Correlation between normal modes in the 20-200 cm-1 frequency range and localized torsion motions related to certain collective motions in proteins

Journal of Molecular Graphics and Modelling

Volumn 21, Issue 4, 2003, Pages 309-319

  Cao, Z W ^a   Chen, X ^a   Chen, Y Z ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Flexible region; Fluctuational motion; Hinge motion; Linker; Molecular modeling; Shear motion; Torsion motion; Vibrational motion

Indexed keywords

CONFORMATIONS; CORRELATION METHODS; MOLECULAR VIBRATIONS;

LOCALIZED MOTIONS;

PROTEINS;

CALBINDIN; CALMODULIN; DNA BINDING PROTEIN; PROTEINASE; TROPONIN C;

ARTICLE; CONFORMATION; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; SHEAR STRESS; VIBRATION;

CALCIUM-BINDING PROTEIN, VITAMIN D-DEPENDENT; CALMODULIN; HIV PROTEASE; MODELS, MOLECULAR; PROTEIN CONFORMATION; STATISTICS; TROPONIN C;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0037212392     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(02)00185-7     Document Type: Article

References (89)

1. Bahar I., Erman B., Haliloglu T., Jernigan R.L. Efficient characterization of collective motions and inter-residue correlations in proteins by low-resolution simulations. Biochemistry. 36:1997;13512-13523.
2. Gerstein M., Lesk A.M., Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry. 33:1994;6739-6749.
3. Zhang M., Yuan T. Molecular mechanisms of calmodulin's functional versatility. Biochem. Cell Biol. 76:1998;313-323.
4. Brooks B., Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. U.S.A. 80:1983;6571-6575.
5. Patel D.J., Ikuta S., Kozlowski S., Itakura K. Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution. Proc. Natl. Acad. Sci. U.S.A. 80:1983;2184-2188.
6. Gueron M., Kochoyan M., Leroy J.L. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 328:1987;89-92.
7. Gerstein M., Krebs W.G. A database of macromolecular motions. Nucleic Acids Res. 26:1998;4280-4290.
8. Chen Y.Z., Mohan V., Griffey R.H. The opening of a single base without perturbations of neighboring nucleotides: a study on crystal B-DNA duplex d(CGCGAATTCGCG)2. J. Biomol. Struct. Dyn. 15:1998;765-777.
9. Van Aalten D.M., Erlanson D.A., Verdine G.L., Joshua-Tor L. Nucleotide, structure: a structural snapshot of base-pair opening in DNA. Proc. Natl. Acad. Sci. U.S.A. 96:1999;11809-11814.
10. Nishikawa T., Go N. Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property. Proteins. 2:1987;308-329.
11. Ma J., Karplus M. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:1997;114-131.
12. Hayward S., Kitao A., Berendsen H.J. Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics of lysozyme. Proteins. 27:1997;425-437.
13. Jaaskelainen S., Verma C.S., Hubbard R.E., Linko P., Caves L.S. Conformational change in the activation of lipase: an analysis in terms of low-frequency normal modes. Protein Sci. 76:1998;1359-1367.
14. Simonson T., Perahia D. Normal modes of symmetric protein assemblies: application to the tobacco mosaic virus protein disk. Biophys. J. 61:1992;410-427.
15. Sheridan R.P., Levy R.M., Englander S.W. Normal mode paths for hydrogen exchange in the peptide ferrichrome. Proc. Natl. Acad. Sci. U.S.A. 80:1983;5569-5572.
16. Tama F., Sanejouand Y.H. Conformational change of proteins arising from normal-mode calculations. Protein Eng. 14:2001;1-6.
17. Hinsen K., Thomas A., Field M.J. Analysis of domain motions in large proteins. Proteins. 34:1999;369-382.
