Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool

Protein Science

Volumn 14, Issue 3, 2005, Pages 633-643

  Alexandrov, Vadim ^a   Lehnert, Ursula ^a   Echols, Nathaniel ^a   Milburn, Duncan ^a   Engelman, Donald ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; CALMODULIN; INSULIN; RNA POLYMERASE;

AMPLITUDE MODULATION; ARTICLE; ATOM; AUTOANALYSIS; BACTERIOPHAGE T7; CONFORMATIONAL TRANSITION; EXPRESSION VECTOR; FREQUENCY MODULATION; GEOMETRY; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; STATISTICAL ANALYSIS; VIBRATION;

DATABASES, PROTEIN; INTERNET; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 14144256567     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04882105     Document Type: Article

References (78)

1. Ahn, J.S., Kanematsu, Y., and Kushida, T. 1993. Site-selective fluorescence spectroscopy in dye-doped polymers. I. Determination of the site-energy distribution and the single-site fluorescence spectrum. Phys. Rev. B Condens. Matter 48: 9058-9065.
2. Alden, R., Schneebeck, M., Ondrias, M., Courtney, S., and Friedman, J. 1992. Mode-specific relaxation dynamics of photoexcited Fe(II) protoporphyrin IX in hemoglobin. J. Raman Spectrosc. 23: 569-574.
3. Alexandrov, V. and Gerstein, M. 2004. Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinformatics 5: 2.
4. Amadei, A., Linssen, A.B., and Berendsen, H.J. 1993. Essential dynamics of proteins. Proteins 17: 412-425.
5. Arfken, G.B. and Weber, H. 2000. Mathematical methods for physicists. Academic Press, New York.
6. Ascher, D., Dubois, P.F., Hinsen, K., Hugunin, J., and Oliphant, T. 2000. Numerical python. Lawrence Livermore National Laboratory, Livermore, CA.
7. Babu, Y.S., Sack, J.S., Greenhough, T.J., Bugg, C.E., Means, A.R., and Cook, W.J. 1985. Three-dimensional structure of calmodulin. Nature 315: 37-40.
8. Babu, Y.S., Bugg, C.E., and Cook, W.J. 1987. X-ray diffraction studies of calmodulin. Methods Enzymol. 139: 632-642.
9. _. 1988. Structure of calmodulin refined at 2.2 Å resolution. J. Mol. Biol. 204: 191-204.
10. Bahar, I. and Jernigan, R.L. 1998. Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms. J. Mol. Biol. 281: 871-884.
11. Bao, S.J., Xie, D.L., Zhang, J.P., Chang, W.R., and Liang, D.C. 1997. Crystal structure of desheptapeptide(B24-B30)insulin at 1.6 Å resolution: Implications for receptor binding. Proc. Natl. Acad. Sci. 94: 2975-2980.
12. Brooks, B. and Karplus, M. 1983. Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. 80: 6571-6575.
13. _. 1985. Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. 82: 4995-4999.
14. Bullough, P.A., Hughson, P.M., Skehel, J.J., and Wiley, D.C. 1994. Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371: 37-43.
15. Chin, D., Winkler, K.E., and Means, A.R. 1997. Characterization of substrate phosphorylation and use of calmodulin mutants to address implications from the enzyme crystal structure of calmodulin-dependent protein kinase I. J. Biol. Chem. 272: 31235-31240.
16. Chothia, C., Lesk, A.M., Dodson, G.G., and Hodgkin, D.C. 1983. Transmission of conformational change in insulin. Nature 302: 500-505.
17. Cook, W.J., Walter, L.J., and Walter, M.R. 1994. Drug binding by calmodulin: Crystal structure of a calmodulin-trifluoperazine complex. Biochemistry 33: 15259-15265.
18. Cui, Q., Li, G., Ma, J., and Karplus, M. 2004. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol. 340: 345-372.
19. 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. Biophys. J. 58: 243-251.
20. Cusack, S., Smith, J., Finney, J., Tidor, B., and Karplus, M. 1988. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. J. Mol. Biol. 202: 903-908.
21. Dupradeau, F.Y., Richard, T., Le Flem, G., Oulyadi, H., Prigent, Y., and Monti, J.P. 2002. A new B-chain mutant of insulin: Comparison with the insulin crystal structure and role of sulfonate groups in the B-chain structure. J. Pept. Res. 60: 56-64.
22. Echols, N., Milburn, D., and Gerstein, M. 2003. MolMovDB: Analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31: 478-482.
23. Elber, R. and Karplus, M. 1987. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235: 318-321.
24. Frauenfelder, H., Parak, F., and Young, R.D. 1988. Conformational substates in proteins. Annu. Rev. Biophys. Biophys. Chem. 17: 451-479.
