Skip to main content Accessibility help
×
Home

Dynamics of proteins in solution

  • Marco Grimaldo (a1) (a2), Felix Roosen-Runge (a1) (a3), Fajun Zhang (a2), Frank Schreiber (a2) and Tilo Seydel (a1)...

Abstract

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Dynamics of proteins in solution
      Available formats
      ×

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Dynamics of proteins in solution
      Available formats
      ×

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Dynamics of proteins in solution
      Available formats
      ×

Copyright

This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work.

Corresponding author

Author for correspondence: Felix Roosen-Runge, E-mail: felix.roosen-runge@fkem1.lu.se; Tilo Seydel, E-mail: seydel@ill.eu

References

Hide All
Abade, GC, Cichocki, B, Ekiel-Jeyewska, ML, Nägele, G and Wajnryb, E (2010) Short-time dynamics of permeable particles in concentrated suspensions. Journal of Chemical Physics 132, 014503.
Acbas, G, Niessen, KA, Snell, EH and Markelz, A (2014) Optical measurements of long-range protein vibrations. Nature Communications 5, 3076.
Achterhold, K, Keppler, C, Ostermann, A, Van Bürck, U, Sturhahn, W, Alp, E and Parak, F (2002) Vibrational dynamics of myoglobin determined by the phonon-assisted Mössbauer effect. Physical Review E 65, 051916.
Agarwal, V, Xue, Y, Reif, B and Skrynnikov, NR (2008) Protein side-chain dynamics as observed by solution- and solid-state NMR spectroscopy: a similarity revealed. Journal of the American Chemical Society 130, 1661116621.
Ahn, S, Kim, KH, Kim, Y, Kim, J and Ihee, H (2009) Protein tertiary structural changes visualized by time-resolved X-ray solution scattering. Journal of Physical Chemistry B 113, 1313113133.
Aihara, T, Ueki, S, Nakamura, M and Arata, T (2006) Calcium-dependent movement of troponin I between troponin C and actin as revealed by spin-labeling EPR. Biochemical and Biophysical Research Communications 340, 462468.
Aisa, D, Aisa, S, Babucci, E, Barocchi, F, Cunsolo, A, D’Anca, F, De Francesco, A, Formisano, F, Gahl, T, Guarini, E, Jahn, S, Laloni, A, Mutka, H, Orecchini, A, Petrillo, C, Pilgrim, W-C, Piluso, A, Sacchetti, F, Suck, J-B and Venturi, G (2006) The Brillouin spectrometer BRISP at the ILL. Physica B: Condensed Matter 385, 10921094.
Akasaka, K (2006) Probing conformational fluctuation of proteins by pressure perturbation. Chemical Reviews 106, 18141835.
Al-Ayoubi, S, Schummel, P, Golub, M, Peters, J and Winter, R (2017) Influence of cosolvents, self-crowding, temperature and pressure on the sub-nanosecond dynamics and folding stability of lysozyme. Physical Chemistry Chemical Physics 19, 1423014237.
Alpert, Y (1980) Tentative use of NSE in biological studies. In Neutron Spin Echo, Budapest, Hungary: Springer, pp. 8793.
Alpert, Y, Cser, L, Farago, B, Franek, F, Mezei, F, Ostanevich, YM (1982) Flexibility and conformational change of IgG molecule. Technical report, Hungarian Academy of Sciences.
Alpert, Y, Cser, L, Faragó, B, Franěk, F, Mezei, F and Ostanevich, YM (1985) Segmental flexibility in pig immunoglobulin G studied by neutron spin-echo technique. Biopolymers 24, 17691784.
Amadei, A, Linssen, ABM and Berendsen, HJC (1993) Essential dynamics of proteins. Proteins 17, 412425.
Ameseder, F, Radulescu, A, Holderer, O, Falus, P, Richter, D and Stadler, AM (2018 a) Relevance of internal friction and structural constraints for the dynamics of denatured bovine serum albumin. Journal of Physical Chemistry Letters 9, 24692473.
Ameseder, F, Radulescu, A, Khaneft, M, Lohstroh, W and Stadler, AM (2018 b) Homogeneous and heterogeneous dynamics in native and denatured bovine serum albumin. Physical Chemistry Chemical Physics 20, 51285139.
Andersson, M, Malmerberg, E, Westenhoff, S, Katona, G, Cammarata, M, Wöri, AB, Johansson, LC, Ewald, F, Eklund, M, Wulff, M, Davidsson, J and Neutze, R (2009) Structural dynamics of light-driven proton pumps. Structure 17, 12651275.
Andersson, C, Martinez, N, Zeller, D, Rondahl, S, Koza, M, Frick, B, Ekström, F, Peters, J and Linusson, A (2017) Changes in dynamics of α-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering. Physical Chemistry Chemical Physics 19, 2536925379.
Ando, T and Skolnick, J (2010) Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proceedings of the National Academy of Sciences (USA) 107, 1845718462.
Ando, T, Kodera, N, Takai, E, Maruyama, D, Saito, K and Toda, A (2001) A high-speed atomic force microscope for studying biological macromolecules. Proceedings of the National Academy of Sciences (USA) 98, 1246812472.
Anunciado, DB, Nyugen, VP, Hurst, GB, Doktycz, MJ, Urban, V, Langan, P, Mamontov, E and O'Neill, H (2017) In vivo protein dynamics on the nanometer length scale and nanosecond timescale. Journal of Physical Chemistry Letters 8, 18991904.
Appavou, M-S, Busch, S, Doster, W, Gaspar, A and Unruh, T (2011) The influence of 2 kbar pressure on the global and internal dynamics of human hemoglobin observed by quasielastic neutron scattering. European Biophysics Journal 40, 705714.
Appel, M, Frick, B, Spehr, TL and Stühn, B (2015) Molecular ring rotation in solid ferrocene revisited. Journal of Chemical Physics 142, 114503.
Appel, M, Frick, B and Magerl, A (2018) A flexible high speed pulse chopper system for an inverted neutron time-of-flight option on backscattering spectrometers. Scientific Reports 8, 13580.
Aquila, A, Hunter, MS, Doak, RB, Kirian, RA, Fromme, P, White, TA, Andreasson, J, Arnlund, D, Bajt, S, Barends, TRM, Barthelmess, M, Bogan, MJ, Bostedt, C, Bottin, H, Bozek, JD, Caleman, C, Coppola, N, Davidsson, J, DePonte, DP, Elser, V, Epp, SW, Erk, B, Fleckenstein, H, Foucar, L, Frank, M, Fromme, R, Graafsma, H, Grotjohann, I, Gumprecht, L, Hajdu, J, Hampton, CY, Hartmann, A, Hartmann, R, Hau-Riege, S, Hauser, G, Hirsemann, H, Holl, P, Holton, JM, Hömke, A, Johansson, L, Kimmel, N, Kassemeyer, S, Krasniqi, F, Kühnel, K-U, Liang, M, Lomb, L, Malmerberg, E, Marchesini, S, Martin, AV, Maia, FR, Messerschmidt, M, Nass, K, Reich, C, Neutze, R, Rolles, D, Rudek, B, Rudenko, A, Schlichting, I, Schmidt, C, Schmidt, KE, Schulz, J, Seibert, MM, Shoeman, RL, Sierra, R, Soltau, H, Starodub, D, Stellato, F, Stern, S, Strüder, L, Timneanu, N, Ullrich, J, Wang, X, Williams, GJ, Weidenspointner, G, Weierstall, U, Wunderer, C, Barty, A, Spence, JCH and Chapman, HN (2012) Time-resolved protein nanocrystallography using an X-ray free-electron laser. Optics Express 20, 27062716.
Arnlund, D, Johansson, LC, Wickstrand, C, Barty, A, Williams, GJ, Malmerberg, E, Davidsson, J, Milathianaki, D, DePonte, DP, Shoeman, RL, Wang, D, James, D, Katona, G, Westenhoff, S, White, TA, Aquila, A, Bari, S, Berntsen, P, Bogan, M, van Driel, TB, Doak, RB, Kjaer, KS, Frank, M, Fromme, R, Grotjohann, I, Henning, R, Hunter, MS, Kirian, RA, Kosheleva, I, Kupitz, C, Liang, M, Martin, AV, Nielsen, MM, Messerschmidt, M, Seibert, MM, Sjohamn, J, Stellato, F, Weierstall, U, Zatsepin, NA, Spence, JCH, Fromme, P, Schlichting, I, Boutet, S, Groenhof, G, Chapman, HN and Neutze, R (2014) Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nature Methods 11, 923926.
Arrio-Dupont, M, Cribier, S, Foucault, G, Devaux, PF and d'Albis, A (1996) Diffusion of fluorescently labeled macromolecules in cultured muscle cells. Biophysical Journal 70, 23272332.
Arrio-Dupont, M, Foucault, G, Vacher, M, Devaux, PF and Cribier, S (2000) Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells. Biophysical Journal 78, 901907.
Arrondo, JLR and Goñi, FM (1999) Structure and dynamics of membrane proteins as studied by infrared spectroscopy. Progress in Biophysics and Molecular Biology 72, 367405.
Arzenšek, D, Kuzman, D and Podgornik, R (2012) Colloidal interactions between monoclonal antibodies in aqueous solutions. Journal of Colloid and Interface Science 384, 207216.
Aznauryan, M, Delgado, L, Soranno, A, Nettels, D, Huang, J-R, Labhardt, AM, Grzesiek, S and Schuler, B (2016) Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS. Proceedings of the National Academy of Sciences (USA) 113, E5389E5398.
Bacia, K, Kim, SA and Schwille, P (2006) Fluorescence cross-correlation spectroscopy in living cells. Nature Methods 3, 8389.
Bai, P, Luo, L and Peng, Z-Y (2000) Side chain accessibility and dynamics in the molten globule state of α-lactalbumin: a 19F-NMR study. Biochemistry 39, 372380.
Bakan, A, Meireles, LM and Bahar, I (2011) Prody: protein dynamics inferred from theory and experiments. Bioinformatics (Oxford, England) 27, 15751577.
Balakrishnan, G, Weeks, CL, Ibrahim, M, Soldatova, AV and Spiro, TG (2008) Protein dynamics from time resolved UV Raman spectroscopy. Current Opinion in Structural Biology 18, 623629.
Ball, P (2008) Water as an active constituent in cell biology. Chemical Reviews 108, 74108.
Balzarotti, F, Eilers, Y, Gwosch, KC, Gynnå, AH, Westphal, V, Stefani, FD, Elf, J and Hell, SW (2016) Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes. Science 355, 606612.
Bancaud, A, Huet, S, Rabut, G and Ellenberg, J (2010) Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, photoconversion, and FLIP. Cold Spring Harbor Protocols, 2010, pdb.top90.
Banchio, AJ and Nägele, G (2008) Short-time transport properties in dense suspensions: from neutral to charge-stabilized colloidal spheres. Journal of Chemical Physics 128, 104903.
Barakat, K, Issack, BB, Stepanova, M and Tuszynski, J (2011) Effects of temperature on the p53-DNA binding interactions and their dynamical behavior: comparing the wild type to the R248Q mutant. PLoS One 6, e27651.
Barth, A (2007) Infrared spectroscopy of proteins. Biochimica et Biophysica Acta Bioenergie 1767, 10731101.
Basu, S, Tan, YL, Taylor, EJR, Laue, ED and Lee, SF (2016) Studying the dynamics of chromatin-binding proteins in mammalian cells using single-molecule localisation microscopy. In Leake, MC (ed.), Chromosome Architecture: Methods and Protocols, New York, NY: Springer, pp. 235263.
Bauer, KC, Göbel, M, Schwab, M-L, Schermeyer, M-T and Hubbuch, J (2016) Concentration-dependent changes in apparent diffusion coefficients as indicator for colloidal stability of protein solutions. International Journal of Pharmaceutics 511, 276287.
Baussay, K, Bon, CL, Nicolai, T, Durand, D and Busnel, J-P (2004) Influence of the ionic strength on the heat-induced aggregation of the globular protein beta-lactoglobulin at pH 7. International Journal of Biological Macromolecules 34, 2128.
Bee, M (1988) Quasielastic Neutron Scattering: Principles and Applications in Solid State Chemistry, Biology and Material Science. Bristol: Adam Hilger.
Bée, M (1992) A physical insight into the elastic incoherent structure factor. Physica B: Condensed Matter 182, 323336.
Beenakker, CWJ and Mazur, P (1984) Diffusion of spheres in a concentrated suspension II. Physica A: Statistical Mechanics and its Applications 126, 349370.
Bellissent-Funel, M-C, Hassanali, A, Havenith, M, Henchman, R, Pohl, P, Sterpone, F, van der Spoel, D, Xu, Y and Garcia, AE (2016) Water determines the structure and dynamics of proteins. Chemical Reviews 116, 76737697.
Benedek, GB (1997) Cataract as a protein condensation disease: the proctor lecture. Investigative Ophthalmology and Visual Science 38, 19111921.
Berg, JM, Tymoczko, JL and Stryer, L (2002) Protein Structure and Function. New York: WH Freeman.
Bernadó, P, Modig, K, Grela, P, Svergun, DI, Tchorzewski, M, Pons, M and Akke, M (2010) Structure and dynamics of ribosomal protein l12: an ensemble model based on SAXS and NMR relaxation. Biophysical Journal 98, 23742382.
Berne, BJ and Pecora, R (2000) Dynamic Light Scattering: With Applications to Chemistry, Biology, and Physics. New York: Dover Publications.
Berry, H and Chaté, H (2014) Anomalous diffusion due to hindering by mobile obstacles undergoing Brownian motion or Ornstein-Uhlenbeck processes. Physical Review E 89, 022708.
Beutel, O, Roder, F, Birkholz, O, Rickert, C, Steinhoff, H-J, Grzybek, M, Coskun, U and Piehler, J (2015) Two-dimensional trap for ultrasensitive quantification of transient protein interactions. ACS Nano 9, 97839791.
Bewley, RI, Taylor, JW and Bennington, SM (2011) LET, a cold neutron multi-disk chopper spectrometer at ISIS. Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 637, 128134.
Bianchi, E, Blaak, R and Likos, C (2011) Patchy colloids: state of the art and perspectives. Physical Chemistry Chemical Physics 13, 63976410.
Bianco, V, Pagès-Gelabert, N, Coluzza, I and Franzese, G (2017) How the stability of a folded protein depends on interfacial water properties and residue–residue interactions. Journal of Molecular Liquids 245, 129139.
Biehl, R and Richter, D (2014) Slow internal protein dynamics in solution. Journal of Physics Condensed Matter 26, 503103.
Biehl, R, Hoffmann, B, Monkenbusch, M, Falus, P, Prévost, S, Merkel, R and Richter, D (2008) Direct observation of correlated interdomain motion in alcohol dehydrogenase. Physical Review Letters 101, 138102.
Biehl, R, Monkenbusch, M and Richter, D (2011) Exploring internal protein dynamics by neutron spin echo spectroscopy. Soft Matter 7, 12991307.