18. D.A. Case, Molecular dynamics and normal mode analysis of biomolecular rigidity. in: M.F. Thorpe, P.M. Duxbury (Eds.), Rigidity Theory and Application. Kluwer Academic/Plenum, New York, 1999.
19. Brooks B., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
20. W.F. Van Gunsteren, Molecular dynamics and stochastic dynamics simulation: a primer. in: Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications, ESCOM, Leiden, 1993.
21. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M. Jr., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
22. Kitao A., Hirata F., Go N. The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and vacuum. Chem. Phys. 158:1991;447-472.
23. D. Frenkel, Monte Carlo simulations: a primer. in: Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications, ESCOM, Leiden, 1993.
24. Matsumoto A., Tomimoto M., Go N. Dynamical structure of transfer RNA studied by normal mode analysis. Eur. Biophys. J. 28:1999;369-379.
25. Ishida H., Jochi Y., Kidera A. Dynamic structure of Subtilisin-Eglin c complex by normal mode analysis. Proteins. 32:1998;324-333.
26. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1996;1905-1908.
27. Tirion M.M., ben-Avraham D. Normal mode analysis of G-actin. J. Mol. Biol. 230:1993;186-195.
28. Nakamura S., Doi J. Dynamics of transfer RNAs analyzed by normal-mode calculation. Nucleic Acids Res. 22:1994;514-521.
29. David W.M., David A.A. Enzyme specificity under dynamic control: a normal mode analysis of α-lytic protease. J. Mol. Biol. 286:1999;267-278.
30. Thomas A., Field M.J., Mouawad L., Perahia D. Analysis of low-frequency normal modes of the T-state of aspartate trans-carbamylase. J. Mol. Biol. 257:1996;1070-1087.
31. Brooks B., Karplus M. Normal mode for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. U.S.A. 82:1985;4995-4999.
32. Levitt M., Sander C., Stern P.S. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysosyme. J. Mol. Biol. 181:1985;147-423.
33. Brown K.G., Erfurth S.C., Small E.W., Peticolas W.L. Conformationally dependent low-frequency motions of proteins by laser Raman spectroscopy. Proc. Nat. Acad. Sci. U.S.A. 69:1972;1467-1469.
34. Peticolas W.L. Low-frequency vibrations and the dynamics of proteins and polypeptides. Methods Enzymol. 61:1979;425-458.
35. Bartunik H.D., Jolles P., Berthou J., Dianoux A.J. Intra-molecular low-frequency vibrations in lysozyme by neutron time-of-flight spectroscopy. Biopolymers. 21:1982;43-50.
36. Powell J.W., Edwards G.S., Genzel L., Kremer F., Wittlin A., Kubasek W., Peticolas W. Investigation of far-infrared vibrational modes in polynucleotides. Phys. Rev. A. 35:1987;3929-3939.
37. Weidlich T., Lindsay S.M., Qi R., Rupprecht A., Peticolas W.L., Thomas G.A. A Raman study of low-frequency intra-helical modes in A-, B-, and C-DNA. J. Biomol. Struct. Dyn. 8:1990;139-171.
38. Edwards G., Liu C. Sequence dependence of low-frequency Raman-active modes in nucleic acids. Phys. Rev. A. 44:1991;2709-2717.
39. Reisdorf W.C., Krimm S. Infrared amide I' band of coiled coil. Biochemistry. 35:1996;1383-1386.
40. 2-. Biophys. J. 66:1994;225-235.
41. Melchers B., Knapp E.W., Parak F., Cordone L., Cupane A., Leone M. Structural fluctuations of myoglobin from normal-modes, Mossbauer, Raman, and absorption spectroscopy. Biophys. J. 70:1996;2092-2099.