25. Gerstein, M. and Krebs, W. 1998. A database of macromolecular motions. Nucleic Acids Res. 26: 4280-4290.
26. Gibrat, J.F. and Go, N. 1990. Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8: 258-279.
27. Go, N., Noguti, T., and Nishikawa, T. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. 80: 3696-3700.
28. Han, X., Bushweller, J.H., Cafiso, D.S., and Tamm, L.K. 2001. Membrane structure and fusion-triggering conformational change of the fusion domain from influenza hemagglutinin. Nat. Struct. Biol. 8: 715-720.
29. Han, B.G., Han, M., Sui, H., Yaswen, P., Walian, P.J., and Jap, B.K. 2002. Crystal structure of human calmodulin-like protein: Insights into its functional role. FEBS Lett. 521: 24-30.
30. Hawkins, B.L., Cross, K.J., and Craik, D.J. 1994. A 1H-NMR determination of the solution structure of the A-chain of insulin: Comparison with the crystal structure and an examination of the role of solvent. Biochim. Biophys. Acta 1209: 177-182.
31. Hawkins, B., Cross, K., and Craik, D. 1995. Solution structure of the B-chain of insulin as determined by 1H NMR spectroscopy. Comparison with the crystal structure of the insulin hexamer and with the solution structure of the insulin monomer. Int. J. Pept. Protein Res. 46: 424-433.
32. Hayward, S., Kitao, A., and Berendsen, H.J. 1997. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27: 425-437.
33. Henry, E.R., Eaton, W.A., and Hochstrasser, R.M. 1986. Molecular dynamics simulations of cooling in laser-excited heme proteins. Proc. Natl. Acad. Sci. 83: 8982-8986.
34. Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins 33: 417-429.
35. _. 2000. The molecular modeling toolkit: A new approach to molecular simulations. J. Comp. Chem. 21: 79-85.
36. Hoelz, A., Nairn, A.C., and Kuriyan, J. 2003. Crystal structure of a tetradecameric assembly of the association domain of Ca2+/calmodulin-dependent kinase II. Mol. Cell 11: 1241-1251.
37. Hong, M. K., Braunstein, D., Cowen, B.R., Frauenfelder, H., Iben, I.E., Mourant, J.R., Ormos, P., Scholl, R., Schulte, A., Steinbach, P.J., et al. 1990. Conformational substates and motions in myoglobin. External influences on structure and dynamics. Biophys. J. 58: 429-436.
38. Horiuchi, T., and Go, N. 1991. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme. Proteins 10: 106-116.
39. Hua, Q.X., Shoelson, S.E., Kochoyan, M., and Weiss, M.A. 1991. Receptor binding redefined by a structural switch in a mutant human insulin. Nature 354: 238-241.
40. Jia, Y. and Patel, S.S. 1997a. Kinetic mechanism of GTP binding and RNA synthesis during transcription initiation by bacteriophage T7 RNA polymerase. J. Biol. Chem. 272: 30147-30153.
41. _. 1997b. Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry 36: 4223-4232.
42. Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Cryst. A32: 922-923.
43. Kottalam, J. and Case, D.A. 1990. Langevin modes of macromolecules: Applications to crambin and DNA hexamers. Biopolymers 29: 1409-1421.
44. Krebs, W.G. and Gerstein, M. 2000. The morph server: A standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28: 1665-1675.
45. Krebs, W.G., Alexandrov, V., Wilson, C.A., Echols, N., Yu, H., and Gerstein, M. 2002. Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins 48: 682-695.
46. Kretsinger, R.H., Rudnick, S.E., and Weissman, L.J. 1986. Crystal structure of calmodulin. J. Inorg. BioChem. 28: 289-302.
47. Kurokawa, H., Osawa, M., Kurihara, H., Katayama, N., Tokumitsu, H., Swindells, M.B., Kainosho, M., and Ikura, M. 2001. Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide. J. Mol. Biol. 312: 59-68.
48. Levitt, M., Sander, C., and Stern, P.S. 1985. Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181: 423-447.
49. Levy, R.M., Srinivasan, A.R., Olson, W.K., and McCammon, J.A. 1984. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 23: 1099-1112.
50. Luecke, H. 2000. Atomic resolution structures of bacteriorhodopsin photocycle intermediates: The role of discrete water molecules in the function of this light-driven ion pump. Biochim. Biophys. Acta 1460: 133-156.
51. Luecke, H., Schobert, B., Richter, H.T., Cartailler, J.P., and Lanyi, J.K. 1999. Structural changes in bacteriorhodopsin during ion transport at 2 Å resolution. Science 286: 255-261.
52. Majumdar, D., Lieberman, K.R., and Wyche, J.H. 1989. Use of modified T7 DNA polymerase in low melting point agarose for DNA gap filling and molecular cloning. Biotechniques 7: 188-191.
