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8 - Diffraction and Simulation

Mary Luckey
Affiliation:
San Francisco State University
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Summary

Important tools for structural determination of membrane components include x-ray and neutron diffraction techniques. While the most familiar use of x-ray diffraction is the solution of crystal structures providing high-resolution structures of proteins and lipids in crystalline arrays, other diffraction techniques can provide structural information on membranes or reconstituted systems with lipids in the fluid phase. Such membrane diffraction studies give information that is one-dimensional, normal to the bilayer plane, because of the liquid nature of the acyl chains. The constant motions of lipids in the Lα phase (see Chapter 2) introduce several types of disorders (Figure 8.1) that prevent precise delineation of their structure at atomic resolution and invite description of their dynamic properties by sophisticated computer modeling. Today the interplay between diffraction techniques and simulation methods contributes even more to understanding the structure of the fluid membrane. This chapter describes diffraction and simulation methods as they apply to the lipid bilayer and then looks at the lipids that are resolved in crystal structures of membrane proteins. It will close with a few comments on the art of crystallography of membrane proteins, which allows solution of their high-resolution structures. The following chapters illustrate how x-ray crystallography of membrane proteins is providing insights toward detailed understanding of their structure and functions.

BACK TO THE BILAYER

A starting point to depict the lipids in a bilayer is a view of the static structures obtained from x-ray crystallography of several pure lipids in crystalline phase (Figure 8.2).

Type
Chapter
Information
Membrane Structural Biology
With Biochemical and Biophysical Foundations
, pp. 191 - 212
Publisher: Cambridge University Press
Print publication year: 2008

