All-atom normal mode calculations of large molecular systems using iterative methods

Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems

Volumn , Issue , 2005, Pages 17-39

  Mouawad, Liliane ^a   Perahia, David ^b  

^a INSTITUT CURIE   (France)

^b UNIVERSITY OF NEVADA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84958545771     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (45)

1. Citri, N., Conformational adaptability of enzymes, Adv. Enzymol.,37, 397, 1973.
2. Carreri, G., Gratton, E., and Fasella, P., Enzyme dynamics: the statistical physics approach, Annu. Rev. Biophys. Bioeng.,8, 69,1979.
3. Gurd, F.R.N., and Rothgeb, M., Motions in proteins, Adv. Prot. Chem.,33, 73, 1979.
4. Yon, J.M., Perahia, D., and Ghelis, C., Conformational dynamics and enzyme activity, Biochimie,80, 33, 1998.
5. Elber, R., and Karplus, M., Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin, Science,235, 318,1987.
6. Go, N., Shape of the conformational energy surface near the global minimum and low-frequency vibrations in the native conformation of globular proteins, Biopolymers,17, 1373, 1978.
7. Brooks, B., and Karplus, M., Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor, Proc. Natl Acad. Sci. USA,80, 6571, 1983.
8. Noguti, T., and Go, N., Collective variable description of small-amplitude conformational fluctuations in a globular protein, Nature,296, 776,1982.
9. Go, N., Noguti, T., and Nishikawa, T., Dynamics of a small globular protein in terms of low-frequency vibrational modes, Proc. Natl Acad. Sci. USA, 80, 3696, 1983.
10. Perahia, D., Levy, R., and Karplus, M., Motions of an alpha helical polypeptide: Comparison of molecular and harmonic dynamics, Biopolymers,29, 645,1990.
11. Frauenfelder, H., Petsko, G., and Tsernoglou, D., Temperature dependent x-ray diffraction as a probe of protein structural dynamics, Nature,280, 558, 1979.
12. Keller, H., and Debrunner, P.G., Evidence for conformational and diffusional mean square displacements in frozen aqueous solutions of oxymyoglobin, Phys. Rev. Lett,54, 68, 1980.
13. Mayo, K.H., Kucheida, D., Parak, F., and Chien, J.C.W., Structural dynamics of human deoxyhemoglobin and hemochrome investigated by nuclear gamma resonance absorption (Mossbauer) spectroscopy, Proc. Natl Acad. Sci. USA,80, 5294, 1983.
14. Smith, J.C., Protein dynamics: Comparison of simulations with inelastic neutron scattering experiments, Quart. Rev. Biophys.,24, 227,1991.
15. Marques, O., and Sanejouand, Y.H., The hinge-bending mode in citrate synthase arising from normal mode calculations, Proteins: Struct. Funct. Genet.,23, 557, 1995.
16. Mouawad, L., and Perahia, D., Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures, J. Mol. Biol.,258, 393, 1996.
17. Thomas, A., Field, M.J., and Perahia, D., 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, 1996.
18. Jaaskelainen, S., Verma, C.S., Hubbard, R.E., Linko, P., and Caves, L.S.D., Conformational change in the activation of lipase: An analysis in terms of low-frequency normal modes, Protein Sci.,7, 1359,1998.
19. Tama, F., and Sanejouand, Y.-H., Conformational change of proteins arising from normal mode calculations, Protein Eng.,14,1,2001.
20. Levitt, M., Sander, C., and Stern, P.S., Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol.,181, 423,1985.
21. Tama, F., Gadea, F.X., Marques, O., and Sanejouand, Y.H., Building blocks approach for determining low-frequency normal modes in macromolecules, Proteins: Struct. Funct. Genet.,41, 1, 2000.
22. Li, G., and Cui, Q., A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca(2+)-ATPase., Biophys. J.,83, 2457, 2002.
23. Tirion, M., Large amplitude elastic motions in proteins from a single parameter, atomic analysis, Phys. Rev. Lett.,77, 1905,1996.
24. Bahar, I., Atilgan, A.R., and Erman, B., Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold. Design,2, 173,1997.
25. Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O., and Bahar, I., Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J.,80, 505, 2001.
26. Hinsen, K., Analysis of domain motions by approximate normal mode calculations, Proteins: Struct. Funct. Genet.,33, 417,1998.
27. Brooks, B., and Karplus, M., Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme, Proc. Natl Acad. Sci. USA,82, 4995,1985.
28. Mouawad, L., and Perahia, D., Diagonalization in a mixed basis: A method to compute low-frequency normal modes for large macromolecules, Biopolymers, 33, 599,1993.
29. Durand, P., Trinquier, G., and Sanejouand, Y.H., A new approach for determining low-frequency normal modes in macromolecules, Biopolymers,34, 759, 1994.
30. Goldstein, H., Classical Mechanics, Addison-Wesley, Reading, MA, 1950.
31. Wilson, E.B., Decius, J.C., and Cross, P.C., Molecular Vibrations, McGraw-Hill, New York, 1955.
32. Brooks, B.R., Janezic, D., and Karplus, M., Harmonic analysis of large systems. I. Methodology, J. Comp. Chem.,16, 1522,1995.
33. Humar, J.L., Dynamics of Structures, Prentice Hall, New Jersey, 1990.
34. Davidson, E.R., The iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of large real-symmetric matrices, J. Comp. Chem.,17, 87, 1975.
35. Lanczos, C.J., An iteration method for the solution of the eigenvalue problem of linear differential and integral operators, J. Res. Natl Bur. Stand.,45, 255,1950.
36. Shavitt, I., Bender, C.F., Pipano, A., and Hosteny, R.P., The iterative calculation of several of the lowest or highest eigenvalues and corresponding eigenvectors of very large symmetric matrices, J. Comp. Phys.,11, 90, 1973.
37. Arnoldi, W.E., The principle of minimized iterations in the solution of the matrix eigenvalue problem, Quart. Appl. Math., IX, 17,1951.
38. Marques, O., BLZPACK: description and user's guide, CERFACS Report TR/PA/95/30, Toulouse, France, 1995.
39. Lehoucq, R.B., Sorensen, D.C., and Yang, C., ARPACK user’s guide: solution of large scale eigenvalue problems with implicitly restarted Arnoldi methods, 1997, http://www.caam.rice.edu/software/ARPACK.
40. Marques, O., and Sanejouand, Y.H., Protein motions through eigenanalyses: A set of study cases, CERFACS Report TR/PA/95/32, Toulouse, France, 1995.
41. Durand, P., and Malrieu, J.-P., Ab-Initio Methods in Quantum Chemistry—I, Lawley, K.P., ed., New York, John Wiley & Sons, 1987, p. 352.
42. Perahia, D., and Mouawad, L., Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin, Comput. Chem.,19, 241, 1995.
43. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comp. Chem.,4,187,1983.
44. Thomas, A., Field, M.J., Mouawad, L., and Perahia, D., Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase, J. Mol. Biol., 257, 1070,1996.
45. Thomas, A., Hinsen, K., Field, M.J., and Perahia, D., Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study, Proteins,34, 96, 1999.