53. Marques, O. and Sanejouand, Y.H. 1995. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23: 557-560.
54. Miller, D.W. and Agard, D.A. 1999. Enzyme specificity under dynamic control: A normal mode analysis of α-lytic protease. J. Mol. Biol. 286: 267-278.
55. Noguti, T. and Go, N. 1982. Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature 296: 776-778.
56. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thomton, J.M. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
57. Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. 85: 2444-2448.
58. Persechini, A. and Kretsinger, R.H. 1988. The central helix of calmodulin functions as a flexible tether. J. Biol. Chem. 263: 12175-12178.
59. Putkey, J.A., Ono, T., VanBerkum, M.F., and Means, A.R. 1988. Functional significance of the central helix in calmodulin. J. Biol. Chem. 263: 11242-11249.
60. Reuland, S.N., Vlasov, A.P., and Krupenko, S.A. 2003. Disruption of a calmodulin central helix-like region of 10-formyltetrahydrofolate dehydrogenase impairs its dehydrogenase activity by uncoupling the functional domains. J. Biol. Chem. 278: 22894-22900.
61. Roe, B.A., Johnston-Dow, L., and Mardis, E. 1988. Use of a chemically modified T7 DNA polymerase for manual and automated sequencing of supercoiled DNA. Biotechniques 6: 520.
62. Sass, H.J., Buldt, G., Gessenich, R., Hehn, D., Neff, D., Schlesinger, R., Berendzen, J., and Ormos, P. 2000. Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin. Nature 406: 649-653.
63. Schlein, M., Havelund, S., Kristensen, C., Dunn, M.F., and Kaarsholm, N.C. 2000. Ligand-induced conformational change in the minimized insulin receptor. J. Mol. Biol. 303: 161-169.
64. Sekharudu, C.Y. and Sundaralingam, M. 1993. A model for the calmodulin-peptide complex based on the troponin C crystal packing and its similarity to the NMR structure of the calmodulin-myosin light chain kinase peptide complex. Protein Sci. 2: 620-625.
65. Smith, J., Cusack, S., Poole, P., and Finney, J. 1987. Direct measurement of hydration-related dynamic changes in lysozyme using inelastic neutron scattering spectroscopy. J. Biomol. Struct. Dyn. 4: 583-588.
66. Subramaniam, S., Lindahl, M., Bullough, P., Faruqi, A.R., Tittor, J., Oesterhelt, D., Brown, L., Lanyi, J., and Henderson, R. 1999. Protein conformational changes in the bacteriorhodopsin photocycle. J. Mol. Biol. 287: 145-161.
67. Tama, F. and Sanejouand, Y.H. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14: 1-6.
68. Thomas, A., Field, M.J., Mouawad, L., and Perahia, D. 1996a. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol. 257: 1070-1087.
69. Thomas, A., Field, M.J., and Perahia, D. 1996b. Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes. J. Mol. Biol. 261: 490-506.
70. Thomas, A., Hinsen, K., Field, M.J., and Perahia, D. 1999. Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study. Proteins 34: 96-112.
71. Valadie, H., Lacapcre, J.J., Sanejouand, Y.H., and Etchebest, C. 2003. Dynamical properties of the MscL of Escherichia coli: A normal mode analysis. J. Mol. Biol. 332: 657-674.
72. Whittingham, J.L., Havelund, S., and Jonassen, I. 1997. Crystal structure of a prolonged-acting insulin with albumin-binding properties. Biochemistry 36: 2826-2831.
73. Wilcox, G.L., Quiocho, F.A., Levinthal, C., Harvey, S.C., Maggiora, G.M., and McCammon, J.A. 1988. Symposium overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J. Comput. Aided Mol. Des. 1: 271-281.
74. Wilson, M.A. and Brunger, A.T. 2000. The 1.0 Å crystal structure of Ca(2+)-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity. J. Mol. Biol. 301: 1237-1256.
75. Yamauchi, E., Nakatsu, T., Matsubara, M., Kato, H., and Taniguchi, H. 2003. Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca2+-calmodulin. Nat. Struct. Biol. 10: 226-231.
76. Ye, S., Wan, Z., Liu, C., Chang, W., and Liang, D. 1996. Crystal structure of (L-Arg)-B0 bovine insulin at 0.21 nm resolution. Sci. China C Life Sci. 39: 465-473.
77. Ye, J., Chang, W., and Liang, D. 2001. Crystal structure of destripeptide (B28-B30) insulin: Implications for insulin dissociation. Biochim. Biophys. Acta 1547: 18-25.
78. Yin, Y.W. and Steitz, T.A. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298: 1387-1395.