Blackledge, M (2005) Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings. Progress in Nuclear Magnetic Resonance Spectroscopy 46, 2361.
Bloemendal, H, De Jong, W, Jaenicke, R, Lubsen, N, Slingsby, C and Tardieu, A (2004) Ageing and vision: structure, stability and function of lens crystallins. Progress in Biophysics and Molecular Biology 86, 407485.
Blumenschein, TM, Stone, DB, Fletterick, RJ, Mendelson, RA and Sykes, BD (2005) Calcium-dependent changes in the flexibility of the regulatory domain of TnC in the troponin complex. Journal of Biological Chemistry 280, 2192421932.
Boehr, DD, Dyson, HJ and Wright, PE (2006) An NMR perspective on enzyme dynamics. Chemical Reviews 106, 30553079.
Bolanños-García, VM, Mas-Oliva, J, Soriano-García, M and Moreno, A (1998) Precrystallization of human apoprotein AI based on its aggregation behavior in solution studied by dynamic light scattering. Journal of Molecular Structure 440, 18.
Borgia, A, Williams, PM and Clarke, J (2008) Single-molecule studies of protein folding. Annual Review of Biochemistry 77, 101125.
Bouchoux, A, Schorr, D, Daffé, A, Cambert, M, Gesan-Guiziou, G and Mariette, F (2012) Molecular mobility in dense protein systems: an investigation through 1H NMR relaxometry and diffusometry. Journal of Physical Chemistry B 116, 1174411753.
Bratko, D, Cellmer, T, Prausnitz, JM and Blanch, HW (2007) Molecular simulation of protein aggregation. Biotechnology and Bioengineering 96, 18.
Braun, MK, Grimaldo, M, Roosen-Runge, F, Hoffmann, I, Czakkel, O, Sztucki, M, Zhang, F, Schreiber, F and Seydel, T (2017) Crowding-controlled cluster size in concentrated aqueous protein solutions: structure, self-and collective diffusion. Journal of Physical Chemistry Letters 8, 25902596.
Bu, Z and Callaway, DJ (2013) Nanoscale protein dynamics and long-range allostery in cell signaling. Biophysical Journal 104, 58a.
Bu, Z, Neumann, DA, Lee, S-H, Brown, CM, Engelman, DM and Han, CC (2000) A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering. Journal of Molecular Biology 301, 525536.
Bu, Z, Cook, J and Callaway, DJ (2001) Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin. Journal of Molecular Biology 312, 865873.
Bu, Z, Biehl, R, Monkenbusch, M, Richter, D and Callaway, DJ (2005) Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. Proceedings of the National Academy of Sciences (USA) 102, 1764617651.
Bucciarelli, S, Casal-Dujat, L, De Michele, C, Sciortino, F, Dhont, J, Bergenholtz, J, Farago, B, Schurtenberger, P and Stradner, A (2015) Unusual dynamics of concentration fluctuations in solutions of weakly attractive globular proteins. Journal of Physical Chemistry Letters 6, 44704474.
Bucciarelli, S, Myung, JS, Farago, B, Das, S, Vliegenthart, GA, Holderer, O, Winkler, RG, Schurtenberger, P, Gompper, G and Stradner, A (2016) Dramatic influence of patchy attractions on short-time protein diffusion under crowded conditions. Science Advances 2, e1601432.
Buck, M, Schwalbe, H and Dobson, CM (1996) Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol. Journal of Molecular Biology 257, 669683.
Busch, NA, Kim, T and Bloomfield, VA (2000) Tracer diffusion of proteins in DNA solutions. 2. Green fluorescent protein in crowded DNA solutions. Macromolecules 33, 59325937.
Busch, S, Doster, W, Longeville, S, Sakai, VG and Unruh, T (2006) Microscopic protein diffusion at high concentration. In Sokol, PE (ed.), Proceedings of the Eighth International Conference on Quasi-Elastic Neutron Scattering held June 14–17, 2006. Bloomington, Indiana, USA, pp. 116117.
Callaway, DJ and Bu, Z (2015) Nanoscale protein domain motion and long-range allostery in signaling proteins – a view from neutron spin echo spectroscopy. Biophysical Reviews 7, 165174.
Callaway, DJE and Bu, Z (2016) Essential strategies for revealing nanoscale protein dynamics by neutron spin echo spectroscopy. In Kelman, Z (ed.), Isotope Labeling of Biomolecules – Applications, Volume 566 of Methods in Enzymology. Cambridge, MA: Academic Press, pp. 253270.
Callaway, DJ and Bu, Z (2017) Visualizing the nanoscale: protein internal dynamics and neutron spin echo spectroscopy. Current Opinion in Structural Biology 42, 15.
Callaway, DJ, Farago, B and Bu, Z (2013) Nanoscale protein dynamics: a new frontier for neutron spin echo spectroscopy. European Physical Journal E: Soft Matter 36, 18.
Callaway, DJ, Matsui, T, Weiss, T, Stingaciu, LR, Stanley, CB, Heller, WT and Bu, Z (2017) Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics. Journal of Molecular Biology 429, 987998.
Calligari, PA, Calandrini, V, Ollivier, J, Artero, J-B, Härtlein, M, Johnson, M and Kneller, GR (2015) Adaptation of extremophilic proteins with temperature and pressure: evidence from initiation factor 6. Journal of Physical Chemistry B 119, 78607873.
Cammarata, M, Levantino, M, Schotte, F, Anfinrud, PA, Ewald, F, Choi, J, Cupane, A, Wulff, M and Ihee, H (2008) Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Nature Methods 5, 881886.
Campbell, SI, Telling, MTF and Carlile, CJ (2000) The optimisation of analyser geometry in near-backscattering spectrometers – IRIS on the ISIS-pulsed source. Physica B: Condensed Matter 276–278, 206207.
Campbell, E, Kaltenbach, M, Correy, GJ, Carr, PD, Porebski, BT, Livingstone, EK, Afriat-Jurnou, L, Buckle, AM, Weik, M, Hollfelder, F, Tokuriki, N and Jackson, C (2016) The role of protein dynamics in the evolution of new enzyme function. Nature Chemical Biology 12, 944950.
Cardarelli, F and Gratton, E (2016) Spatiotemporal fluorescence correlation spectroscopy of inert tracers: a journey within cells, one molecule at a time. In Jameson, D (ed.), Perspectives on Fluorescence. Cham, Switzerland: Springer, pp. 287309.
Cardinaux, F, Zaccarelli, E, Stradner, A, Bucciarelli, S, Farago, B, Egelhaaf, SU, Sciortino, F and Schurtenberger, P (2011) Cluster-driven dynamical arrest in concentrated lysozyme solutions. Journal of Physical Chemistry B 115, 72277237.
Caronna, C, Natali, F and Cupane, A (2005) Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics. Biophysical Chemistry 116, 219225.
Castro-Camus, E and Johnston, MB (2008) Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chemical Physics Letters 455, 289292.
Casuso, I, Rico, F and Scheuring, S (2011) High-speed atomic force microscopy: structure and dynamics of single proteins. Current Opinion in Chemical Biology 15, 704709.
Cerveny, S, Alegría, A and Colmenero, J (2008) Universal features of water dynamics in solutions of hydrophilic polymers, biopolymers, and small glass-forming materials. Physical Review E 77, 031803.
Charras, GT, Hu, C-K, Coughlin, M and Mitchison, TJ (2006) Reassembly of contractile actin cortex in cell blebs. Journal of Cell Biology 175, 477490.
Cheung, MS, Klimov, D and Thirumalai, D (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins. Proceedings of the National Academy of Sciences (USA) 102, 47534758.
Chevelkov, V, Xue, Y, Linser, R, Skrynnikov, NR and Reif, B (2010) Comparison of solid-state dipolar couplings and solution relaxation data provides insight into protein backbone dynamics. Journal of the American Chemical Society 132, 50155017.
Chin, JK, Jimenez, R and Romesberg, FE (2002) Protein dynamics and cytochrome c: correlations between ligand vibrations and redox activity. Journal of the American Chemical Society 124, 18461847.
Cho, HS, Dashdorj, N, Schotte, F, Graber, T, Henning, R and Anfinrud, P (2010) Protein structural dynamics in solution unveiled via 100-ps time-resolved X-ray scattering. Proceedings of the National Academy of Sciences (USA) 107, 72817286.
Choi, Y-G, Park, C-J, Kim, H-E, Seo, Y-J, Lee, A-R, Choi, S-R, Lee, SS and Lee, J-H (2015) Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase. Journal of Biomolecular NMR 61, 137150.
Chu, X-Q, Mamontov, E, O'Neill, H and Zhang, Q (2012) Apparent decoupling of the dynamics of a protein from the dynamics of its aqueous solvent. Journal of Physical Chemistry Letters 3, 380385.
Cilia, E, Pancsa, R, Tompa, P, Lenaerts, T and Vranken, WF (2013) From protein sequence to dynamics and disorder with DynaMine. Nature Communications 4, 2741.
Ciliberti, S, De Los Rios, P and Piazza, F (2006) Glasslike structure of globular proteins and the boson peak. Physical Review Letters 96, 198103.
Cino, EA, Karttunen, M and Choy, W-Y (2012) Effects of molecular crowding on the dynamics of intrinsically disordered proteins. PLoS One 7, e49876.
Cioni, P and Gabellieri, E (2011) Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility? BBA-Protein Proteomics 1814, 934941.
Constantine, KL, Friedrichs, MS, Wittekind, M, Jamil, H, Chu, C-H, Parker, RA, Goldfarb, V, Mueller, L and Farmer, BT (1998) Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins. Biochemistry 37, 79657980.
Copley, JRD and Cook, JC (2003) The disk chopper spectrometer at NIST: a new instrument for quasielastic neutron scattering studies. Chemical Physics 292, 477485.
Cordina, NM, Liew, CK, Potluri, PR, Curmi, PM, Fajer, PG, Logan, TM, Mackay, JP and Brown, LJ (2014) Ca2+-induced PRE-NMR changes in the troponin complex reveal the possessive nature of the cardiac isoform for its regulatory switch. PLoS One 9, e112976.
CSPEC. European Spallation Source. Available at https://europeanspallationsource.se/instruments/cspec. Accessed 23 October 2018.
Cui, Q and Bahar, I (2006) Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Boca Raton: Chapman & Hall/CRC.
Cusack, S and Doster, W (1990) Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering. Biophysical Journal 58, 243.
Daniel, RM, Smith, JC, Ferrand, M, Hry, S, Dunn, R and Finney, JL (1998) Enzyme activity below the dynamical transition at 220 K. Biophysical Journal 75, 25042507.
Daniel, RM, Finney, JL, Réat, V, Dunn, R, Ferrand, M and Smith, JC (1999) Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution. Biophysical Journal 77, 21842190.
Daniel, RM, Dunn, RV, Finney, JL and Smith, JC (2003) The role of dynamics in enzyme activity. Annual Review of Biophysics and Biomolecular Structure 32, 6992.
Das, S, Riest, J, Winkler, RG, Gompper, G, Dhont, JK and Nägele, G (2018) Clustering and dynamics of particles in dispersions with competing interactions: theory and simulation. Soft Matter 14, 92103.
Dauty, E and Verkman, A (2005) Actin cytoskeleton as the principal determinant of size-dependent DNA mobility in cytoplasm a new barrier for non-viral gene delivery. Journal of Biological Chemistry 280, 78237828.
d'Auvergne, EJ and Gooley, PR (2008) Optimisation of NMR dynamic models I. minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. Journal of Biomolecular NMR 40, 107.
Da Vela, S, Roosen-Runge, F, Skoda, MW, Jacobs, RM, Seydel, T, Frielinghaus, H, Sztucki, M, Schweins, R, Zhang, F and Schreiber, F (2017) Effective interactions and colloidal stability of bovine γ-globulin in solution. Journal of Physical Chemistry B 121, 57595769.
Dee, DR, Myers, B and Yada, RY (2011) Dynamics of thermodynamically stable, kinetically trapped, and inhibitor-bound states of pepsin. Biophysical Journal 101, 16991709.
DeLano, WL (2002) The PyMOL molecular graphics system. Available at http://www.pymol.org.
de la Torre, JG, Huertas, ML and Carrasco, B (2000) Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophysical Journal 78, 719730.
Demmel, F, McPhail, D, French, C, Maxwell, D, Harrison, S, Boxall, J, Rhodes, N, Mukhopadhyay, S, Silverwood, I, Sakai, VG and Fernandez-Alonso, F (2018) ToF-backscattering spectroscopy at the ISIS facility: status and perspectives. Journal of Physics Conference Series 1021, 012027.
Deniz, AA, Laurence, TA, Dahan, M, Chemla, DS, Schultz, PG and Weiss, S (2001) Ratiometric single-molecule studies of freely diffusing biomolecules. Annual Review of Physical Chemistry 52, 233253.
de Souza, NR, Klapproth, A and Iles, GN (2016) EMU: high-resolution backscattering spectrometer at ANSTO. Neutron News 27, 2021.
Dharmaraj, VL, Godfrin, PD, Liu, Y and Hudson, SD (2016) Rheology of clustering protein solutions. Biomicrofluidics 10, 043509.
Dhont, JK (1996). An Introduction to Dynamics of Colloids. Amsterdam, Netherlands: Elsevier Science.
Diakova, G, Goddard, YA, Korb, J-P and Bryant, RG (2007) Changes in protein structure and dynamics as a function of hydration from 1H second moments. Journal of Magnetic Resonance 189, 166172.
Diehl, M, Doster, W, Petry, W and Schober, H (1997) Water-coupled low-frequency modes of myoglobin and lysozyme observed by inelastic neutron scattering. Biophysical Journal 73, 2726.
Diekmann, S and Hoischen, C (2014) Biomolecular dynamics and binding studies in the living cell. Physics of Life Reviews 11, 130.
Dierker, S, Pindak, R, Fleming, R, Robinson, I and Berman, L (1995) X-ray photon correlation spectroscopy study of Brownian motion of gold colloids in glycerol. Physical Review Letters 75, 449.
Dilg, AW, Grantner, K, Iakovleva, O, Parak, FG, Babini, E, Bertini, I, Capozzi, F, Luchinat, C and Meyer-Klaucke, W (2002) Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP. Journal of Biological Inorganic Chemistry 7, 691703.
Di Rienzo, C, Piazza, V, Gratton, E, Beltram, F and Cardarelli, F (2014) Probing short-range protein Brownian motion in the cytoplasm of living cells. Nature Communications 5, 5891.
Długosz, M and Antosiewicz, JM (2013) Evaluation of proteins’ rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments. Journal of Chemical Theory and Computation 10, 481491.
Dobson, CM and Hore, PJ (1998) Kinetic studies of protein folding using NMR spectroscopy. Nature Structural and Molecular Biology 5, 504507.
Doi, M and Edwards, SF (1986) Oxford: The Theory of Polymer Dynamics Clarendon Press.
Dorosh, L, Kharenko, OA, Rajagopalan, N, Loewen, MC and Stepanova, M (2013) Molecular mechanisms in the activation of abscisic acid receptor PYR1. PLoS Computational Biology 9, e1003114.