42. Wang J., Takahashi S., Rousseau D.L. Identification of the overtone of the Fe-CO stretching mode in heme proteins: a probe of the heme active site. Proc. Natl. Acad. Sci. U.S.A. 92:1995;9402-9406.
43. 2+. Biophys. J. 69:1995;2623-2641.
44. Chen Y.Z., Prohofsky E.W. Normal-mode calculation of a netropsin-DNA complex: effect of structural deformation on vibrational spectrum. Biopolymers. 35:1995;657-666.
45. Chen Y.Z., Prohofsky E.W. Sequence and temperature dependence of the inter-base hydrogen bond breathing modes in B-DNA polymers: comparison with low-frequency Raman peaks and their role in helix melting. Biopolymers. 35:1995;573-582.
46. Lee S.A., Rupprecht A., Chen Y.Z. Drug binding to DNA: observation of the drug-DNA hydrogen bond-stretching modes of netropsin bound to DNA via Raman spectroscopy. Phys. Rev. Lett. 80:1998;2241-2244.
47. Tidor B., Karplus M. The contribution of vibrational entropy to molecular association: the dimerization of insulin. J. Mol. Biol. 238:1994;405-414.
48. Miura T., Thomas G.J. Jr. Structure and dynamics of inter-strand guanine association in quadruplex telomeric DNA. Biochemistry. 34:1995;9645-9654.
49. Lawson C.L., Zhang R., Schevitz R.W., Otwinowski Z., Joachimiak A., Sigler P.B. Flexibility of the DNA-binding domains of the TRP repressor. Proteins. 3:1988;18-31.
50. Meador W.E., Means A.R., Quiocho F.A. Modulation of calmodulin plasticity in molecular recognition on the basis of X-ray structures. Science. 262:1993;1718-1721.
51. Jia Z., Barford D., Flint A.J., Tonks N.K. Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B. Science. 268:1995;1754-1758.
52. Fitzgerald P.M.D., McKeever B.M., VanMiddlesworth J.F., Springer J.P., Heimbach J.C., Leu C.-T., Herber W.K., Dixon R.A.F., Darke P.L. Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Å resolution. J. Biol. Chem. 265:1990;14209-14219.
53. Service R.F. Flexing muscle with just one amino acid. Science. 271:1996;31-33.
54. Taylor D.A., Sack J.S., Maune J.F., Beckingham K., Quiocho F.A. Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-Å resolution. J. Biol. Chem. 266:1991;21375-21380.
55. Ikura M., Clore G.M., Gronenborn A.M., Zhu G., Klee C.B., Bax A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 256:1992;632-638.
56. 9k by NMR spectroscopy. J. Mol. Biol. 249:1995;441-462.
57. 2+) I,II2 binding pathway J. Mol. Biol. 252:1995;102-121.
58. 9k observed by X-ray crystallography. J. Mol. Biol. 223:1992;601-606.
59. Spinelli S., Liu Q.Z., Alzari P.M., Hirel P.H., Poljak R.J. The 3D structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie. 73:1991;1391-1396.
60. Thanki N., Rao J.K., Foundling S.I., Howe W.J., Moon J.B., Hui J.O., Tomasselli A.G., Heinrikson R.L., Thaisrivongs S., Wlodawer A. Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling. Protein Sci. 1:1992;1061-1072.
61. Slupsky C.M., Sykes B.D. NMR solution structure of calcium-saturated skeletal muscle troponin C. Biochemistry. 34:1995;15953-15964.
62. Sundaralingam M., Bergstrom R., Strasburg G., Rao S.T., Roychowdhury P., Greaser M., Wang B.C. Protein, structure molecular structure of troponin C from chicken skeletal muscle at 3-Å resolution. Science. 227:1985;945-948.
63. McCammon J.A., Karplus M. Internal motions of antibody molecules. Nature. 268:1977;765-766.
64. Chen Y.Z., Prohofsky E.W. The role of a minor groove spine of hydration in stabilizing poly(dA)·poly(dT) against fluctuational inter-base H-bond disruption in the premelting temperature regime. Nucleic Acids Res. 20:1992;415-419.