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References

White, S. H., and M. C. Wiener, The liquid-crystallographic structure of fluid lipid bilayer membranes, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment. Boston: Birkhauser, 1996.Google Scholar
Wiener, M. C., and White, S. H., Fluid bilayer structure determined by the combined use of x-ray and neutron diffraction. Biophys J. 1991, 59:162–173.CrossRefGoogle ScholarPubMed
Nagle, J. F., and Tristram-Nagle, S., Structure of lipid bilayers. Biochim Biophys Acta. 2000, 1469:159–195.CrossRefGoogle ScholarPubMed
Tristram-Nagle, S., and Nagle, J. F., Lipid bilayers: thermodynamics, structure, fluctuations and interactions. Chem Phys Lipids. 2004, 127:3–14.CrossRefGoogle ScholarPubMed
Pastor, R. W., and S. E. Feller, Time scales of lipid dynamics and molecular dynamics, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996.Google Scholar
Scott, H. L., Statistical mechanics and Monte Carlo studies of lipid membranes, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996.Google Scholar
Scott, H. L., Modeling the lipid component of membranes. Curr Opin Struct Biol. 2002, 12:495–502.CrossRefGoogle ScholarPubMed
Schlenkrich, M., et al., An empirical potential energy function for phospholipids, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996, pp. 31–81.Google Scholar
Gumbart, J.. Wang, A.Aksimentiev, E.Tajkhorshid, , and Schulten, K., Molecular dynamics simulations of proteins in lipid bilayers. Curr Opin Struct Biol. 2005, 15:423–431.CrossRefGoogle ScholarPubMed
Marsh, D., and Pali, T., The protein–lipid interface: perspectives from magnetic resonance and crystal structures. Biochim Biophys Acta. 2004, 1666:118–141.CrossRefGoogle ScholarPubMed
Palsdottir, H., and Hunte, C., Lipids in membrane protein structures. Biochim Biophys Acta. 2004, 1666:2–18.CrossRefGoogle ScholarPubMed
Lee, A. G., Lipid–protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta. 2003, 1612:1–40.CrossRefGoogle ScholarPubMed
Cartailler, J.-P., and Luecke, H., x-ray crystallographic analysis of lipid–protein interactions in the bacteriorhodopsin purple membrane. Annu Rev Biophys Biomol Struct. 2003, 32:285–310.CrossRefGoogle ScholarPubMed
Fyfe, P. K., et al., Probing the interface between membrane proteins and membrane lipids by x-ray crystallography. Trends Biochem Sci. 2001, 26:106–112.CrossRefGoogle ScholarPubMed
Pebay-Peyroula, E., and Rosenbusch, J. P., High-resolution structures and dynamics of membrane protein–lipid complexes: a critique. Curr Opin Struct Biol. 2001, 11:427–432.CrossRefGoogle ScholarPubMed
Hunte, C., and Michel, H., Crystallisation of membrane proteins mediated by antibody fragments. Curr Opin Struct Biol. 2002, 12:503–508.CrossRefGoogle ScholarPubMed
Landau, E. M., and Rosenbusch, J. P., Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A. 1996, 93:14532–14535.CrossRefGoogle ScholarPubMed
Faham, S., and Bowie, J. U., Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J Mol Biol. 2002, 316:1–6.CrossRefGoogle ScholarPubMed
White, S. H., and M. C. Wiener, The liquid-crystallographic structure of fluid lipid bilayer membranes, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment. Boston: Birkhauser, 1996.Google Scholar
Wiener, M. C., and White, S. H., Fluid bilayer structure determined by the combined use of x-ray and neutron diffraction. Biophys J. 1991, 59:162–173.CrossRefGoogle ScholarPubMed
Nagle, J. F., and Tristram-Nagle, S., Structure of lipid bilayers. Biochim Biophys Acta. 2000, 1469:159–195.CrossRefGoogle ScholarPubMed
Tristram-Nagle, S., and Nagle, J. F., Lipid bilayers: thermodynamics, structure, fluctuations and interactions. Chem Phys Lipids. 2004, 127:3–14.CrossRefGoogle ScholarPubMed
Pastor, R. W., and S. E. Feller, Time scales of lipid dynamics and molecular dynamics, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996.Google Scholar
Scott, H. L., Statistical mechanics and Monte Carlo studies of lipid membranes, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996.Google Scholar
Scott, H. L., Modeling the lipid component of membranes. Curr Opin Struct Biol. 2002, 12:495–502.CrossRefGoogle ScholarPubMed
Schlenkrich, M., et al., An empirical potential energy function for phospholipids, in Merz, K. M. Jr., and Roux, B. (eds.), Biological Membranes, A Molecular Perspective from Computation and Experiment, Boston: Birkhauser, 1996, pp. 31–81.Google Scholar
Gumbart, J.. Wang, A.Aksimentiev, E.Tajkhorshid, , and Schulten, K., Molecular dynamics simulations of proteins in lipid bilayers. Curr Opin Struct Biol. 2005, 15:423–431.CrossRefGoogle ScholarPubMed
Marsh, D., and Pali, T., The protein–lipid interface: perspectives from magnetic resonance and crystal structures. Biochim Biophys Acta. 2004, 1666:118–141.CrossRefGoogle ScholarPubMed
Palsdottir, H., and Hunte, C., Lipids in membrane protein structures. Biochim Biophys Acta. 2004, 1666:2–18.CrossRefGoogle ScholarPubMed
Lee, A. G., Lipid–protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta. 2003, 1612:1–40.CrossRefGoogle ScholarPubMed
Cartailler, J.-P., and Luecke, H., x-ray crystallographic analysis of lipid–protein interactions in the bacteriorhodopsin purple membrane. Annu Rev Biophys Biomol Struct. 2003, 32:285–310.CrossRefGoogle ScholarPubMed
Fyfe, P. K., et al., Probing the interface between membrane proteins and membrane lipids by x-ray crystallography. Trends Biochem Sci. 2001, 26:106–112.CrossRefGoogle ScholarPubMed
Pebay-Peyroula, E., and Rosenbusch, J. P., High-resolution structures and dynamics of membrane protein–lipid complexes: a critique. Curr Opin Struct Biol. 2001, 11:427–432.CrossRefGoogle ScholarPubMed
Hunte, C., and Michel, H., Crystallisation of membrane proteins mediated by antibody fragments. Curr Opin Struct Biol. 2002, 12:503–508.CrossRefGoogle ScholarPubMed
Landau, E. M., and Rosenbusch, J. P., Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc Natl Acad Sci U S A. 1996, 93:14532–14535.CrossRefGoogle ScholarPubMed
Faham, S., and Bowie, J. U., Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. J Mol Biol. 2002, 316:1–6.CrossRefGoogle ScholarPubMed

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  • Diffraction and Simulation
  • Mary Luckey, San Francisco State University
  • Book: Membrane Structural Biology
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511811098.009
Available formats
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  • Diffraction and Simulation
  • Mary Luckey, San Francisco State University
  • Book: Membrane Structural Biology
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511811098.009
Available formats
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Save book to Google Drive

To save content items to your account, please 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 account. Find out more about saving content to Google Drive.

  • Diffraction and Simulation
  • Mary Luckey, San Francisco State University
  • Book: Membrane Structural Biology
  • Online publication: 05 June 2012
  • Chapter DOI: https://doi.org/10.1017/CBO9780511811098.009
Available formats
×