Doruker, P, Atilgan, AR and Bahar, I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins 40, 512524.
Dosset, P, Hus, J-C, Blackledge, M and Marion, D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. Journal of Biomolecular NMR 16, 2328.
Doster, W and Longeville, S (2007) Microscopic diffusion and hydrodynamic interactions of hemoglobin in red blood cells. Biophysical Journal 93, 13601368.
Doster, W, Cusack, S and Petry, W (1989) Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature 337, 754756.
Dubin, SB, Clark, NA and Benedek, GB (1971) Measurement of the rotational diffusion coefficient of lysozyme by depolarized light scattering: configuration of lysozyme in solution. Journal of Chemical Physics 54, 51585164.
Dunkel, S, Pulagam, L, Steinhoff, H-J and Klare, J (2015) In vivo EPR on spin labeled colicin A reveals an oligomeric assembly of the pore-forming domain in E. coli membranes. Physical Chemistry Chemical Physics 17, 48754878.
Dutta, A, Altenbach, C, Mangahas, S, Yanamala, N, Gardner, E, Hubbell, WL and Klein-Seetharaman, J (2014) Differential dynamics of extracellular and cytoplasmic domains in denatured states of rhodopsin. Biochemistry 53, 71607169.
Dyson, HJ and Wright, PE (2004) Unfolded proteins and protein folding studied by NMR. Chemical Reviews 104, 36073622.
Ebbinghaus, S, Kim, SJ, Heyden, M, Yu, X, Gruebele, M, Leitner, DM and Havenith, M (2008) Protein sequence- and pH-dependent hydration probed by terahertz spectroscopy. Journal of the American Chemical Society 130, 23742375.
Echeverria, I, Makarov, DE and Papoian, GA (2014) Concerted dihedral rotations give rise to internal friction in unfolded proteins. Journal of the American Chemical Society 136, 87088713.
Ehlers, G, Podlesnyak, AA, Niedziela, JL, Iverson, EB and Sokol, PE (2011) The new cold neutron chopper spectrometer at the spallation neutron source: design and performance. Review of Scientific Instruments 82, 085108.
Eisenmesser, EZ, Bosco, DA, Akke, M and Kern, D (2002) Enzyme dynamics during catalysis. Science 295, 15201523.
Ellis, RJ (2001) Macromolecular crowding: an important but neglected aspect of the intracellular environment. Current Opinion in Structural Biology 11, 114119.
Elowitz, MB, Surette, MG, Wolf, P-E, Stock, JB and Leibler, S (1999) Protein mobility in the cytoplasm of Escherichia coli. Journal of Bacteriology 181, 197203.
Erlkamp, M, Grobelny, S, Faraone, A, Czeslik, C and Winter, R (2014) Solvent effects on the dynamics of amyloidogenic insulin revealed by neutron spin echo spectroscopy. Journal of Physical Chemistry B 118, 33103316.
Erlkamp, M, Marion, J, Martinez, N, Czeslik, C, Peters, J and Winter, R (2015) Influence of pressure and crowding on the sub-nanosecond dynamics of globular proteins. Journal of Physical Chemistry B 119, 48424848.
Eyal, E, Lum, G and Bahar, I (2015) The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics (Oxford, England) 31, 14871489.
Fabiani, E, Stadler, A, Madern, D, Koza, M, Tehei, M, Hirai, M and Zaccai, G (2009) Dynamics of apomyoglobin in the α-to-β transition and of partially unfolded aggregated protein. European Biophysics Journal 38, 237.
Falconer, RJ and Markelz, AG (2012) Terahertz spectroscopic analysis of peptides and proteins. Journal of Infrared, Millimeter and Terahertz Waves 33, 973988.
Farago, B (1999) Recent neutron spin-echo developments at the ILL (IN11 and IN15). Physica B: Condensed Matter 267–268, 270276.
Farago, B, Li, J, Cornilescu, G, Callaway, DJ and Bu, Z (2010) Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy. Biophysical Journal 99, 34733482.
Farago, B, Falus, P, Hoffmann, I, Gradzielski, M, Thomas, F and Gomez, C (2015) The IN15 upgrade. Neutron News 26, 1517.
Fayer, M (2009) Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy. Annual Review of Physical Chemistry 60, 2138.
Feig, M, Yu, I, Wang, P-h, Nawrocki, G and Sugita, Y (2017) Crowding in cellular environments at an atomistic level from computer simulations. Journal of Physical Chemistry B 121, 80098025.
Feller, G (2003) Molecular adaptations to cold in psychrophilic enzymes. Cellular and Molecular Life Sciences 60, 648662.
Feller, G and Gerday, C (1997) Psychrophilic enzymes: molecular basis of cold adaptation. Cellular and Molecular Life Sciences 53, 830841.
Fenimore, PW, Frauenfelder, H, Magazù, S, McMahon, BH, Mezei, F, Migliardo, F, Young, RD and Stroe, I (2013) Concepts and problems in protein dynamics. Chemical Physics 424, 26.
Fenwick, RB, Schwieters, CD and Vögeli, B (2016) Direct investigation of slow correlated dynamics in proteins via dipolar interactions. Journal of the American Chemical Society 138, 84128421.
Ferré-D'Amaré, AR and Burley, SK (1994) Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure 2, 357359.
Ferreon, ACM and Deniz, AA (2011) Protein folding at single-molecule resolution. BBA-Proteins and Proteomics 1814, 10211029.
Ferrer, M, Duchowicz, R, Carrasco, B and Torre, JDL (2001) The conformation of serum albumin in solution: a combined phosphorescence depolarization-hydrodynamic modeling study. Biophysical Journal 80, 24222430.
Finkenstaedt-Quinn, SA, Qiu, TA, Shin, K and Haynes, CL (2016) Super-resolution imaging for monitoring cytoskeleton dynamics. The Analyst 141, 56745688.
Fitter, J (2000) Confined molecular motions of globular proteins studied in powder samples and in solution. Journal de Physique IV 10, 265270.
Fitter, J (2003 a) Conformational dynamics of a protein in the folded and the unfolded state. Chemical Physics 292, 405411.
Fitter, J (2003 b) A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy. Biophysical Journal 84, 39243930.
Fitter, J, Ernst, O, Hauß, T, Lechner, R, Hofmann, K and Dencher, N (1998) Molecular motions and hydration of purple membranes and disk membranes studied by neutron scattering. European Biophysics Journal 27, 638645.
Fitter, J, Gutberlet, T and Katsaras, J (2006) Neutron Scattering in Biology: Techniques and Applications. Springer, Berlin Heidelberg.
Foffi, G, Savin, G, Bucciarelli, S, Dorsaz, N, Thurston, GM, Stradner, A and Schurtenberger, P (2014) Hard sphere-like glass transition in eye lens-crystallin solutions. Proceedings of the National Academy of Sciences (USA) 111, 1674816753.
Fomina, M, Schirò, G and Cupane, A (2014) Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectroscopy. Biophysical Chemistry 185, 2531.
Fouquet, P, Ehlers, G, Farago, B, Pappas, C and Mezei, F (2007) The wide-angle neutron spin echo spectrometer project WASP. Journal of Neutron Research 15, 3947.
Frauenfelder, H (1998) Protein dynamics and function. In Jardetzky, O, Lefèvre, J-F and Holbrook, RE (eds), Protein Dynamics, Function, and Design. Boston, MA: Springer US, pp. 95102.
Frauenfelder, H, Petsko, GA and Tsernoglou, D (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280, 558563.
Frauenfelder, H, Parak, F and Young, RD (1988) Conformational substrates in proteins. Annual Review of Biophysics and Biophysical Chemistry 17, 451479.
Frauenfelder, H, Chen, G, Berendzen, J, Fenimore, PW, Jansson, H, McMahon, BH, Stroe, IR, Swenson, J and Young, RD (2009) A unified model of protein dynamics. Proceedings of the National Academy of Sciences (USA) 106, 51295134.
Freedberg, DI and Selenko, P (2014) Live cell NMR. Annual Review of Biophysics 43, 171192.
Frick, B, Mamontov, E, Eijck, LV and Seydel, T (2010) Recent backscattering instrument developments at the ILL and SNS. Zeitschrift für Physikalische Chemie 224, 3360.
Frick, B, Combet, J and van Eijck, L (2012) New possibilities with inelastic fixed window scans and linear motor Doppler drives on high resolution neutron backscattering spectrometers. Nuclear Instruments and Methods Section A 669, 713.
Fritzsche, M and Charras, G (2015) Dissecting protein reaction dynamics in living cells by fluorescence recovery after photobleaching. Nature Protocols 10, 660680.
Fujiwara, S, Araki, K, Matsuo, T, Yagi, H, Yamada, T, Shibata, K and Mochizuki, H (2016) Dynamical behavior of human α-synuclein studied by quasielastic neutron scattering. PLoS One 11, e0151447.
Fujiwara, S, Chatake, T, Matsuo, T, Kono, F, Tominaga, T, Shibata, K, Sato-Tomita, A and Shibayama, N (2017) Ligation-dependent picosecond dynamics in human hemoglobin as revealed by quasielastic neutron scattering. Journal of Physical Chemistry B 121, 80698077.
Furukawa, R, Arauz-Lara, JL and Ware, BR (1991) Self-diffusion and probe diffusion in dilute and semidilute aqueous solutions of dextran. Macromolecules 24, 599605.
Gabel, F, Bicout, D, Lehnert, U, Tehei, M, Weik, M and Zaccai, G (2003) Protein dynamics studied by neutron scattering. Quarterly Reviews of Biophysics 35, 327367.
Gall, A, Seguin, J, Robert, B and Bellissent-Funel, M-C (2002) Membrane proteins in bulk solution can be used for quasi-elastic neutron scattering studies: the case for the photochemical reaction center. Journal of Physical Chemistry B 106, 63036309.
Garczarek, F and Gerwert, K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439, 109.
Gaspar, AM, Appavou, M-S, Busch, S, Unruh, T and Doster, W (2008) Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study. European Biophysics Journal 37, 573582.
Ghahghaei, A, Rekas, A, Price, WE and Carver, JA (2007) The effect of dextran on subunit exchange of the molecular chaperone αa-crystallin. BBA-Proteins and Proteomics 1774, 102111.
Ghosh, S, Ghosh, C, Nandi, S and Bhattacharyya, K (2015) Unfolding and refolding of a protein by cholesterol and cyclodextrin: a single molecule study. Physical Chemistry Chemical Physics 17, 80178027.
Gibrat, G, Assairi, F, Blouquit, Y, Craescu, C and Bellissentfunel, M (2008) Biophysical study of thermal denaturation of apo-calmodulin: dynamics of native and unfolded states. Biophysical Journal 95, 52475256.
Godfrin, PD, Hudson, SD, Hong, K, Porcar, L, Falus, P, Wagner, NJ and Liu, Y (2015) Short-time glassy dynamics in viscous protein solutions with competing interactions. Physical Review Letters 115, 228302.
Gögelein, C, Nägele, G, Tuinier, R, Gibaud, T, Stradner, A and Schurtenberger, P (2008) A simple patchy colloid model for the phase behavior of lysozyme dispersions. Journal of Chemical Physics 129, 085102.
Golub, M, Lehofer, B, Martinez, N, Ollivier, J, Kohlbrecher, J, Prassl, R and Peters, J (2017) High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles. Scientific Reports 7, 46034.
Goluguri, RR and Udgaonkar, JB (2016) Microsecond rearrangements of hydrophobic clusters in an initially collapsed globule prime structure formation during the folding of a small protein. Journal of Molecular Biology 428, 31023117.
Goodman, JL, Pagel, MD and Stone, MJ (2000) Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters. Journal of Molecular Biology 295, 963978.
Goret, G, Aoun, B and Pellegrini, E (2017) MDANSE: an interactive analysis environment for molecular dynamics simulations. Journal of Chemical Information and Modeling 57, 15.
Griffiths, AJ, Gelbart, WM, Miller, JH and Lewontin, RC (1999) Modern Genetic Analysis. New York: WH Freeman.
Grimaldo, M, Roosen-Runge, F, Zhang, F, Seydel, T and Schreiber, F (2014) Diffusion and dynamics of γ-globulin in crowded aqueous solutions. Journal of Physical Chemistry B 118, 72037209.
Grimaldo, M, Roosen-Runge, F, Hennig, M, Zanini, F, Zhang, F, Jalarvo, N, Zamponi, M, Schreiber, F and Seydel, T (2015 a) Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation. Physical Chemistry Chemical Physics 17, 46454655.
Grimaldo, M, Roosen-Runge, F, Hennig, M, Zanini, F, Zhang, F, Zamponi, M, Jalarvo, N, Schreiber, F and Seydel, T (2015 b) Salt-induced universal slowing down of the short-time self-diffusion of a globular protein in aqueous solution. Journal of Physical Chemistry Letters 6, 25772582.
Grimaldo, M, Roosen-Runge, F, Jalarvo, N, Zamponi, M, Zanini, F, Hennig, M, Zhang, F, Schreiber, F and Seydel, T (2015 c) High-resolution neutron spectroscopy on protein solution samples. EPJ Web of Conferences 83, 02005.
Grübel, G, Madsen, A and Robert, A (2008) X-ray photon correlation spectroscopy (XPCS). In Borsali, R and Pecora, R (eds), Soft Matter Characterization. Dordrecht: Springer, pp. 953995.
Gun'ko, VM, Klyueva, AV, Levchuk, YN and Leboda, R (2003) Photon correlation spectroscopy investigations of proteins. Advances in Colloid and Interface Science 105, 201328.
Gunton, JD, Shiryayev, A and Pagan, DL (2007) Protein Condensation: Kinetic Pathways to Crystallization and Disease. Cambridge, UK: Cambridge University Press.
Gupta, S, Biehl, R, Sill, C, Allgaier, J, Sharp, M, Ohl, M and Richter, D (2016) Protein entrapment in polymeric mesh: diffusion in crowded environment with fast process on short scales. Macromolecules 49, 19411949.
Hall, PL and Ross, DK (1981) Incoherent neutron scattering functions for random jump diffusion in bounded and infinite media. Molecular Physics 42, 673682.
Halle, B (2002) Flexibility and packing in proteins. Proceedings of the National Academy of Sciences (USA) 99, 12741279.
Halle, B (2004) Protein hydration dynamics in solution: a critical survey. Philosophical Transactions of the Royal Society, London, B Biological Sciences 359, 12071224.
Hänsel, R, Luh, LM, Corbeski, I, Trantirek, L and Doetsch, V (2014) In-cell NMR and EPR spectroscopy of biomacromolecules. Angewandte Chemie International Edition 53, 1030010314.
Harding, SE (1995) On the hydrodynamic analysis of macromolecular conformation. Biophysical Chemistry 55, 6993.
Harpole, KW, O'Brien, ES, Clark, MA, McKnight, CJ, Vugmeyster, L and Wand, AJ (2016) The unusual internal motion of the villin headpiece subdomain. Protein Science 25, 423432.
