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  • Print publication year: 2010
  • Online publication date: July 2013

13 - Spectroscopic techniques: II Structure and interactions

Summary

INTRODUCTION

The overarching theme of techniques such as mass spectrometry (Chapter 9), electron microscopy and imaging (Chapter 4), analytical centrifugation (Chapter 3) and molecular exclusion chromatography (Chapter 11) is the aim to obtain clues about the structure of biomolecules and larger assemblies thereof. The spectroscopic techniques discussed in Chapters 12 and 13 are further complementary methods, and by assembling the jigsaw of pieces of information, one can gain a comprehensive picture of the structure of the biological object under study. In addition, the spectroscopic principles established in Chapter 12 are often employed as read-out in a huge variety of biochemical assays, and several more sophisticated technologies employ these basic principles in a ‘hidden’ way.

In the previous chapter, we established that the electromagnetic spectrum is a continuum of frequencies from the long wavelength region of the radio frequencies to the high-energy γ-rays of nuclear origin. While the methods and techniques discussed in Chapter 12 concentrated on the use of visible and UV light, there are other spectroscopic techniques that employ electromagnetic radiation of higher as well as lower energy. Another shared property of the techniques in this chapter is the higher level of complexity in undertaking. These applications are usually employed at a later stage of biochemical characterisation and aimed more at investigation of the three-dimensional structure, and in the case of proteins and peptides, address the tertiary and quaternary structure.

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Ciulli, A. and Abell, C. (2007). Fragment-based approaches to enzyme inhibition. Current Opinion in Biotechnology, 18, 489–496.
Beekes, M., Lasch, P. and Naumann, D. (2007). Analytical applications of Fourier transform-infrared (FT–IR) spectroscopy in microbiology and prion research. Veterinary Microbiology, 123, 305–319.
Ganim, Z., Chung, H. S., Smith, A. W., Deflores, L. P., Jones, K. C. and Tokmakoff, A. (2008). Amide I two-dimensional infrared spectroscopy of proteins. Accounts of Chemical Research, 41, 432–441.
Tonouchi, M. (2007). Cutting-edge terahertz technology. Nature Photonics, 1, 97–105.
http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/InfraRed/infrared.htm
http://www.chem.uic.edu/web1/ocol/spec/IR.htm
http://orgchem.colorado.edu/hndbksupport/irtutor/tutorial.html
http://www.umd.umich.edu/casl/natsci/slc/slconline/IR/
http://www.biophysik.uni-freiburg.de/Spectroscopy/Time-Resolved/spectroscopy.html
Benevides, J. M., Overman, S. A. and Thomas, G. J. (2004). Raman spectroscopy of proteins. Current Protocols in Protein Science, Chapter 17, Unit 17.8. New York: Wiley Interscience.
Wen, Z. Q. (2007). Raman spectroscopy of protein pharmaceuticals. Journal of Pharmaceutical Sciences, 96, 2861–2878.
http://www.jobinyvon.com/Raman%20Tutorial%20Intro
http://people.bath.ac.uk/pysdw/newpage11.htm
Anker, J. N., Hall, W. P., Lyandres, O., Shah, N. C., Zhao, J. and Duyne, R. P. (2008). Biosensing with plasmonic nanosensors. Nature Materials, 7, 442–453.
Campbell, C. T. and Kim, G. (2007). SPR microscopy and its applications to high-throughput analyses of biomolecular binding events and their kinetics. Biomaterials, 28, 2380–2392.
Majka, J. and Speck, C. (2007). Analysis of protein–DNA interactions using surface plasmon resonance. Advances in Biochemical Engineering and Biotechnology, 104, 13–36.
Neumann, T., Junker, H. D., Schmidt, K. and Sekul, R. (2007). SPR-based fragment screening: advantages and applications. Current Topics in Medicinal Chemistry, 7, 1630–1642.
Phillips, K. S. and Cheng, Q. (2007). Recent advances in surface plasmon resonance based techniques for bioanalysis. Analytical and Bioanalytical Chemistry, 387, 1831–1840.
http://www.biacore.com/
http://www.uksaf.org/tech/spr.html
http://people.clarkson.edu/~ekatz/spr.htm
Matsumoto, K., Subramanian, S., Murugesan, R., Mitchell, J. B. and Krishna, M. C. (2007). Spatially resolved biologic information from in vivo EPRI, OMRI, and MRI. Antioxidants and Redox Signaling, 9, 1125–1141.
Schiemann, O. and Prisner, T. F. (2007). Long-range distance determinations in biomacromolecules by EPR spectroscopy. Quarterly Reviews in Biophysics, 40, 1–53.
http://hyperphysics.phy-astr.gsu.edu/hbase/molecule/esr.html
http://www.chemistry.nmsu.edu/studntres/chem435/Lab7/intro.html
Blamire, A. M. (2008). The technology of MRI: the next 10 years?British Journal of Radiology, 81, 601–617.
Ishima, R. and Torchia, D. A. (2000). Protein dynamics from NMR. Nature Structural Biology, 7, 740–743.
McDermott, A. and Polenova, T. (2007). Solid state NMR: new tools for insight into enzyme function. Current Opinion in Structural Biology, 17, 617–622.
Skinner, A. L. and Laurence, J. S. (2008). High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands. Journal of Pharmaceutical Science, 97, 4670–4695.
Spiess, H. W. (2008). NMR spectroscopy: pushing the limits of sensitivity. Angewandte Chemie International Edition (English), 47, 639–642.
http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/nmr/nmr1.htm#nmr1
http://arrhenius.rider.edu/nmr/NMR_tutor/pages/nmr_tutor_home.html
http://www.cis.rit.edu/htbooks/nmr/
http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr1.htm
http://www.chem.queensu.ca/FACILITIES/NMR/nmr/webcourse/
Hickman, A. B. and Davies, D. R. (2001). Principles of macromolecular X-ray crystallography. Current Protocols in Protein Science, Chapter 17, Unit 17.3. New York: Wiley Interscience.
Miao, J., Ishikawa, T., Shen, Q. and Earnest, T. (2008). Extending X-ray crystallography to allow the imaging of noncrystalline materials, cells, and single protein complexes. Annual Reviews in Physical Chemistry, 59, 387–410.
Mueller, M., Jenni, S. and Ban, N. (2007). Strategies for crystallization and structure determination of very large macromolecular assemblies. Current Opinion in Structural Biology, 17, 572–579.
Wlodawer, A., Minor, W., Dauter, Z. and Jaskolski, M. (2008). Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS Journal, 275, 1–21.
http://www.colorado.edu/physics/2000/xray/index.html
http://www.physics.upenn.edu/~heiney/talks/hires/hires.html
http://www.matter.org.uk/diffraction/x-ray/default.htm
Lipfert, J. and Doniach, S. (2007). Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Reviews of Biophysical and Biomolecular Structure, 36, 307–327.
Neylon, C. (2008). Small angle neutron and X-ray scattering in structural biology: recent examples from the literature. European Biophysics Journal, 37, 531–541.
Putnam, C. D., Hammel, M., Hura, G. L. and Tainer, J. A. (2007). X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Quarterly Reviews in Biophysics, 40, 191–285.
http://www.ncnr.nist.gov/programs/sans/tutorials/index.html
http://www.isis.rl.ac.uk/largescale/loq/documents/sans.htm
http://www.embl-hamburg.de/workshops/2001/EMBO/