Backbone entropy of loops as a measure of their flexibility: Application to a Ras protein simulated by Molecular Dynamics

Proteins: Structure, Function and Genetics

Volumn 29, Issue 2, 1997, Pages 127-140

  Meirovitch, Hagai ^a   Hendrickson, Thomas F ^b  

^a FLORIDA STATE UNIVERSITY   (United States)

^b AGOURON PHARMACEUTICALS INC   (United States)

Author keywords

Backbone entropy; Flexibility; Loops; Molecular Dynamics; Proteins; Ras protein

Indexed keywords

RAS PROTEIN;

ARTICLE; ENTROPY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ENTROPY; MODELS, CHEMICAL; PROTEIN CONFORMATION; RAS PROTEINS;

EID: 0030961098     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199710)29:2<127::AID-PROT1>3.0.CO;2-A     Document Type: Article

References (76)

1. Getzoff, E.D., Geysen, H.M., Rodda, S.J., Alexander, H., Tainer, J.A., Lerner, R.A. Mechanisms of antibody binding to a protein. Science 235:1191-1196, 1987.
2. Colman, P.M., Laver, W.G., Varghese, J.N., Baker, A.T., Tulloch, P.A., Air, G.M., Webster, R.G. Three-dimensional structure of a complex of antibody with influenza virus neuraminidase. Nature 326:358-363, 1987.
3. Bhat, T.N., Bentley, G.A., Fischmann, T.O., Boulot, G., Poljak, R.J. Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding. Nature 347:483-485, 1990.
4. Stanfield, R.L., Fieser, T.M., Lerner, R.A., Wilson, I.A. Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science 248:712-719, 1990.
5. Rini, J.M., Schulze-Gahmen, U., Wilson, I.A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 255:959-965, 1992.
6. Nicholson, L.K., Yamazaki, T., Torchia, D.A., Grzesiek, S., Bax, A., Stahl, S.J., Kaufman, J.D., Wingfield, P.T., Lam, P.Y.S., Jadhav, P.K., Hodge, C.N., Domaille, P.J., Chang C.-H. Flexibility and function in HIV-1 protease. Struct. Biol. 2:274-280, 1995.
7. Collins, J.R., Burt, S.K., Erickson, J.W. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Struct. Biol. 2:334-338, 1995.
8. Wagner, G. The importance of being floppy. Struct. Biol. 2:255-257, 1995.
9. Lois, E., Petsko, B.A. Crystallographic analysis of the complex between triose phosphate isomerase and the 2-phosphoglycolate at 2.5 Å resolution. Biochemistry 29:6619-6625, 1990.
10. Joseph, D., Petsko, G.A., Karplus, M. Anatomy of conformational change: hinged "lid" motion of the triose phosphate isomerase loop. Science 249:1425-1428, 1990.
11. Brzovic, P.S., Sawa, Y., Hyde, C.C., Miles, E.W., Dunn, M.F. Evidence that mutations in a loop region of the α-subunit inhibit the transition from an open to a closed conformation in the tryptophan synthase bienzyme complex. J. Biol. Chem. 267:13028-13038, 1992.
12. Brzovic, P.S., Hyde, C.C., Miles, E.W., Dunn, M.F. Characterization of the functional role of a flexible loop in the α subunit of tryptophan synthase from Salmonella typhimurium by rapid scanning, stopped-flow spectroscopy and site directed mutagenesis. Biochemistry 32:10404-10413, 1993.
13. Fetrow, J.S. Omega loops: Nonregular secondary structures significant in protein function and stability. FASEB J. 9:708-717, 1995.
14. Gō, N., Scheraga, H.A. Ring closure and local conformational deformations of chain molecules. Macromolecules 3:178-187, 1970.
15. Bruccoleri, R.E., Karplus, M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137-168, 1987.
16. Moult, J., James, M.N.G. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1:146-163, 1986.
17. Fine, R.M., Wang, H., Shenkin, P.S., Yarmush, D.L., Levinthal, C. Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins 1:342-362, 1986.
18. Bruccoleri, R.E., Haber, E., Novotný, J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 335:564-568, 1988.
19. Dudek, M.J., Scheraga, H.A. Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops. J. Comp. Chem. 11:121-151, 1990.
20. Higo, J., Collura, V., Garnier, J. Development of extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins. Biopolymers 32:33-43, 1992.
21. Carlacci, L., Englander, S.W. Loop problem in proteins: Developments on the Monte Carlo simulated annealing approach. J. Comp. Chem. 17:1002-1012, 1996.