Harris, LJ, Larson, SB, Hasel, KW and McPherson, A (1997) Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 36, 15811597.
Häußler, W (2008) Neutron spin echo studies on ferritin: free-particle diffusion and interacting solutions. European Biophysics Journal 37, 563571.
Häußler, W and Farago, B (2003) Diffusive dynamics of ordered solutions of apoferritin near the structure factor peak. Journal of Physics Condensed Matter 15, S197.
He, Y, Ku, PI, Knab, J, Chen, J and Markelz, A (2008) Protein dynamical transition does not require protein structure. Physical Review Letters 101, 178103.
Heinen, M, Zanini, F, Roosen-Runge, F, Fedunova, D, Zhang, F, Hennig, M, Seydel, T, Schweins, R, Sztucki, M, Antalik, M, Schreiber, F and Nägele, G (2012) Viscosity and diffusion: crowding and salt effects in protein solutions. Soft Matter 8, 14041419.
Hellenkamp, B, Wortmann, P, Kandzia, F, Zacharias, M and Hugel, T (2017) Multidomain structure and correlated dynamics determined by self-consistent FRET networks. Nature Methods 14, 174.
Hennig, M (2011) Dynamics of Globular Proteins in Crowded Electrolyte Solutions Studied by Neutron Scattering (PhD thesis). Institut Für Angewandte Physik - Eberhard Karls University of Tübingen, Institute Laue Langevin.
Hennig, M, Frick, B and Seydel, T (2011) Optimum velocity of a phase-space transformer for cold-neutron backscattering spectroscopy. Journal of Applied Crystallography 44, 467472.
Hennig, M, Roosen-Runge, F, Zhang, F, Zorn, S, Skoda, MW, Jacobs, RM, Seydel, T and Schreiber, F (2012) Dynamics of highly concentrated protein solutions around the denaturing transition. Soft Matter 8, 16281633.
Henzler-Wildman, KA, Lei, M, Thai, V, Kerns, SJ, Karplus, M and Kern, D (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913916.
Hill, RB, Bracken, C, DeGrado, WF and Palmer, AG (2000) Molecular motions and protein folding: characterization of the backbone dynamics and folding equilibrium of α2d using 13C NMR spin relaxation. Journal of the American Chemical Society 122, 1161011619.
Hinsen, K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33, 417429.
Hinsen, K (2000) The molecular modeling toolkit: a new approach to molecular simulations. Journal of Computational Chemistry 21, 7985.
Hinsen, K, Petrescu, A-J, Dellerue, S, Bellissent-Funel, M-C and Kneller, GR (2000) Harmonicity in slow protein dynamics. Chemical Physics 261, 2537.
Hoffmann, I (2014) Neutrons for the study of dynamics in soft matter systems. Colloid and Polymer Science 292, 20532069.
Höfling, F and Franosch, T (2013) Anomalous transport in the crowded world of biological cells. Reports on Progress in Physics 76, 046602.
Holderer, O, Monkenbusch, M, Schätzler, R, Kleines, H, Westerhausen, W and Richter, D (2008) The JCNS neutron spin-echo spectrometer J-NSE at the FRM II. Measurement Science and Technology 19, 034022.
Hong, L, Sharp, MA, Poblete, S, Biehl, R, Zamponi, M, Szekely, N, Appavou, M-S, Winkler, RG, Nauss, RE, Johs, A, Parks, JM, Yi, Z, Cheng, H, Liang, L, Ohl, M, Miller, SM, Richter, D, Gompper, G and Smith, JC (2014 a) Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophysical Journal 107, 393400.
Hong, L, Smolin, N and Smith, JC (2014 b) de Gennes narrowing describes the relative motion of protein domains. Physical Review Letters 112, 158102.
Hong, L, Jain, N, Cheng, X, Bernal, A, Tyagi, M and Smith, JC (2016) Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. Science Advances 2, e1600886.
Huang, F, Rajagopalan, S, Settanni, G, Marsh, RJ, Armoogum, DA, Nicolaou, N, Bain, AJ, Lerner, E, Haas, E, Ying, L and Fersht, AR (2009) Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer. Proceedings of the National Academy of Sciences (USA) 106, 2075820763.
Hwang, J, Kim, J and Sung, BJ (2016) Dynamics of highly polydisperse colloidal suspensions as a model system for bacterial cytoplasm. Physical Review E 94, 022614.
Ibrahim, Z, Martel, A, Moulin, M, Kim, HS, Härtlein, M, Franzetti, B and Gabel, F (2017) Time-resolved neutron scattering provides new insight into protein substrate processing by a AAA+ unfoldase. Scientific Reports 7, 40948.
Igumenova, TI, Frederick, KK and Wand, AJ (2006) Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chemical Reviews 106, 16721699.
Ihee, H, Wulff, M, Kim, J and Adachi, S-i (2010) Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules. International Reviews in Physical Chemistry 29, 453520.
Inoue, R, Biehl, R, Rosenkranz, T, Fitter, J, Monkenbusch, M, Radulescu, A, Farago, B and Richter, D (2010) Large domain fluctuations on 50-ns timescale enable catalytic activity in phosphoglycerate kinase. Biophysical Journal 99, 23092317.
Institut Laue-Langevin. (2008) The Yellow Book – Guide to Neutron Facilities. Available at http://www.ill.eu/instruments-support/instruments-groups/yellowbook/
Ishima, R and Torchia, DA (2000) Protein dynamics from NMR. Nature Structural and Molecular Biology 7, 740743.
Ishima, R, Petkova, AP, Louis, JM and Torchia, DA (2001) Comparison of methyl rotation axis order parameters derived from model-free analyses of 2H and 13C longitudinal and transverse relaxation rates measured in the same protein sample. Journal of the American Chemical Society 123, 61646171.
Issack, BB, Berjanskii, M, Wishart, DS and Stepanova, M (2012) Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers. Proteins 80, 18471865.
Itoh, S, Yokoo, T, Satoh, S, ichiro Yano, S, Kawana, D, Suzuki, J and Sato, TJ (2011) High resolution chopper spectrometer (HRC) at J-PARC. Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 631, 9097.
Jachimska, B, Wasilewska, M and Adamczyk, Z (2008) Characterization of globular protein solutions by dynamic light scattering, electrophoretic mobility, and viscosity measurements. Langmuir 24, 68666872.
Janßen, S, Mesot, J, Holitzner, L, Furrer, A and Hempelmann, R (1997) FOCUS: a hybrid TOF-spectrometer at SINQ. Physica B: Condensed Matter 234, 11741176.
Jansson, H and Swenson, J (2008) Dynamical changes of hemoglobin and its surrounding water during thermal denaturation as studied by quasielastic neutron scattering and temperature modulated differential scanning calorimetry. Journal of Chemical Physics 128, 245104.
Jansson, H, Kargl, F, Fernandez-Alonso, F and Swenson, J (2009) Dynamics of a protein and its surrounding environment: a quasielastic neutron scattering study of myoglobin in water and glycerol mixtures. Journal of Chemical Physics 130, 05B613.
Jasnin, M, Moulin, M, Härtlein, M, Zaccai, G and Tehei, M (2008 a) In vivo measurement of internal and global macromolecular motions in Escherichia coli. Biophysical Journal 95, 857864.
Jasnin, M, Tehei, M, Moulin, M, Härtlein, M and Zaccai, G (2008 b) Solvent isotope effect on macromolecular dynamics in E. coli. European Biophysics Journal 37, 613617.
Jennings, BR and Parslow, K (1988) Particle size measurement: the equivalent spherical diameter. Proceedings of the Royal Society London A 419, 137149.
Jepsen, PU, Cooke, DG and Koch, M (2011) Terahertz spectroscopy and imaging – modern techniques and applications. Laser & Photonics Reviews 5, 124166.
Johnson, CSJ (1999) Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Progress in Nuclear Magnetic Resonance Spectroscopy 34, 203256.
Joti, Y, Kitao, A and Go, N (2005) Protein boson peak originated from hydration-related multiple minima energy landscape. Journal of the American Chemical Society 127, 87058709.
Kajimoto, R, Nakamura, M, Inamura, Y, Mizuno, F, Nakajima, K, Ohira-Kawamura, S, Yokoo, T, Nakatani, T, Maruyama, R, Soyama, K, Shibata, K, Suzuya, K, Sato, S, Aizawa, K, Arai, M, Wakimoto, S, Ishikado, M, Shamoto, S-i, Fujita, M, Hiraka, H, Ohoyama, K, Yamada, K and Lee, C-H (2011) The Fermi chopper spectrometer 4SEASONS at J-PARC. Journal of the Physical Society of Japan, 80(Suppl. B), SB025.
Kalinin, IV, Morozov, VM, Novikov, AG, Puchkov, AV, Savostin, VV, Sudarev, VV, Bulkin, AP, Kalinin, SI, Pusenkov, VM and Ul'yanov, VA (2014) Characteristics of the DIN-2PI spectrometer with a neutron concentrator. Technical Physics 59, 307310.
Karplus, M and McCammon, JA (2002) Molecular dynamics simulations of biomolecules. Nature Structural and Molecular Biology 9, 646.
Katan, AJ and Dekker, C (2011) High-speed AFM reveals the dynamics of single biomolecules at the nanometer scale. Cell 147, 979982.
Kataoka, M, Ferrand, M, Goupil-Lamy, A, Kamikubo, H, Yunoki, J, Oka, T and Smith, J (1999 a) Dynamical and structural modifications of staphylococcal nuclease on C-terminal truncation. Physica B Condensed Matter 266, 2026.
Kataoka, M, Kamikubo, H, Yunoki, J, Tokunaga, F, Kanaya, T, Izumi, Y and Shibata, K (1999 b) Low energy dynamics of globular proteins studied by inelastic neutron scattering. Journal of Physics and Chemistry of Solids 60, 12851289.
Kay, LE (2005) NMR studies of protein structure and dynamics. Journal of Magnetic Resonance 173, 193207.
Keeler, C, Dannies, PS and Hodsdon, ME (2003) The tertiary structure and backbone dynamics of human prolactin. Journal of Molecular Biology 328, 11051121.
Kern, D and Zuiderweg, ER (2003) The role of dynamics in allosteric regulation. Current Opinion in Structural Biology 13, 748757.
Khodadadi, S and Sokolov, AP (2015) Protein dynamics: from rattling in a cage to structural relaxation. Soft Matter 11, 49844998.
Khodadadi, S and Sokolov, AP (2017) Atomistic details of protein dynamics and the role of hydration water. Biochimica et Biophysica Acta General Subjects 1861, 35463552.
Khodadadi, S, Pawlus, S and Sokolov, A (2008) Influence of hydration on protein dynamics: combining dielectric and neutron scattering spectroscopy data. Journal of Physical Chemistry B 112, 1427314280.
Kim, YS and Hochstrasser, RM (2009) Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics. Journal of Physical Chemistry B 113, 82318251.
Kim, KH, Muniyappan, S, Oang, KY, Kim, JG, Nozawa, S, Sato, T, Koshihara, S-y, Henning, R, Kosheleva, I, Ki, H, Kim, Y, Kim, TW, Kim, J, Adachi, S-i and Ihee, H (2012 a) Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump–probe X-ray solution scattering. Journal of the American Chemical Society 134, 70017008.
Kim, TW, Lee, JH, Choi, J, Kim, KH, van Wilderen, LJ, Guerin, L, Kim, Y, Jung, YO, Yang, C, Kim, J, Wulff, M, van Thor, JJ and Ihee, H (2012 b) Protein structural dynamics of photoactive yellow protein in solution revealed by pump–probe X-ray solution scattering. Journal of the American Chemical Society 134, 31453153.
Kim, JG, Kim, TW, Kim, J and Ihee, H (2015) Protein structural dynamics revealed by time-resolved X-ray solution scattering. Accounts of Chemical Research 48, 22002208.
Kirby, NM and Cowieson, NP (2014) Time-resolved studies of dynamic biomolecules using small angle X-ray scattering. Current Opinion in Structural Biology 28, 4146.
Kleckner, IR and Foster, MP (2011) An introduction to NMR-based approaches for measuring protein dynamics. BBA-Proteins and Proteomics 1814, 942968.
Klose, D, Voskoboynikova, N, Orban-Glass, I, Rickert, C, Engelhard, M, Klare, JP and Steinhoff, H-J (2014) Light-induced switching of HAMP domain conformation and dynamics revealed by time-resolved EPR spectroscopy. FEBS Letters 588, 39703976.
Kneller, GR (2000) Inelastic neutron scattering from damped collective vibrations of macromolecules. Chemical Physics 261, 124.
Kneller, GR (2005) Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models. Physical Chemistry Chemical Physics 7, 26412655.
Kneller, GR (2018) Franck–Condon picture of incoherent neutron scattering. Proceedings of the National Academy of Sciences (USA) 115, 94509455.
Kneller, GR and Hinsen, K (2004) Fractional Brownian dynamics in proteins. The Journal of Chemical Physics 121, 1027810283.
Kneller, GR, Keiner, V, Kneller, M and Schiller, M (1995) nMOLDYN: a program package for a neutron scattering oriented analysis of molecular dynamics simulations. Computer Physics Communications 91, 191214.
Kolano, C, Helbing, J, Kozinski, M, Sander, W and Hamm, P (2006) Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy. Nature 444, 469.
Kong, J and Yu, S (2007) Fourier transform infrared spectroscopic analysis of protein secondary structures. Acta Biochimica et Biophysica Sinica 39, 549559.
Kornev, AP and Taylor, SS (2015) Dynamics-driven allostery in protein kinases. Trends in Biochemical Sciences 40, 628647.
Korzhnev, D, Billeter, M, Arseniev, A and Orekhov, VY (2001) NMR studies of Brownian tumbling and internal motions in proteins. Progress in Nuclear Magnetic Resonance Spectroscopy 3, 197266.
Kötting, C and Gerwert, K (2015) What vibrations tell us about GTPases. Biological Chemistry 396, 131144.
Kowlessur, D and Tobacman, LS (2010 a) Troponin regulatory function and dynamics revealed by H/D exchange-mass spectrometry. Journal of Biological Chemistry 285, 26862694.
Kowlessur, D and Tobacman, LS (2010 b) Low temperature dynamic mapping reveals unexpected order and disorder in troponin. Journal of Biological Chemistry 285, 3897838986.
Kowlessur, D and Tobacman, LS (2012) Significance of troponin dynamics for Ca2+-mediated regulation of contraction and inherited cardiomyopathy. Journal of Biological Chemistry 287, 4229942311.
Krichevsky, O and Bonnet, G (2002) Fluorescence correlation spectroscopy: the technique and its applications. Reports on Progress in Physics 65, 251.
Krushelnitsky, A, Zinkevich, T, Mukhametshina, N, Tarasova, N, Gogolev, Y, Gnezdilov, O, Fedotov, V, Belton, P and Reichert, D (2009) 13C and 15N NMR study of the hydration response of T4 lysozyme and αb-crystallin internal dynamics. Journal of Physical Chemistry B 113, 1002210034.
