Protein dynamics from X-ray crystallography: Anisotropic, global motion in diffuse scattering patterns

Proteins: Structure, Function and Genetics

Volumn 66, Issue 4, 2007, Pages 941-953

  Meinhold, Lars ^a   Smith, Jeremy C ^a,b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Collective motion; Correlation; Damping; Harmonicity; Principal component analysis; Variance covariance matrix

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; HYDROGEN; NUCLEASE;

ARTICLE; CORRELATION ANALYSIS; COVARIANCE; MODEL; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RADIATION SCATTERING; STAPHYLOCOCCUS; VIBRATION; X RAY CRYSTALLOGRAPHY;

ANISOTROPY; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIFFUSION; ESTERASES; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; STAPHYLOCOCCUS; VIBRATION;

EID: 33847060038     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21246     Document Type: Article

References (62)

1. Brooks CL, III, Karplus M, Pettitt BM. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. New York: Wiley; 1988.
2. Creighton TE. Protein: structure and molecular properties. New York: WH Freeman; 1992.
3. van Holde KE, Johnson WC, Ho PS. Principles of physical biochemistry. Englewood Cliffs, NJ: Prentice Hall; 1998.
4. McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids. Cambridge: Cambridge University Press; 1988.
5. Amadei A, Linssen ABM, Berendsen HJC. Essential dynamics of proteins. Proteins 1993;17:412-425.
6. Brooks BR, Janezic D, Karplus M. Harmonic analyis of large systems. J Comput Chem 1995;16:1522-1542.
7. Héry S, Genest D, Smith JC. Rigid-body motion and X-ray diffuse scattering in crystalline lysozyme. J Mol Biol 1998;279:303-318.
8. Hayward S, Kitao A, Berendsen HJC. Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 1997;27:425-437.
9. Kitao A, Gō N. Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 1999;9:164-169.
10. Benoit JP, Doucet J. Diffuse scattering in protein crystallography. Q Rev Biophys 1995;28:131-169.
11. Moss DS, Harris GW, Wostrack A, Sansom C. Diffuse X-Ray scattering from molecular crystals. Cryst Rev 2003;9:229-277.
12. Meinhold L, Smith JC. Correlated dynamics determining X-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. Phys Rev Lett 2005;95:218103.
13. Moss DS, Harris GW, Wostrack A. Diffuse X-ray scattering from molecular crystals. In: Franchon E, Geissler E, Hodeau J-L, Regnard J-R, Timmins PA, editors. Structure and dynamics of biomolecules: neutron and synchrotron radiation for condensed matter studies. Oxford, UK: Oxford University Press; 2000.
14. Göttlicher S. Der Beitrag der thermisch diffusen streustrahlung zur Intensität der röntgeninterferenzen und die elektronendichteverteilung im NaCl. Acta Crystallogr Sect B 1968;24:122-129.
15. Cochran W. The correction of measured structure factors for thermal diffuse scattering. Acta Crystallogr Sect A 1996;25:95-101.
16. Glover ID, Harris GW, Helliwell JR, Moss DS. The variety of x-ray diffuse scattering from macromolecular crystals and its respective components. Acta Crystallogr Sect B 1991;47:960-968.
17. Lovesey SW Theory of neutron scattering from condensed matter. Oxford, UK: Oxford University Press; 1984.
18. Doucet J, Benoit JP. Molecular dynamics studied by analysis of X-ray diffuse scattering from lysozyme crystals. Nature 1987;325:643-646.
19. Kolatkar AR, Clarage JB, Phillips GN, Jr. Analysis of diffuse scattering from yeast initiator tRNA crystals. Acta Crystallogr Sect D 1994;50:210-218.
20. Wall ME, Clarage JB, Phillips GN, Jr. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 1997;5:1599-1612.
21. Phillips GN, Jr, Fillers JP, Cohen C. Motions of tropomyosin. Crystal as metaphor. Biophys J 1980;32:485-502.
22. Chacko S, Phillips GN, Jr. Diffuse x-ray scattering from tropomyosin crystals. Biophys J 1992;61:1256-1266.
23. Pérez J, Faure P, Benoit J-P. Molecular rigid-body displacements in a tetragonal lysozyme crystal confirmed by x-ray diffuse scattering. Acta Crystallogr Sect D 1996;52:722-729.
24. Caspar DLD, Clarage J, Salunke DM, Clarage M. Liquid-like movements in crystalline insulin. Nature 1988;332:659-662.
25. Faure P, Micu A, Perahia D, Doucet J, Smith JC, Benoit JP. Correlated motions and X-ray diffuse scattering in lysozyme. Nat Struct Biol 1994;1:124-128.
26. Wall ME, Ealick SE, Gruner SM. Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease. Proc Natl Acad Sci USA 1997;94:6180-6184.