22. Zheng, Q., Kyle, D.J. Accuracy and reliability of the scaling-relaxation method for loop closure: An evaluation based on extensive and multiple copy conformational sampling. Proteins 24:209-217, 1996.
23. Leszcynski, J.F., Rose, G.D. Loops in globular proteins: A novel category of secondary structure. Science 234:849-855, 1986.
24. Ring, C.S., Kneller, D.G., Langridge, R., Cohen, F.E. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224:685-699, 1992.
25. Chothia, C., Lesk, A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:901-917, 1987.
26. Chothia, C., Lesk, A.M., Tramontano, A., Levitt, M., Smith-Gill, S.J., Air, G., Sheriff, F., Padlan, A.A., Davis, D., Tulip, W.R., Colman, P.M., Spinelli, S., Alzari, P.M., Poljak, R.J. Conformations of immunoglobulin hypervariable regions. Nature 342:877-883, 1989.
27. Kwasigroch, J.-M., Chomilier, J., Mormon, J.-P. A global taxonomy of loops in globular proteins. J. Mol. Biol. 259:855-872, 1996.
28. Karplus, P.A., Schulz, G.E. Prediction of chain flexibility in proteins. Naturwissenschaften 72:212-213, 1985.
29. Dykes, D.C., Brandt-Rauf, P.W., Luster, S.M., Chung, D., Friedman, F.K., Pincus, M.R. Activated conformations of the ras-gene-encoded p21 protein. 1. An energy refined structure for the normal p21 protein complexed with GDP. J. Biomol. Struct. Dynam. 9:1025-1044, 1992.
30. Dykes, D.C., Friedman, F.K., Luster-Dykes, S., Murphy, R.B., Brandt-Rauf, P.W., Pincus, M.R. Molecular dynamics of the H-ras-gene-encoded p21 protein: Identification of flexible regions and possible effector domains. J. Biomol. Struct. Dynam. 11:443-458, 1993.
31. Thomas, A., Roux, B., Smith, J.C. Computer simulations of the flexibility of a series of synthetic cyclic peptide analogs. Biopolymers 33:1249-1270, 1993.
32. Liwo, A., Gibson, K.D., Scheraga, H.A., Brandt-Rauf, P.W., Monaco, R., Pincus, M.R. Comparison of the low energy conformations of an oncogenic and non-oncogenic p21 protein, neither which binds GTP or GDP. J. Prot. Chem. 13:237-251, 1994.
33. Díaz, J.F., Wroblowski, B., Engelborghs, Y. Molecular dynamic simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: Flexibility, possible hinges, and levers of the conformational transition. Biochemistry 34: 12038-12047, 1995.
34. Meirovitch, H. Calculation of entropy with computer simulation methods. Chem. Phys. Lett. 45:389-392, 1977.
35. Meirovitch, H. Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions. Phys. Rev. A 32:3709-3715, 1985.
36. Meirovitch, H., Vásquez, M., Scheraga, H.A. Stability of polypeptides conformational states as determined by computer simulation of the free energy. Biopolymers 26:651-671, 1987.
37. 2 in vacuum and the crystal. J. Am. Chem. Soc. 114:5386-5399, 1992.
38. Meirovitch, H., Koerber, S.C., Rivier, J., Hagler, A.T. Computer simulation of the free energy of peptides with the local states method: Analogues of gonadotropin releasing hormone in the random coil and stable states. Biopolymers 34:815-839, 1994.
39. Meirovitch, H., Meirovitch, E. New theoretical methodology for elucidating the solution structure of peptides from NMR data. 3. Solvation effects. J. Phys. Chem. 100:5123-5133, 1996.
40. Lipari, G., Szabo, A. A model free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:4545-4549, 1982.
41. Lipari, G., Szabo, A. A model free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:4549-4570, 1982.
42. 1H NMR spectroscopy. Biochemistry 29:7387-7401, 1990.
43. 15N NMR relaxation measurements. Biochemistry 31:4394-4406, 1992.
44. Peng, J.W., Wagner, G. Mapping of the spectral densities of N - H bond motions in eglin c using heteronuclear relaxation experiments. Biochemistry 31:8571-8586, 1992.
45. Brüschweiler, R., Wright, P.E. NMR order parameters of biomolecules: a new analytical representation and application to the Gaussian axial fluctuation model. J. Am. Chem. Soc. 116:8426-8427, 1994.
46. Farrow, N.A., Zhang, O., Forman-Kay, J.D., Kay, L.E. Comparison of backbone dynamics of a folded and unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry 34:868-878, 1995.