Krushelnitsky, A, Reichert, D and Saalwächter, K (2013) Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds. Accounts of Chemical Research 46, 20282036.
Kuehner, DE, Heyer, C, Rämsch, C, Fornefeld, UM, Blanch, HW and Prausnitz, JM (1997) Interactions of lysozyme in concentrated electrolyte solutions from dynamic light-scattering measurements. Biophysical Journal 73, 32113224.
Kuhne, J, Eisenhauer, K, Ritter, E, Hegemann, P, Gerwert, K and Bartl, F (2015) Early formation of the ion-conducting pore in channel rhodopsin-2. Angewandte Chemie International Edition 54, 49534957.
Kuzmenkina, EV, Heyes, CD and Nienhaus, GU (2005) Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions. Proceedings of the National Academy of Sciences (USA) 102, 1547115476.
Lakshmikanth, G and Krishnamoorthy, G (1999) Solvent-exposed tryptophans probe the dynamics at protein surfaces. Biophysical Journal 77, 11001106.
Lal, J, Fouquet, P, Maccarini, M and Makowski, L (2010) Neutron spin-echo studies of hemoglobin and myoglobin: multiscale internal dynamics. Journal of Molecular Biology 397, 423435.
Lal, J, Maccarini, M, Fouquet, P, Ho, NT, Ho, C and Makowski, L (2017) Modulation of hemoglobin dynamics by an allosteric effector. Protein Science 26, 505514.
Lamboy, JA, Kim, H, Lee, KS, Ha, T and Komives, EA (2011) Visualization of the nanospring dynamics of the iκbα ankyrin repeat domain in real time. Proceedings of the National Academy of Sciences (USA) 108, 1017810183.
Latham, MP and Kay, LE (2012) Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate. PLoS One 7, e48226.
Le Bon, C, Nicolai, T, Kuil, ME and Hollander, JG (1999) Self-diffusion and cooperative diffusion of globular proteins in solution. Journal of Physical Chemistry B 103, 1029410299.
Le Coeur, C and Longeville, S (2008) Microscopic protein diffusion at high concentration by neutron spin-echo spectroscopy. Chemical Physics 345, 298304.
Lee, J, Jeong, K-W, Jin, B, Ryu, K-S, Kim, E-H, Ahn, J-H and Kim, Y (2013) Structural and dynamic features of cold-shock proteins of listeria monocytogenes, a psychrophilic bacterium. Biochemistry 52, 24922504.
Leheny, RL (2012) XPCS: nanoscale motion and rheology. Current Opinion in Colloid and Interface Science 17, 312.
Lehnert, U, Réat, V, Weik, M, Zaccai, G and Pfister, C (1998) Thermal motions in bacteriorhodopsin at different hydration levels studied by neutron scattering: correlation with kinetics and light-induced conformational changes. Biophysical Journal 75, 19451952.
Lenton, S, Grimaldo, M, Roosen-Runge, F, Schreiber, F, Nylander, T, Clegg, R, Holt, C, Härtlein, M, Sakai, VG, Seydel, T and Teixeira, SCM (2017) Effect of phosphorylation on a human-like osteopontin peptide. Biophysical Journal 112, 15861596.
Leone, M, Di Lello, P, Ohlenschläger, O, Pedone, EM, Bartolucci, S, Rossi, M, Di Blasio, B, Pedone, C, Saviano, M, Isernia, C and Fattorusso, R (2004) Solution structure and backbone dynamics of the K18G/R82E alicyclobacillus acidocaldarius thioredoxin mutant: a molecular analysis of its reduced thermal stability. Biochemistry 43, 60436058.
Lerbret, A, Hdoux, A, Annighfer, B and Bellissent-Funel, M-C (2013) Influence of pressure on the low-frequency vibrational modes of lysozyme and water: a complementary inelastic neutron scattering and molecular dynamics simulation study. Proteins: Structure, Function, and Bioinformatics 81, 326340.
Levantino, M, Lemke, HT, Schiro, G, Glownia, M, Cupane, A and Cammarata, M (2015) Observing heme doming in myoglobin with femtosecond X-ray absorption spectroscopy). Structural Dynamics 2, 041713.
Lewis, EN, Qi, W, Kidder, LH, Amin, S, Kenyon, SM and Blake, S (2014) Combined dynamic light scattering and Raman spectroscopy approach for characterizing the aggregation of therapeutic proteins. Molecules 19, 2088820905.
Leyser, H, Doster, W and Diehl, M (1999) Far-infrared emission by Boson peak vibrations in a globular protein. Physical Review Letters 82, 29872990.
Li, H and Akasaka, K (2006) Conformational fluctuations of proteins revealed by variable pressure NMR. BBA-Proteins and Proteomics 1764, 331345.
Li, C, Charlton, LM, Lakkavaram, A, Seagle, C, Wang, G, Young, GB, Macdonald, JM and Pielak, GJ (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy. Journal of the American Chemical Society 130, 63106311.
Li, Y, Lubchenko, V and Vekilov, PG (2011) The use of dynamic light scattering and Brownian microscopy to characterize protein aggregation. Review of Scientific Instruments 82, 053106.
Lima, FA, Milne, CJ, Amarasinghe, DC, Rittmann-Frank, MH, Veen, RMvd, Reinhard, M, Pham, V-T, Karlsson, S, Johnson, SL, Grolimund, D, Borca, C, Huthwelker, T, Janousch, M, van Mourik, F, Abela, R and Chergui, M (2011) A high-repetition rate scheme for synchrotron-based picosecond laser pump/X-ray probe experiments on chemical and biological systems in solution. Review of Scientific Instruments 82, 063111.
Lippincott-Schwartz, J, Snapp, E and Kenworthy, A (2001) Studying protein dynamics in living cells. Nature Reviews. Molecular Cell Biology 2, 444456.
Liu, Y, Porcar, L, Chen, J, Chen, W-R, Falus, P, Faraone, A, Fratini, E, Hong, K and Baglioni, P (2010) Lysozyme protein solution with an intermediate range order structure. Journal of Physical Chemistry B 115, 72387247.
Liu, B, Chia, D, Csizmok, V, Farber, P, Forman-Kay, JD and Gradinaru, CC (2014) The effect of intrachain electrostatic repulsion on conformational disorder and dynamics of the Sic1 protein. Journal of Physical Chemistry B 118, 40884097.
Liu, X, Shi, D, Zhou, S, Liu, H, Liu, H and Yao, X (2018) Molecular dynamics simulations and novel drug discovery. Expert Opinion on Drug Discovery 13, 2337.
Longeville, S, Doster, W, Diehl, M, Gaehler, R and Petry, W (2003 a) Neutron resonance spin echo: oxygen transport in crowded protein solutions. In Mezei, F, Pappas, C, Gutberlet, T (eds), Neutron Spin Echo Spectroscopy. Berlin, Heidelberg: Springer, pp. 325335.
Longeville, S, Doster, W and Kali, G (2003 b) Myoglobin in crowded solutions: structure and diffusion. Chemical Physics 292, 413424.
Longeville, S and Stingaciu, L-R (2017) Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells. Scientific Reports 7, 10448.
López-Peña, I, Leigh, BS, Schlamadinger, DE and Kim, JE (2015) Insights into protein structure and dynamics by ultraviolet and visible resonance Raman spectroscopy. Biochemistry 54, 47704783.
Luby-Phelps, K, Castle, PE, Taylor, DL and Lanni, F (1987) Hindered diffusion of inert tracer particles in the cytoplasm of mouse 3t3 cells. Proceedings of the National Academy of Sciences (USA) 84, 49104913.
Maes, D, Vorontsova, MA, Potenza, MA, Sanvito, T, Sleutel, M, Giglio, M and Vekilov, PG (2015) Do protein crystals nucleate within dense liquid clusters? Acta Crystallographica Section F 71, 815822.
Magazu, S, Maisano, G, Migliardo, F and Mondelli, C (2004) Mean-square displacement relationship in bioprotectant systems by elastic neutron scattering. Biophysical Journal 86, 32413249.
Magazù, S, Mezei, F, Falus, P, Farago, B, Mamontov, E, Russina, M and Migliardo, F (2017) Protein dynamics as seen by (quasi) elastic neutron scattering. Biochimica et Biophysica Acta General Subjects 1861, 35043512.
Makowski, L, Rodi, DJ, Mandava, S, Minh, DDL, Gore, DB and Fischetti, RF (2008) Molecular crowding inhibits intramolecular breathing motions in proteins. Journal of Molecular Biology 375, 529546.
Mamontov, E (2018) Microscopic diffusion processes measured in living planarians. Scientific Reports 8, 4190.
Mamontov, E and Herwig, KW (2011) A time-of-flight backscattering spectrometer at the spallation neutron source, BASIS. Review of Scientific Instruments 82, 085109.
Mandel, AM, Akke, M and Palmer, AG III (1995) Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. Journal of Molecular Biology, 246, 144163.
Marconi, M, Cornicchi, E, Onori, G and Paciaroni, A (2008) Comparative study of protein dynamics in hydrated powders and in solutions: a neutron scattering investigation. Chemical Physics 345, 224229.
Marion, J, Trovaslet, M, Martinez, N, Masson, P, Schweins, R, Nachon, F, Trapp, M and Peters, J (2015) Pressure-induced molten globule state of human acetylcholinesterase: structural and dynamical changes monitored by neutron scattering. Physical Chemistry Chemical Physics 17, 31573163.
Markelz, AG, Roitberg, A and Heilweil, EJ (2000) Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz. Chemical Physics Letters 320, 4248.
Markelz, AG, Knab, JR, Chen, JY and He, Y (2007) Protein dynamical transition in terahertz dielectric response. Chemical Physics Letters 442, 413417.
Martinez, N, Michoud, G, Cario, A, Ollivier, J, Franzetti, B, Jebbar, M, Oger, P and Peters, J (2016) High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes. Scientific Reports 6, 32816.
Matsuo, T, Tominaga, T, Kono, F, Shibata, K and Fujiwara, S (2017) Modulation of the picosecond dynamics of troponin by the cardiomyopathy-causing mutation K247R of troponin T observed by quasielastic neutron scattering. Biochimica et Biophysica Acta Proteins and Proteomics 1865, 17811789.
Matthies, M, Glinka, K, Theiling, M, Hideg, K and Steinhoff, H-J (2016) Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels. Applied Magnetic Resonance 47, 627641.
McCammon, JA (1984) Protein dynamics. Reports on Progress in Physics 47, 1.
Medina-Noyola, M (1988) Long-time self-diffusion in concentrated colloidal dispersions. Physical Review Letters 60, 27052708.
Mewis, J and Wagner, NJ (2012) Colloidal Suspension Rheology. Cambridge, UK: Cambridge University Press.
Meyer, A, Dimeo, R, Gehring, P and Neumann, D (2003) The high-flux backscattering spectrometer at the NIST center for neutron research. Review of Scientific Instruments 74, 27592777.
Mezei, F (1972) Neutron spin echo: a new concept in polarized thermal neutron techniques. Zeitschrift für Physik A: Hadrons and Nuclei 255, 146160.
Mezei, F, Pappas, C and Gutberlet, T (2002) Neutron Spin echo Spectroscopy: Basics, Trends and Applications, Volume 601. Berlin, Heidelberg, Germany: Springer Science & Business Media.
Mijovic, J, Bian, Y, Gross, RA and Chen, B (2005) Dynamics of proteins in hydrated state and in solution as studied by dielectric relaxation spectroscopy. Macromolecules 38, 1081210819.
Minh, DD, Chang, C-E, Trylska, J, Tozzini, V and McCammon, JA (2006) The influence of macromolecular crowding on HIV-1 protease internal dynamics. Journal of the American Chemical Society 128, 60066007.
Mitsutake, A and Takano, H (2018) Relaxation mode analysis for molecular dynamics simulations of proteins. Biophysical Reviews 10, 375389.
Mittermaier, AK and Kay, LE (2009) Observing biological dynamics at atomic resolution using NMR. Trends in Biochemical Sciences 34, 601611.
Mok, KH, Nagashima, T, Day, IJ, Jones, JA, Jones, CJ, Dobson, CM and Hore, P (2003) Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: applications to real-time protein folding. Journal of the American Chemical Society 125, 1248412492.
Möller, J, Chushkin, Y, Prévost, S and Narayanan, T (2016) Multi-speckle X-ray photon correlation spectroscopy in the ultra-small-angle X-ray scattering range. Journal of Synchrotron Radiation 23, 929936.
Mondal, S, Kallianpur, MV, Udgaonkar, JB and Krishnamoorthy, G (2015) Molecular crowding causes narrowing of population heterogeneity and restricts internal dynamics in a protein. Methods and Applications in Fluorescence 4, 014003.
Monkenbusch, M and Richter, D (2007) High resolution neutron spectroscopy – a tool for the investigation of dynamics of polymers and soft matter. Comptes Rendus Physique 8, 845864.
Monkenbusch, M, Richter, D and Biehl, R (2010) Observation of protein domain motions by neutron spectroscopy. ChemPhysChem 11, 11881194.
Monkenbusch, M, Stadler, A, Biehl, R, Ollivier, J, Zamponi, M and Richter, D (2015) Fast internal dynamics in alcohol dehydrogenase. Journal of Chemical Physics 143, 075101.
Morone, N, Fujiwara, T, Murase, K, Kasai, RS, Ike, H, Yuasa, S, Usukura, J and Kusumi, A (2006) Three-dimensional reconstruction of the membrane skeleton at the plasma membrane interface by electron tomography. Journal of Cell Biology 174, 851862.
Motlagh, HN, Wrabl, JO, Li, J and Hilser, VJ (2014) The ensemble nature of allostery. Nature 508, 331.
Mukhopadhyay, S, Nayak, PK, Udgaonkar, JB and Krishnamoorthy, G (2006) Characterization of the formation of amyloid protofibrils from barstar by mapping residue-specific fluorescence dynamics. Journal of Molecular Biology 358, 935942.
Mukhopadhyay, S, Krishnan, R, Lemke, EA, Lindquist, S and Deniz, AA (2007) A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. Proceedings of the National Academy of Sciences (USA) 104, 26492654.
Müller-Späth, S, Soranno, A, Hirschfeld, V, Hofmann, H, Rüegger, S, Reymond, L, Nettels, D and Schuler, B (2010) Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proceedings of the National Academy of Sciences (USA) 107, 1460914614.
Murphy, RM (1997) Static and dynamic light scattering of biological macromolecules: what can we learn? Current Opinion in Biotechnology 8, 2530.
Muschol, M and Rosenberger, F (1995) Interactions in undersaturated and supersaturated lysozyme solutions: static and dynamic light scattering results. Journal of Chemical Physics 103, 1042410432.
Myung, JS, Roosen-Runge, F, Winkler, RG, Gompper, G, Schurtenberger, P and Stradner, A (2018) Weak shape anisotropy leads to a nonmonotonic contribution to crowding, impacting protein dynamics under physiologically relevant conditions. Journal of Physical Chemistry B 122, 1239612402.