65. Cao Z.W., Chen Y.Z. Hydrogen bond disruption probability in proteins by a modified self-consistent harmonic approach. Biopolymers. 58:2001;319-328.
66. 4+. Int. J. Quantum. Chem. Symp. 1:1974;49-53.
67. Chen Y.Z., Prohofsky E.W. Premelting base pair opening probability and drug binding constant of a daunomycin - Poly d(GCAT)-Poly d(ATGC) complex. Biophys. J. 66:1994;820-826.
68. E. Anderson, Z. Bai, C. Bischof, C. Demmel, LAPACK User's Guide, Society for Industrial and Applied Mathematics, Philadelphia, 1992.
69. Lawson C.L., Carey J. Tandem binding in crystals of a TRP repressor/operator half-site complex. Nature. 366:1993;178-182.
70. Schevitz R.W., Otwinowski Z., Joachimiak A., Lawson C.L., Sigler P.B. The 3D structure of TRP repressor. Nature. 317:1985;782-786.
71. McCary L.C., Staun M., DeLuca H.F. A characterization of Vitamin D-independent intestinal calcium absorption in the osteopetrotic (op/op) mouse. Arch. Biochem. Biophys. 368:1999;249-256.
72. 9k in the apo, singly and doubly calcium-loaded states. Proteins. 33:1998;265-284.
73. 2+ binding and dissociation. Biochemistry. 37:1998;8926-8937.
74. Ababou A., Desjarlais J.R. Solvation energetics and conformational change in EF-hand proteins. Protein Sci. 10:2001;301-312.
75. 9k. Nat. Struct. Boil. 7:2000;245-250.
76. 9k strongly affects backbone dynamics: measurements of exchange rates of individual amide protons using 1H NMR. Biochemistry. 29:1990;5925-5934.
77. York D.M., Darden T.A., Pedersen L.G., Anderson M.W. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry. 32:1993;1443-1453.
78. Collins J.R., Burt S.K., Erickson J.W. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nat. Struct. Biol. 2:1995;334-338.
79. Skalka A.M. Retroviral proteases: first glimpses at the anatomy of a processing machine. Cell. 56:1989;911-913.
80. Blundell T., Pearl L. Retroviral proteinases: a second front against AIDS. Nature. 337:1989;596-597.
81. Wilderspin A.F., Sugrue R.J. Alternative native flap conformation revealed by 2.3-Å resolution structure of SIV proteinase. J. Mol. Biol. 239:1994;97-103.
82. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:1993;283-291.
83. Jacobs D.J., Rader A.J., Kuhn L.A., Thorpe M.F. Protein flexibility prediction using graph theory. Proteins. 44:2001;150-165.
84. Harte W.E. Jr., Swaminathan S., Mansuri M.M., Martin J.C., Rosenberg I.E., Beveridge D.L. Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. Proc. Natl. Acad. Sci. U.S.A. 87:1990;8864-8868.
85. Satyshur K.A., Rao S.T., Pyzalska D., Drendel W., Greaser M., Sundaralingam M. Refined structure of chicken skeletal muscle troponin C in the two-calcium states at 2-Å resolution. J. Biol. Chem. 263:1998;1628-1647.
86. Digel J., Abugo O., Kobayashi T., Gryczynski Z., Lakowicz J.R., Collins J.H. Calcium- and magnesium-dependent interactions between the C-terminus of troponin I and the N-terminal, regulatory domain of troponin C. Arch. Biochem. Biophys. 387:2001;243-249.
87. Ngai S.M., Hodges R.S. Structural and functional studies on troponin I and troponin C interactions. J. Cell Biochem. 83:2001;33-46.
88. Li H.C., Hideg K., Fajer P.G. The mobility of troponin C and troponin I in muscle. J. Mol. Recognit. 10:1997;194-201.
89. Moncrieffe M.C., Eaton S., Bajzer Z., Haydock C., Potter J.D., Laue T.M., Prendergast F.G. Rotational and translational motion of troponin C. J. Biol. Chem. 274:1999;17464-17470.