27. Meinhold L, Smith JC. Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of Staphylococcal nuclease. Biophys J 2005;88:2554-2563.
28. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
29. MacKerell AD, Bashford D, Bellot M, Dunbrack JR, Evenseck RL, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher IWE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin J, Karplus M. All-atom empirical potential for molecular modelling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
30. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
31. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth partice mesh Ewald method. J Chem Phys 1995;103:8577-8593.
32. Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 1980;72:2384-2393.
33. Nose S, Klein ML. Constant pressure molecular dynamics for molecular systems. Mol Phys 1983;50:1055-1076.
34. Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A: At Mol Opt Phys 1985;31:1695-1697.
35. Legg MJ. Protein crystallography: new approaches to X-ray data collection, direct space refinement and model building. PhD Thesis, Agricultural and Mechanical University, Texas, 1977.
36. Waller I. Theoretische studien zur interferenz- und dispersion-theorie der röntgenstrahlen. PhD Thesis, Uppsala University, 1925.
37. Zachariasen WH. Theory of X-Ray diffraction in crystals. New York: Wiley; 1946.
38. Cochran W. Lattice vibrations. Rep Prog Phys 1963;26:1-45.
39. Kitao A, Hayward S, Gō N. Energy landscape of a native protein: jumping-among-minima model. Proteins 1998;33:496-517.
40. Hess B. Similarities between principal components of protein dynamics and random diffusion. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Top 2000;62:8438-8448.
41. Tournier AL, Smith JC. Principal components of the protein dynamical transition. Phys Rev Lett 2003;91:208106.
42. Reichl LE. A Modern course in statistical physics. New York: Wiley-Interscience; 1998.
43. The MathWorks, Inc. http://www.mathworks.com/.
44. Luzatti V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst 1952;5:802-810.
45. Mizuguchi K, Kidera A, Gō N. Collective motions in proteins investigated by X-ray diffuse scattering. Proteins 1994;18:34-48.
46. Kuriyan J, Petsko GA, Levy RM, Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. J Mol Biol 1986;190:227-254.
47. Vitkup D, Ringe D, Karplus M, Petsko GA. Why protein R-factors are so large: a self-consistent analysis. Proteins 2002;46:345-354.
48. Leach AR. Molecular modelling: principles and applications. Harlow: Pearson Education Ltd; 2001.
49. Elber R, Karplus M. Low-Frequency Modes in Proteins: Use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements. Phys Rev Lett 1986;56:394-397.
50. ben Avraham D. Vibrational normal-mode spectrum of globular proteins. Phys Rev B: Condens Matter 1993;47:14559-14560.
51. Nöllmann M, Etchegoin P. Universal low-frequency vibrations in proteins from a simple interaction potential. Phys Rev E: Stat Phys Plasmas Fluids Relat Interdiscip Top 1999;60:4593-4596.
52. Giraud G, Karolin J, Wynne K. Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy. Biophys J 2003;85:1903-1913.
53. Balog E, Becker T, Oettl M, Lechner R, Daniel R, Finney JL, Smith JC. Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett 2004;93:028103.
54. Cusack S, Smith JC, Finney JL, Tidor B, Karplus M. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. J Mol Biol 1988;202:903-908.
55. Smith JC, Cusack S, Tidor B, Karplus M. Inelastic neutron scattering analysis of low-frequency motions in proteins: harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor. J Chem Phys 1990;93:2974-2991.
56. Hayward S, Kitao A, Hirata F, Gō N. Effect of solvent on collective motions in globular protein. J Mol Biol 1993;234:1207-1217.
57. Clarage JB, Clarage MS, Phillips WC, Sweet RM, Caspar DL. Correlations of atomic movements in lysozyme crystals. Proteins 1992;12:145-157.
58. Faure P, Pérez J, Doucet J, Benoit JP. X-ray diffuse scattering and molecular dynamics in proteins. J Phys IV 1994;4:293-298.
59. Durand P, Trinquier G, Sanejouand Y-H. A new approach for determining low-frequency normal modes in macromoleculs. Biopolymers 1994;34:759-771.
60. Tama F, Gadea FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000;41:1-7.
61. Hess B. Convergence of sampling in protein simulations. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Top 2002;65:031910.
62. Moritsugu K, Smith JC. Langevin model of the temperature and hydration dependence of protein vibrational dynamics. J Phys Chem B 2005;109:12182-12194.