Nägele, G (1996) On the dynamics and structure of charge-stabilized suspensions. Physics Reports 272, 215372.
Nakajima, K, Ohira-Kawamura, S, Kikuchi, T, Nakamura, M, Kajimoto, R, Inamura, Y, Takahashi, N, Aizawa, K, Suzuya, K, Shibata, K, Nakatani, T, Soyama, K, Maruyama, R, Tanaka, H, Kambara, W, Iwahashi, T, Itoh, Y, Osakabe, T, Wakimoto, S, Kakurai, K, Maekawa, F, Harada, M, Oikawa, K, Lechner, RE, Mezei, F and Arai, M (2011) AMATERAS: a cold-neutron disk chopper spectrometer. Journal of the Physical Society of Japan, 80(Suppl. B), SB028.
Nakamura, M, Ueki, S, Hara, H and Arata, T (2005) Calcium structural transition of human cardiac troponin C in reconstituted muscle fibres as studied by site-directed spin labelling. Journal of Molecular Biology 348, 127137.
Nakanishi, M and Sokolov, AP (2015) Protein dynamics in a broad frequency range: dielectric spectroscopy studies. Journal of Non-Crystalline Solids 407, 478485.
Nandi, N, Bhattacharyya, K and Bagchi, B (2000) Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems. Chemical Reviews 100, 20132046.
Narayanan, T, Wacklin, H, Konovalov, O and Lund, R (2017) Recent applications of synchrotron radiation and neutrons in the study of soft matter. Crystallography Reviews 23, 160226.
Natali, F, Peters, J, Russo, D, Barbieri, S, Chiapponi, C, Cupane, A, Deriu, A, Bari, MTD, Farhi, E, Gerelli, Y, Mariani, P, Paciaroni, A, Rivasseau, C, Schiro, G and Sonvico, F (2008) IN13 backscattering spectrometer at ILL: looking for motions in biological macromolecules and organisms. Neutron News 19, 1418.
Nath, A and Rhoades, E (2013) A flash in the pan: dissecting dynamic amyloid intermediates using fluorescence. FEBS Letters 587, 10961105.
Nath, S, Meuvis, J, Hendrix, J, Carl, SA and Engelborghs, Y (2010) Early aggregation steps in α-synuclein as measured by FCS and FRET: evidence for a contagious conformational change. Biophysical Journal 98, 13021311.
Navirian, HA, Herzog, M, Goldshteyn, J, Leitenberger, W, Vrejoiu, I, Khakhulin, D, Wulff, M, Shayduk, R, Gaal, P and Bargheer, M (2011) Shortening X-ray pulses for pump-probe experiments at synchrotrons. Journal of Applied Physics 109, 126104.
Nawrocki, G, Wang, P-H, Yu, I, Sugita, Y and Feig, M (2017) Slow-down in diffusion in crowded protein solutions correlates with transient cluster formation. Journal of Physical Chemistry B 121, 1107211084.
Neuman, KC and Nagy, A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nature Methods 5, 491505.
Nibbering, ETJ, Fidder, H and Pines, E (2005) Ultrafast chemistry: using time-resolved vibrational spectroscopy for interrogation of structural dynamics. Annual Review of Physical Chemistry 56, 337367.
Nickels, JD, O'Neill, H, Hong, L, Tyagi, M, Ehlers, G, Weiss, KL, Zhang, Q, Yi, Z, Mamontov, E, Smith, JC and Sokolov, AP (2012) Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophysical Journal 103, 15661575.
Nienhaus, GU (2006) Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromolecular Bioscience 6, 907922.
Nienhaus, K and Nienhaus, GU (2016) Where do we stand with super-resolution optical microscopy? Journal of Molecular Biology 428, 308322.
Ohl, M, Monkenbusch, M, Arend, N, Kozielewski, T, Vehres, G, Tiemann, C, Butzek, M, Soltner, H, Giesen, U, Achten, R, Stelzer, H, Lindenau, B, Budwig, A, Kleines, H, Drochner, M, Kaemmerling, P, Wagener, M, Müller, R, Iverson, E, Sharp, M and Richter, D (2012) The spin-echo spectrometer at the Spallation Neutron Source (SNS). Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 696, 8599.
Okumura, H, Higashi, M, Yoshida, Y, Sato, H and Akiyama, R (2017) Theoretical approaches for dynamical ordering of biomolecular systems. Biochimica et Biophysica Acta (BBA)-General Subjects 1862, 212228.
Oleinikova, A, Sasisanker, P and Weingärtner, H (2004) What can really be learned from dielectric spectroscopy of protein solutions? A case study of ribonuclease A. Journal of Physical Chemistry B 108, 84678474.
Ollivier, J, Mutka, H and Didier, L (2010) The new cold neutron time-of-flight spectrometer IN5. Neutron News 21, 2225.
Olsson, C, Jansson, H and Swenson, J (2016) The role of trehalose for the stabilization of proteins. Journal of Physical Chemistry B 120, 47234731.
Ortega, A, Amorós, D and García De La Torre, J (2011) Prediction of hydrodynamic and other solution properties of rigid proteins from atomic- and residue-level models. Biophysical Journal 101, 892898.
Ortore, MG, Spinozzi, F, Mariani, P, Paciaroni, A, Barbosa, LR, Amenitsch, H, Steinhart, M, Ollivier, J and Russo, D (2009) Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution. Journal of the Royal Society, Interface 6, S619.
Papaleo, E, Parravicini, F, Grandori, R, De Gioia, L and Brocca, S (2014) Structural investigation of the cold-adapted acylaminoacyl peptidase from sporosarcina psychrophila by atomistic simulations and biophysical methods. BBA-Proteins and Proteomics 1844, 22032213.
Papaleo, E, Saladino, G, Lambrughi, M, Lindorff-Larsen, K, Gervasio, FL and Nussinov, R (2016) The role of protein loops and linkers in conformational dynamics and allostery. Chemical Reviews 116, 63916423.
Parak, FG (2003 a) Physical aspects of protein dynamics. Reports on Progress in Physics 66, 103.
Parak, FG (2003 b) Proteins in action: the physics of structural fluctuations and conformational changes. Current Opinion in Structural Biology 13, 552557.
Parak, F, Knapp, E and Kucheida, D (1982) Protein dynamics: Mössbauer spectroscopy on deoxymyoglobin crystals. Journal of Molecular Biology 161, 177194.
Parigi, G, Rezaei-Ghaleh, N, Giachetti, A, Becker, S, Fernandez, C, Blackledge, M, Griesinger, C, Zweckstetter, M and Luchinat, C (2014) Long-range correlated dynamics in intrinsically disordered proteins. Journal of the American Chemical Society 136, 1620116209.
Partikian, A, Ölveczky, B, Swaminathan, R, Li, Y and Verkman, A (1998) Rapid diffusion of green fluorescent protein in the mitochondrial matrix. Journal of Cell Biology 140, 821829.
Peng, H-L, Egawa, T, Chang, E, Deng, H and Callender, R (2015) Mechanism of thermal adaptation in the lactate dehydrogenases. Journal of Physical Chemistry B 119, 1525615262.
Pérez, J, Zanotti, J and Durand, D (1999) Evolution of the internal dynamics of two globular proteins from dry powder to solution. Biophysical Journal 77, 454469.
Perilla, JR, Goh, BC, Cassidy, CK, Liu, B, Bernardi, RC, Rudack, T, Yu, H, Wu, Z and Schulten, K (2015) Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology 31, 6474.
Perticaroli, S, Nickels, JD, Ehlers, G, Mamontov, E and Sokolov, AP (2014) Dynamics and rigidity in an intrinsically disordered protein, β-casein. Journal of Physical Chemistry B 118, 73177326.
Phair, RD and Misteli, T (2000) High mobility of proteins in the mammalian cell nucleus. Nature 404, 604609.
Phillies, GD (2016) Diffusion in crowded solutions. Advances in Chemical Physics 48, 277358.
Phillies, GDJ, Benedek, GB and Mazer, NA (1976) Diffusion in protein solutions at high concentrations: a study by quasielastic light scattering spectroscopy. Journal of Chemical Physics 65, 18831892.
Piazza, R (2004) Protein interactions and association: an open challenge for colloid science. Current Opinion in Colloid & Interface Science 8, 515522.
Piazza, R and Iacopini, S (2002) Transient clustering in a protein solution. European Physical Journal E: Soft Matter 7, 4548.
Pieper, J and Renger, G (2009) Protein dynamics investigated by neutron scattering. Photosynthesis Research 102, 281.
Piston, DW and Kremers, G-J (2007) Fluorescent protein FRET: the good, the bad and the ugly. Trends in Biochemical Sciences 32, 407414.
Pollack, L, Tate, M, Finnefrock, A, Kalidas, C, Trotter, S, Darnton, N, Lurio, L, Austin, R, Batt, C, Gruner, S, Mochrie, S (ed.), (2001) Time resolved collapse of a folding protein observed with small angle X-ray scattering. Physical Review Letters 86, 4962.
Porcar, L, Falus, P, Chen, W-R, Faraone, A, Fratini, E, Hong, K, Baglioni, P and Liu, Y (2009) Formation of the dynamic clusters in concentrated lysozyme protein solutions. Journal of Physical Chemistry Letters 1, 126129.
Poznański, J, Szymaǹski, J, Basiǹska, T, Słomkowski, S and Zielenkiewicz, W (2005) Aggregation of aqueous lysozyme solutions followed by dynamic light scattering and 1H NMR spectroscopy. Journal of Molecular Liquids 121, 2126.
Press, W (1981) Single-particle Rotations in Molecular Crystals. Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 1126.
Price, WS (1997) Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion: part 1. Basic theory. Concepts in Magnetic Resonance 9, 299336.
Price, WS (2000) NMR gradient methods in the study of proteins. Annual Reports on the Progress of Chemistry, Section C 96, 353.
Price, WS, Tsuchiya, F and Arata, Y (1999) Lysozyme aggregation and solution properties studied using PGSE NMR diffusion measurements. Journal of the American Chemical Society 121, 1150311512.
Protopapas, P, Andersen, HC and Parlee, NAD (1973) Theory of transport in liquid metals. I. Calculation of self-diffusion coefficients. Journal of Chemical Physics 59, 1525.
Pynn, R (1978) Neutron spin-echo and three-axis spectrometers. Journal of Physics E 11, 1133.
Quinn, M, Gnan, N, James, S, Ninarello, A, Sciortino, F, Zaccarelli, E and McManus, JJ (2015) How fluorescent labelling alters the solution behaviour of proteins. Physical Chemistry Chemical Physics 17, 3117731187.
Radestock, S and Gohlke, H (2011) Protein rigidity and thermophilic adaptation. Proteins 79, 10891108.
Ramboarina, S and Redfield, C (2008) Probing the effect of temperature on the backbone dynamics of the human α-lactalbumin molten globule. Journal of the American Chemical Society 130, 1531815326.
Réat, V, Patzelt, H, Ferrand, M, Pfister, C, Oesterhelt, D and Zaccai, G (1998) Dynamics of different functional parts of bacteriorhodopsin: H-2H labeling and neutron scattering. Proceedings of the National Academy of Sciences (USA) 95, 49704975.
Réat, V, Dunn, R, Ferrand, M, Finney, JL, Daniel, RM and Smith, JC (2000) Solvent dependence of dynamic transitions in protein solutions. Proceedings of the National Academy of Sciences (USA) 97, 99619966.
Receveur, V, Calmettes, P, Smith, JC, Desmadril, M, Coddens, G and Durand, D (1997) Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering. Proteins 28, 380387.
Reif, B, Xue, Y, Agarwal, V, Pavlova, MS, Hologne, M, Diehl, A, Ryabov, YE and Skrynnikov, NR (2006) Protein side-chain dynamics observed by solution-and solid-state NMR: comparative analysis of methyl 2 h relaxation data. Journal of the American Chemical Society 128, 1235412355.
Richter, D (2012) Future perspectives: moving to longer length and timescales, from polymers to biological macromolecules. In Garcia Sakai, V, Alba-Simionesco, C, Chen, SH (eds), Dynamics of Soft Matter. Boston, MA: Springer, pp. 145186..
Riest, J and Nägele, G (2015) Short-time dynamics in dispersions with competing short-range attraction and long-range repulsion. Soft Matter 11, 92739280.
Riest, J, Eckert, T, Richtering, W and Nägele, G (2015) Dynamics of suspensions of hydrodynamically structured particles: analytic theory and applications to experiments. Soft Matter 11, 28212843.
Riest, J, Nägele, G, Liu, Y, Wagner, NJ and Godfrin, PD (2018) Short-time dynamics of lysozyme solutions with competing short-range attraction and long-range repulsion: experiment and theory. Journal of Chemical Physics 148, 065101.
Rivas, G and Minton, AP (2016) Macromolecular crowding in vitro, in vivo, and in between. Trends in Biochemical Sciences 41, 970981.
Roberti, MJ, Jovin, TM and Jares-Erijman, E (2011) Confocal fluorescence anisotropy and FRAP imaging of α-synuclein amyloid aggregates in living cells. PLoS One 6, e23338.
Róg, T, Murzyn, K, Hinsen, K and Kneller, GR (2003) Nmoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations. Journal of Computational Chemistry 24, 657667.
Roh, JH, Curtis, JE, Azzam, S, Novikov, VN, Peral, I, Chowdhuri, Z, Gregory, RB and Sokolov, AP (2006) Influence of hydration on the dynamics of lysozyme. Biophysical Journal 91, 25732588.
Roos, M, Link, S, Balbach, J, Krushelnitsky, A and Saalwächter, K (2015) NMR-detected Brownian dynamics of αb-crystallin over a wide range of concentrations. Biophysical Journal 108, 98106.
Roos, M, Ott, M, Hofmann, M, Link, S, Roössler, E, Balbach, J, Krushelnitsky, A and Saalwächter, K (2016) Coupling and decoupling of rotational and translational diffusion of proteins under crowding conditions. Journal of the American Chemical Society 138, 1036510372.
Roosen-Runge, F and Seydel, T (2015) A generalized mean-squared displacement from inelastic fixed window scans of incoherent neutron scattering as a model-free indicator of anomalous diffusion confinement. EPJ Web of Conferences 83, 02015.
Roosen-Runge, F, Hennig, M, Seydel, T, Zhang, F, Skoda, MWA, Zorn, S, Jacobs, RMJ, Maccarini, M, Fouquet, P and Schreiber, F (2010) Protein diffusion in crowded electrolyte solutions. BBA-Proteins and Proteomics 1804, 6875.
Roosen-Runge, F, Hennig, M, Zhang, F, Jacobs, RMJ, Sztucki, M, Schober, H, Seydel, T and Schreiber, F (2011) Protein self-diffusion in crowded solutions. Proceedings of the National Academy of Sciences (USA) 108, 1181511820.
Roosen-Runge, F, Zhang, F, Schreiber, F and Roth, R (2014) Ion-activated attractive patches as a mechanism for controlled protein interactions. Scientific Reports 4, 07016.
Roosen-Runge, F, Bicout, DJ and Barrat, J-L (2016) Analytical correlation functions for motion through diffusivity landscapes. Journal of Chemical Physics 144, 204109.
Roseker, W, Hruszkewycz, S, Lehmkühler, F, Walther, M, Schulte-Schrepping, H, Lee, S, Osaka, T, Strüder, L, Hartmann, R, Sikorski, M, Song, S, Robert, A, Fuoss, PH, Sutton, M, Stephenson, GB and Grübel, G (2018) Towards ultrafast dynamics with split-pulse X-ray photon correlation spectroscopy at free electron laser sources. Nature Communications 9, 1704.
Rosov, N, Rathgeber, S and Monkenbusch, M (1999) Neutron spin echo spectroscopy at the NIST center for neutron research. In Cebe, P, Hsiao, BS and Lohse, DJ (eds), Scattering from Polymers, Chapter 7. Washington, DC: American Chemical Society, pp. 103116
Ross, C and Poirier, M (2004) Protein aggregation and neurodegenerative disease. Nature Medicine 10(Suppl): S10S17.
Roy, R, Hohng, S and Ha, T (2008) A practical guide to single-molecule FRET. Nature Methods 5, 507516.
Ruffle, B, Ollivier, J, Longeville, S and Lechner, RE (2000) Neutron time-of-flight measurement techniques: new possibilities of TOF spectroscopy with NEAT at BENSC. Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 449, 322330.
Russo, D, Pérez, J, Zanotti, J-M, Desmadril, M and Durand, D (2002) Dynamic transition associated with the thermal denaturation of a small beta protein. Biophysical Journal 83, 27922800.
Russo, D, Hura, GL and Copley, JR (2007) Effects of hydration water on protein methyl group dynamics in solution. Physical Review E 75, 040902.
Russo, D, Teixeira, J and Ollivier, J (2009) The impact of hydration water on the dynamics of side chains of hydrophobic peptides: from dry powder to highly concentrated solutions. Journal of Chemical Physics 130, 235101.
Sakai, VG and Arbe, A (2009) Quasielastic neutron scattering in soft matter. Current Opinion in Colloid & Interface Science 14, 381390.
Sakai, VG, Alba-Simionesco, C and Chen, SH (2011) Dynamics of Soft Matter: Neutron Applications. Berlin, Heidelberg, Germany: Springer Science & Business Media.
Sakai, VG, Khodadadi, S, Cicerone, MT, Curtis, JE, Sokolov, AP and Roh, JH (2013) Solvent effects on protein fast dynamics: implications for biopreservation. Soft Matter 9, 53365340.
Salbreux, G, Charras, G and Paluch, E (2012) Actin cortex mechanics and cellular morphogenesis. Trends in Cell Biology 22, 536545.
Sánchez-Rico, C, Voith von Voithenberg, L, Warner, L, Lamb, DC and Sattler, M (2017) Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR spectroscopy. Chemistry 23, 1426714277.
Santero, SP, Favretto, F, Zanzoni, S, Chignola, R, Assfalg, M and D'Onofrio, M (2016) Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level. Archives of Biochemistry and Biophysics 606, 99110.
Santo, KP, Berjanskii, M, Wishart, DS and Stepanova, M (2011) Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion 5, 188200.
Santos, A, Duarte, AG, Fedorov, A, Martinho, JM and Moura, I (2010) Rubredoxin mutant a51c unfolding dynamics: a Förster resonance energy transfer study. Biophysical Chemistry 148, 131137.
Saphire, EO, Stanfield, RL, Crispin, MDM, Parren, PWHI, Rudd, PM, Dwek, RA, Burton, DR and Wilson, IA (2002) Contrasting IgG structures reveal extreme asymmetry and flexibility. Journal of Molecular Biology 319, 918.
Sauter, A, Roosen-Runge, F, Zhang, F, Lotze, G, Jacobs, RMJ, and Schreiber, F (2015) Real-time observation of nonclassical protein crystallization kinetics. Journal of the American Chemical Society 137, 14851491.
Scheffold, F and Cerbino, R (2007) New trends in light scattering. Current Opinion in Colloid & Interface Science 12, 5057.
Schiro, G, Caronna, C, Natali, F, Koza, MM and Cupane, A (2011) The ‘protein dynamical transition’ does not require the protein polypeptide chain. Journal of Physical Chemistry Letters 2, 22752279.
Schmitz, KS (2012) An Introduction to Dynamic Light Scattering by Macromolecules. Boston: Academic Press.
Schneider, J, Zahn, J, Maglione, M, Sigrist, SJ, Marquard, J, Chojnacki, J, Krausslich, H-G, Sahl, SJ, Engelhardt, J and Hell, SW (2015) Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics. Nature Methods 12, 827830.
Schober, H (2014) An introduction to the theory of nuclear neutron scattering in condensed matter. Journal of Neutron Research 17, 109357.
Schöneberg, J, Ullrich, A and Noé, F (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics 7, 11.
Schotte, F, Lim, M, Jackson, TA, Smirnov, AV, Soman, J, Olson, JS, Phillips, GN, Wulff, M and Anfinrud, PA (2003) Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science 300, 19441947.
Schotte, F, Cho, HS, Kaila, VRI, Kamikubo, H, Dashdorj, N, Henry, ER, Graber, TJ, Henning, R, Wulff, M, Hummer, G, Kataoka, M and Anfinrud, PA (2012) Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Sciences (USA), 109 : 1925619261.
Schrank, TP, Bolen, DW and Hilser, VJ (2009) Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins. Proceedings of the National Academy of Sciences (USA) 106, 1698416989.
Schröter, G, Mann, D, Kötting, C and Gerwert, K (2015) Integration of Fourier transform infrared spectroscopy, fluorescence spectroscopy, steady-state kinetics and molecular dynamics simulations of g αi1 distinguishes between the gtp hydrolysis and GDP release mechanism. Journal of Biological Chemistry 290, 1708517095.
Schuler, B and Eaton, WA (2008) Protein folding studied by single-molecule FRET. Current Opinion in Structural Biology 18, 1626.
Schurtenberger, P and Augusteyn, RC (1991) Structural properties of polydisperse biopolymer solutions: a light scattering study of bovine alpha-crystallin. Biopolymers 31, 12291240.
Schweitzer-Stenner, R (2005) Structure and dynamics of biomolecules probed by Raman spectroscopy. Journal of Raman Spectroscopy 36, 276278.
Schwille, P, Haupts, U, Maiti, S and Webb, WW (1999) Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one-and two-photon excitation. Biophysical Journal 77, 22512265.
Sears, VF (1992) Neutron scattering lengths and cross sections. Neutron News 3, 2637.
Sekar, RB and Periasamy, A (2003) Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. Journal of Cell Biology 160, 629633.
Selhuber-Unkel, C, Yde, P, Berg-Sørensen, K and Oddershede, LB (2009) Variety in intracellular diffusion during the cell cycle. Physical Biology 6, 025015.
Senff, H and Richtering, W (1999) Temperature sensitive microgel suspensions: colloidal phase behavior and rheology of soft spheres. Journal of Chemical Physics 111, 17051711.
Sentjabrskaja, T, Zaccarelli, E, De Michele, C, Sciortino, F, Tartaglia, P, Voigtmann, T, Egelhaaf, SU and Laurati, M (2016) Anomalous dynamics of intruders in a crowded environment of mobile obstacles. Nature Communications 7, 11133.
Separovic, F, Lam, Y, Ke, X and Chan, H-K (1998) A solid-state NMR study of protein hydration and stability. Pharmaceutical Research 15, 18161821.
Seto, H, Itoh, S, Yokoo, T, Endo, H, Nakajima, K, Shibata, K, Kajimoto, R, Ohira-Kawamura, S, Nakamura, M, Kawakita, Y, Nakagawa, H and Yamada, T (2017) Inelastic and quasi-elastic neutron scattering spectrometers in J-PARC. Biochimica et Biophysica Acta General Subjects 1861, 36513660.
Seydel, T, Madsen, A, Tolan, M, Grübel, G and Press, W (2001) Capillary waves in slow motion. Physical Review B 63, 073409.
Shen, CL, Scott, GL, Merchant, F and Murphy, RM (1993) Light scattering analysis of fibril growth from the amino-terminal fragment beta(1–28) of beta-amyloid peptide. Biophysical Journal 65, 23832395.
Shi, L, Lake, EM, Ahmed, MA, Brown, LS and Ladizhansky, V (2009) Solid-state NMR study of proteorhodopsin in the lipid environment: secondary structure and dynamics. Biochimica et Biophysica Acta Biomembranes 1788, 25632574.
Shibata, K, Takahashi, N, Kawakita, Y, Matsuura, M, Yamada, T, Tominaga, T, Kambara, W, Kobayashi, M, Inamura, Y, Nakatani, T, Nakajima, K and Arai, M (2015) The performance of TOF near backscattering spectrometer DNA in MLF, J-PARC. JPS Conference Proceedings 8, 036022.
Shirane, G, Shapiro, SM and Tranquada, JM (2002) Neutron scattering with a triple-axis spectrometer: basic techniques. Cambridge, UK: Cambridge University Press.
Shrestha, UR, Bhowmik, D, Copley, JRD, Tyagi, M, Leo, JB and Chu, X-q (2015) Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile. Proceedings of the National Academy of Sciences (USA) 112, 1388613891.
Shrestha, UR, Perera, SM, Bhowmik, D, Chawla, U, Mamontov, E, Brown, MF and Chu, X-Q (2016) Quasi-elastic neutron scattering reveals ligand-induced protein dynamics of a g-protein-coupled receptor. Journal of Physical Chemistry Letters 7, 41304136.
Siglioccolo, A, Gerace, R and Pascarella, S (2010) ‘Cold spots’ in protein cold adaptation: insights from normalized atomic displacement parameters (B’-factors). Biophysical Chemistry 153, 104114.
Sill, C, Biehl, R, Hoffmann, B, Radulescu, A, Appavou, M-S, Farago, B, Merkel, R and Richter, D (2016) Structure and domain dynamics of human lactoferrin in solution and the influence of Fe(III)-ion ligand binding. BMC Biophysics 9, 7.
Singwi, KS and Sjölander, A (1960) Diffusive motions in water and cold neutron scattering. Physical Review 119, 863871.
Skrynnikov, NR, Millet, O and Kay, LE (2002) Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions. Journal of the American Chemical Society 124, 64496460.
Smith, J (1991) Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Quarterly Reviews of Biophysics 87, 16011605.
Smith, J, Kuczera, K and Karplus, M (1990) Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra. Proceedings of the National Academy of Sciences (USA) 87, 16011605.
Smith, JC, Tan, P, Petridis, L and Hong, L (2018) Dynamic neutron scattering by biological systems. Annual Review of Biophysics 47, 335354.
Smolin, N, Biehl, R, Kneller, G, Richter, D and Smith, JC (2012) Functional domain motions in proteins on the 1–100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation. Biophysical Journal 102, 11081117.
Soranno, A, Buchli, B, Nettels, D, Cheng, RR, Müller-Späth, S, Pfeil, SH, Hoffmann, A, Lipman, EA, Makarov, DE and Schuler, B (2012) Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Proceedings of the National Academy of Sciences (USA) 109, 178017806.
Soraruf, D, Roosen-Runge, F, Grimaldo, M, Zanini, F, Schweins, R, Seydel, T, Zhang, F, Roth, R, Oettel, M and Schreiber, F (2014) Protein cluster formation in aqueous solution in the presence of multivalent metal ions – a light scattering study. Soft Matter 10, 894902.
Spencer Kimball PM and the GIMP Development Team. Gimp 2.8.16. Available at www.gimp.org (accessed April 11, 2019).
Spiga, E, Abriata, LA, Piazza, F and Dal Peraro, M (2014) Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics. Journal of Physical Chemistry B 118, 53105321.
Squires, GL (2012) Introduction to the Theory of Thermal Neutron Scattering. Cambridge University Press.
Srajer, V, Ren, Z, Teng, T-Y, Schmidt, M, Ursby, T, Bourgeois, D, Pradervand, C, Schildkamp, W, Wulff, M and Moffat, K (2001) Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochemistry 40, 1380213815.
Stadler, AM (2018) Conformational motions of disordered proteins. In Artmann, G, Artmann, A, Zhubanova, A, Digel, I (eds), Biological, Physical and Technical Basics of Cell Engineering. Singapore: Springer, pp. 381399.
Stadler, A, Digel, I, Artmann, GM, Embs, JP, Zaccai, G and Büldt, G (2008) Hemoglobin dynamics in red blood cells: correlation to body temperature. Biophysical Journal 95, 54495461.
Stadler, A, Digel, I, Embs, J, Unruh, T, Tehei, M, Zaccai, G, Büldt, G and Artmann, G (2009) From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature. Biophysical Journal 96, 50735081.
Stadler, AM, Van Eijck, L, Demmel, F and Artmann, G (2010) Macromolecular dynamics in red blood cells investigated using neutron spectroscopy. Journal of the Royal Society Interface 8, 590600.
Stadler, AM, Fabiani, E and Zaccai, G (2012 a) Changes in molecular dynamics of apomyoglobin during amyloid formation. Journal of Physics Conference Series 340, 012092.
Stadler, AM, Pellegrini, E, Johnson, M, Fitter, J and Zaccai, G (2012 b) Dynamics-stability relationships in apo- and holomyoglobin: a combined neutron scattering and molecular dynamics simulations study. Biophysical Journal 102, 351359.
Stadler, AM, Garvey, CJ, Bocahut, A, Sacquin-Mora, S, Digel, I, Schneider, GJ, Natali, F, Artmann, GM and Zaccai, G (2012 c) Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics. Journal of the Royal Society Interface 9, 28452855.
Stadler, A, Monkenbusch, M, Biehl, R, Richter, D and Ollivier, J (2013 a) Neutron spin-echo and ToF reveals protein dynamics in solution. Journal of the Physical Society of Japan, 82 (Suppl. A), SA016.
Stadler, AM, Unruh, T, Namba, K, Samatey, F and Zaccai, G (2013 b) Correlation between supercoiling and conformational motions of the bacterial flagellar filament. Biophysical Journal 105, 21572165.
Stadler, AM, Garvey, CJ, Embs, JP, Koza, MM, Unruh, T, Artmann, G and Zaccai, G (2014 a) Picosecond dynamics in haemoglobin from different species: a quasielastic neutron scattering study. Biochimica et Biophysica Acta 1840, 29892999.
Stadler, AM, Stingaciu, L, Radulescu, A, Holderer, O, Monkenbusch, M, Biehl, R and Richter, D (2014 b) Internal nanosecond dynamics in the intrinsically disordered myelin basic protein. Journal of the American Chemical Society 136, 69876994.
Stadler, AM, Demmel, F, Ollivier, J and Seydel, T (2016 a) Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding. Physical Chemistry Chemical Physics 18, 2152721538.
Stadler, AM, Knieps-Grnhagen, E, Bocola, M, Lohstroh, W, Zamponi, M and Krauss, U (2016 b) Photoactivation reduces side-chain dynamics of a LOV photoreceptor. Biophysical Journal 110, 10641074.
Stafford, KA, Robustelli, P and Palmer, AG III (2013) Thermal adaptation of conformational dynamics in ribonuclease H. PLoS Computational Biology 9, e1003218.
Stagg, L, Zhang, S, Cheung, M and Pernilla, W (2007) Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. Proceedings of the National Academy of Sciences (USA) 104, 1897618981.
Steinhoff, H-J, Mollaaghababa, R, Altenbach, C, Hideg, K, Krebs, M, Khorana, HG and Hubbell, WL (1994) Time-resolved detection of structural changes during the photocycle of spin-labeled bacteriorhodopsin. Science 266, 105107.
Stepanova, M (2007) Dynamics of essential collective motions in proteins: theory. Physical Review E 76, 051918.
Stingaciu, LR, Ivanova, O, Ohl, M, Biehl, R and Richter, D (2016) Fast antibody fragment motion: flexible linkers act as entropic spring. Scientific Reports 6, 22148.
Stone, MJ, Chandrasekhar, K, Holmgren, A, Wright, PE and Dyson, HJ (1993) Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Escherichia coli thioredoxin using nitrogen-15 NMR relaxation measurements. Biochemistry 32, 426435.
Stradner, A, Sedgwick, H, Cardinaux, F, Poon, WC, Egelhaaf, SU and Schurtenberger, P (2004) Equilibrium cluster formation in concentrated protein solutions and colloids. Nature 432, 492495.
Stueker, O, Ortega, VA, Goss, GG and Stepanova, M (2014) Understanding interactions of functionalized nanoparticles with proteins: a case study on lactate dehydrogenase. Small 10, 20062021.
Sun, Y, Zhu, D, Song, S, Decker, F-J, Sutton, M, Ludwig, K, Roseker, W, Grübel, G, Hruszkewycz, S, Stephenson, GB, Fuoss, PH and Robert, A (2017) Characterization of the LCLS nanosecond two-bunch mode for X-ray speckle visibility spectroscopy experiments. In Proc. SPIE 10237. Advances in X-ray Free-Electron Lasers Instrumentation IV, 102370N.
Svergun, DI and Koch, MHJ (2003) Small-angle scattering studies of biological macromolecules in solution. Reports on Progress in Physics 66, 1735.
Swaminathan, R, Hoang, CP and Verkman, AS (1997) Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-s65t in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophysical Journal 72, 19001907.
T-REX. European Spallation Source. Available at https://europeanspallationsource.se/instruments/t-rex.last. Accessed 23 October 2018.
Tada, M, Kobashigawa, Y, Mizuguchi, M, Miura, K, Kouno, T, Kumaki, Y, Demura, M, Nitta, K and Kawano, K (2002) Stabilization of protein by replacement of a fluctuating loop: structural analysis of a chimera of bovine α-lactalbumin and equine lysozyme. Biochemistry 41, 1380713813.
Takahashi, S, Kamagata, K and Oikawa, H (2016) Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics. Current Opinion in Structural Biology 36, 19.
Tama, F, Gadea, FX, Marques, O and Sanejouand, Y-H (2000) Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 41, 17.
Tarek, M and Tobias, DJ (2002) Single-particle and collective dynamics of protein hydration water: a molecular dynamics study. Physical Review Letters 89, 275501.
Tarek, M, Neumann, DA and Tobias, DJ (2003) Characterization of sub-nanosecond dynamics of the molten globule state of α-lactalbumin using quasielastic neutron scattering and molecular dynamics simulations. Chemical Physics 292, 435443.
Teague, SJ (2003) Implications of protein flexibility for drug discovery. Nature Reviews Drug Discovery 2, 527541.
Tehei, M and Zaccai, G (2005) Adaptation to extreme environments: macromolecular dynamics in complex systems. Biochimica et Biophysica Acta 1724, 404410.
Tehei, M and Zaccai, G (2007) Adaptation to high temperatures through macromolecular dynamics by neutron scattering. FEBS Journal 274, 40344043.
Tehei, M, Madern, D, Pfister, C and Zaccai, G (2001) Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability. Proceedings of the National Academy of Sciences (USA) 98, 1435614361.
Tehei, M, Franzetti, B, Madern, D, Ginzburg, M, Ginzburg, BZ, Giudici-Orticoni, M-T, Bruschi, M and Zaccai, G (2004) Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering. EMBO Reports 5, 6670.
Tehei, M, Madern, D, Franzetti, B and Zaccai, G (2005) Neutron scattering reveals the dynamic basis of protein adaptation to extreme temperature. Journal of Biological Chemistry 280, 4097440979.
Tehei, M, Smith, JC, Monk, C, Ollivier, J, Oettl, M, Kurkal, V, Finney, JL and Daniel, RM (2006) Dynamics of immobilized and native Escherichia coli dihydrofolate reductase by quasielastic neutron scattering. Biophysical Journal 90, 10901097.
Telling, MTF and Andersen, KH (2005) Spectroscopic characteristics of the OSIRIS near-backscattering crystal analyser spectrometer on the ISIS pulsed neutron source. Physical Chemistry Chemical Physics 7, 12551261.
Thurn-Albrecht, T, Steffen, W, Patkowski, A, Meier, G, Fischer, EW, Grübel, G and Abernathy, D (1996) Photon correlation spectroscopy of colloidal palladium using a coherent X-ray beam. Physical Review Letters 77, 5437.
Tokuyama, M and Oppenheim, I (1994) Dynamics of hard-sphere suspensions. Physical Review E 50, 1619.
Toppozini, L, Roosen-Runge, F, Bewley, RI, Dalgliesh, RM, Perring, T, Seydel, T, Glyde, HR, Sakai, VG and Rheinstädter, MC (2015) Anomalous and anisotropic nanoscale diffusion of hydration water molecules in fluid lipid membranes. Soft Matter 11, 83548371.
Tournier, AL, Xu, J and Smith, JC (2003) Translational hydration water dynamics drives the protein glass transition. Biophysical Journal 85, 18711875.
Tregenna-Piggott, PLW, Juranyi, F and Allenspach, P (2008) Introducing the inverted-geometry time-of-flight backscattering instrument, MARS at SINQ. Journal of Neutron Research 16, 112.
Tsapatsaris, N, Lechner, RE, Marko, M and Bordallo, HN (2016) Conceptual design of the time-of-flight backscattering spectrometer, MIRACLES, at the European spallation source. Review of Scientific Instruments 87, 085118.
Tzeng, S-R and Kalodimos, CG (2011) Protein dynamics and allostery: an NMR view. Current Opinion in Structural Biology 21, 6267.
Unruh, T, Neuhaus, J and Petry, W (2007) The high-resolution time-of-flight spectrometer TOFTOF. Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 580, 14141422.
van Hove, L (1954) Correlations in space and time and born approximation scattering in systems of interacting particles. Physical Review 95, 249262.
van Nuland, NA, Forge, V, Balbach, J and Dobson, CM (1998) Real-time NMR studies of protein folding. Accounts of Chemical Research 31, 773780.
Verkman, AS (2002) Solute and macromolecule diffusion in cellular aqueous compartments. Trends in Biochemical Sciences 27, 2733.
Verrier, S, Notingher, I, Polak, JM and Hench, LL (2004) In situ monitoring of cell death using Raman microspectroscopy. Biopolymers 74, 157162.
Verwohlt, J, Reiser, M, Randolph, L, Matic, A, Medina, LA, Madsen, A, Sprung, M, Zozulya, A and Gutt, C (2018) Low dose X-ray speckle visibility spectroscopy reveals nanoscale dynamics in radiation sensitive ionic liquids. Physical Review Letters 120, 168001.
Viani, MB, Schäffer, TE, Chand, A, Rief, M, Gaub, HE and Hansma, PK (1999) Small cantilevers for force spectroscopy of single molecules. Journal of Applied Physics 86, 22582262.
Vineyard, GH (1958) Scattering of slow neutrons by a liquid. Physical Review 110, 999.
Vodnala, P, Karunaratne, N, Lurio, L, Thurston, GM, Vega, M, Gaillard, E, Narayanan, S, Sandy, A, Zhang, Q, Dufresne, EM, Foffi, G, Grybos, P, Kmon, P, Maj, P and Szczygiel, R (2018) Hard-sphere-like dynamics in highly concentrated alpha-crystallin suspensions. Physical Review E 97, 020601.
Vogel, R and Siebert, F (2000) Vibrational spectroscopy as a tool for probing protein function. Current Opinion in Chemical Biology 4, 518523.
Vögeli, B and Yao, L (2009) Correlated dynamics between protein HN and HC bonds observed by NMR cross relaxation. Journal of the American Chemical Society 131, 36683678.
Volino, F and Dianoux, AJ (1980) Neutron incoherent scattering law for diffusion in a potential of spherical symmetry: general formalism and application to diffusion inside a sphere. Molecular Physics 41, 271279.
Volino, F, Perrin, J-C and Lyonnard, S (2006) Gaussian model for localized translational motion: application to incoherent neutron scattering. Journal of Physical Chemistry B 110, 1121711223.
Vural, D, Hu, X, Lindner, B, Jain, N, Miao, Y, Cheng, X, Liu, Z, Hong, L and Smith, JC (2017) Quasielastic neutron scattering in biology: theory and applications. Biochimica et Biophysica Acta General Subjects 1861, 36383650.
Wachsmuth, M (2014) Molecular diffusion and binding analyzed with FRAP. Protoplasma 251, 373382.
Wachsmuth, M, Waldeck, W and Langowski, J (2000) Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. Journal of Molecular Biology 298, 677689.
Wand, AJ, Urbauer, JL, McEvoy, RP and Bieber, RJ (1996) Internal dynamics of human ubiquitin revealed by 13C-relaxation studies of randomly fractionally labeled protein. Biochemistry 35, 61166125.
Wang, Y, Li, C and Pielak, GJ (2010) Effects of proteins on protein diffusion. Journal of the American Chemical Society 132, 93929397.
Wattenbarger, M, Bloomfield, V, Bu, Z and Russo, P (1992) Tracer diffusion of proteins in DNA solutions. Macromolecules 25, 52635265.
Whitelam, S (2010) Control of pathways and yields of protein crystallization through the interplay of nonspecific and specific attractions. Physical Review Letters 105, 088102.
Wilkins, DK, Grimshaw, SB, Receveur, V, Dobson, CM, Jones, JA and Smith, LJ (1999) Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques. Biochemistry 38, 1642416431.
Williams, G and Watts, DC (1970) Non-symmetrical dielectric relaxation behaviour arising from a simple empirical decay function. Transactions of the Faraday Society 66, 8085.
Williamson, MP (2015) Pressure-dependent conformation and fluctuation in folded protein molecules. In Akasaka, K, Matsuki, H (eds), High Pressure Bioscience. Dordrecht: Springer, pp. 109127.
Wojcieszyn, JW, Schlegel, RA, Wu, E-S and Jacobson, KA (1981) Diffusion of injected macromolecules within the cytoplasm of living cells. Proceedings of the National Academy of Sciences (USA) 78, 44074410.
Wolf-Watz, M, Thai, V, Henzler-Wildman, K, Hadjipavlou, G, Eisenmesser, EZ and Kern, D (2004) Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nature Structural and Molecular Biology 11, 945949.
Wolfram Research, Inc. Mathematica, Version 10.1.
Wood, K, Caronna, C, Fouquet, P, Haussler, W, Natali, F, Ollivier, J, Orecchini, A, Plazanet, M and Zaccai, G (2008) A benchmark for protein dynamics: ribonuclease a measured by neutron scattering in a large wavevector-energy transfer range. Chemical Physics 345, 305314.
Wulff, M, Schotte, F, Naylor, G, Bourgeois, D, Moffat, K and Mourou, G (1997) Time-resolved structures of macromolecules at the ESRF: single-pulse Laue diffraction, stroboscopic data collection and femtosecond flash photolysis. Nuclear Instruments & Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment 398, 6984.
Wuttke, J, Budwig, A, Drochner, M, Kämmerling, H, Kayser, F-J, Kleines, H, Ossovyi, V, Pardo, LC, Prager, M, Richter, D, Schneider, GJ, Schneider, H and Staringer, S (2012) SPHERES, Jülich's high-flux neutron backscattering spectrometer at FRM II. Review of Scientific Instruments 83, 075109.
Xu, J, Plaxco, KW and Allen, SJ (2006) Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy. Protein Science 15, 11751181.
Yadav, R, Sengupta, B and Sen, P (2014) Conformational fluctuation dynamics of domain i of human serum albumin in the course of chemically and thermally induced unfolding using fluorescence correlation spectroscopy. Journal of Physical Chemistry B 118, 54285438.
Yang, L, Song, G and Jernigan, RL (2007) How well can we understand large-scale protein motions using normal modes of elastic network models? Biophysical Journal 93, 920929.
Yang, L-Q, Sang, P, Tao, Y, Fu, Y-X, Zhang, K-Q, Xie, Y-H and Liu, S-Q (2014) Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. Journal of Biomolecular Structure and Dynamics 32, 372393.
Yearley, EJ, Godfrin, PD, Perevozchikova, T, Zhang, H, Falus, P, Porcar, L, Nagao, M, Curtis, JE, Gawande, P, Taing, R, Zarraga, IE, Wagner, NJ and Liu, Y (2014) Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity. Biophysical Journal 106, 17631770.
Yu, D, Mole, R, Noakes, T, Kennedy, S and Robinson, R (2013) Pelican – a time of flight cold neutron polarization analysis spectrometer at OPAL. Journal of the Physical Society of Japan, 82(Suppl. A), SA027.
Zaccai, G (2000) How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288, 16041607.
Zaccai, G (2003) Proteins as nano-machines: dynamics–function relations studied by neutron scattering. Journal of Physics Condensed Matter 15, S1673.
Zaccai, G, Natali, F, Peters, J, Řihová, M, Zimmerman, E, Ollivier, J, Combet, J, Maurel, M-C, Bashan, A and Yonath, A (2016) The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Scientific Reports 6, 37138.
Zanni, MT and Hochstrasser, RM (2001) Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures. Current Opinion in Structural Biology 11, 516522.
Závodszky, P, Kardos, J, Svingor, Á and Petsko, GA (1998) Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proceedings of the National Academy of Sciences (USA) 95, 74067411.
Zhang, Z and Liu, Y (2017) Recent progresses of understanding the viscosity of concentrated protein solutions. Current Opinion in Chemical Engineering 16, 4855.
Zhu, L, Sage, J and Champion, P (1994) Observation of coherent reaction dynamics in heme proteins. Science 266, 629632.
Zhuang, X and Rief, M (2003) Single-molecule folding. Current Opinion in Structural Biology 13, 8897.
Zorn, R (2009) On the evaluation of neutron scattering elastic scan data. Nuclear Instruments and Methods Section A 603, 439445.
Zuckerman, DM and Chong, LT (2017) Weighted ensemble simulation: review of methodology, applications, and software. Annual Reviews of Biophysics 46, 4357.