47. 9k. J. Am. Chem. Soc. 115:9832-9833, 1993.
48. Yang, D., Kay, L.E. Contribution to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: Application to protein folding. J. Mol. Biol. 263:369-382, 1996.
49. 15NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: Backbone dynamics and entropy changes of an enzyme upon inhibitor binding. Biochemistry 35:16036-16047, 1996.
50. DeVos, A.M., Tong, L., Milburn, M.V., Matias, P.M., Jancarik, J., Noguchi, S., Nishimura, S., Miura, K., Ohtsuka, E., Kim, S.-H. Three dimensional structure of an oncogene protein: Catalytic domain of human c-H-ras p21. Science 239:888-893, 1988.
51. Tong, L., DeVos, A.M., Milburn, M.V., Kim, S.-H. Crystal structure at 2.2 Å resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP. J. Mol. Biol. 217:503-516, 1991.
52. Milburn, M.V., Tong, L., DeVos, A.M., Brünger, A.T., Yamaizumi, Z., Nishimura, S., Kim, S.-H. Molecular Switch for signal transduction: Structural differences between active and inactive forms of protooncogenic ras proteins. Science 247:939-945, 1990.
53. Pai, E.F., Krengel, U., Petsko, G.A., Goody, R.S., Kabsh, W., Wittinghofer, A. Refined Crystal structure of the triphosphate conformation of H-ras p21 at 1.35 Å resolution: Implications for the mechanism of GTP hydrolysis. EMBO J. 9:2351-2359, 1990.
54. Kraulis, P.J., Domaille, P.J., Campbell-Burk, S.L., Van Aken, T., Laue, E.D. Solution structure and dynamics of Ras p21-GDP determined by hetronuclear three-and four-dimensional NMR spectroscopy. Biochemistry 33:3515-3531, 1994.
55. Foley, C.K., Pedersen, L.G., Charifson, P.S., Darden, T.A., Wittinghofer, A., Pai, E.F., Anderson, M.W. Simulation of the solution structure of the H-ras p21-GTP complex. Biochemistry 31:4951-4959, 1992.
56. Brooks III, C.L., Brünger, A.T., Karplus, M. Active site dynamics in protein molecules: A stochastic boundary molecular dynamics approach. Biopolymers 24:843-865, 1985.
57. Brünger, A.T., Brooks C.L. III, Karplus, M. Active site dynamics of ribonuclease. Proc. Natl. Acad. Sci. U.S.A. 82:8458-8462, 1985.
58. Nadler, W., Brünger, A.T., Schulten, K., Karplus, M. Molecular and stochastic dynamics of proteins. Proc. Natl. Acad. Sci., U.S.A. 84:7933-7937, 1987.
59. Brooks C.L. III, Karplus, M. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site of lysozyme. J. Mol. Biol. 208:159-181, 1989.
60. Fleischman, S.H., Brooks, C.L. III. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes. J. Chem. Phys. 87:3029-3037, 1987.
61. Fleischman, S.H., Brooks, C.L. III. Protein-drug interactions: Characterization of inhibitor binding complexes of DHFR with trimethoprim and related derivatives. Proteins 7:52-61, 1990.
62. Matthews, D.A., Smith, W.W., Ferre, R.A., Condon, B., Budahazi, G., Sisson, W., Villafranca, J.E., Janson, C.A., McElroy H.E., Gribskov, C.L., Worland, S. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77:761-771, 1994.
63. Brooks, B.R., Bruccoleri, R.E., Olafson, B.O., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program of macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217, 1983.
64. Chirlian, L.E., Francl, M.M. Atomic charges derived from electrostatic potentials: A detailed study. J. Comp. Chem. 8:894-905, 1987.
65. Frisch, M.J., Head-Gordon, M., Schlegel, H.B., Raghavachari, K., Binkley, J.S., Gonzalez, C., Defrees, D.J., Fox, D.J., Whiteside, R.A., Seeger, R., Melius, C.F., Baker, J., Kahn, L.R., Stewert, J.P.P., Fluser, E.M., Topial, S., Pople, J.A., "Gaussian 90," Gaussian, Inc., Pittsburgh, PA 15213.
66. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
67. Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341, 1977.
68. Lifson, S., Oppenheim, I. Neighbor interactions and internal rotations in polymer molecules. IV. Solvent effect on internal rotations. J. Chem. Phys. 33:109-115, 1960.
69. Gō, N., Scheraga, H.A. Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. Chem. Phys. 51:4751-4767, 1969.
70. Gō, N., Scheraga, H.A. On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules 9:535-542, 1976.
71. Edholm, O., Berendsen, H.J.C. Entropy estimation trom simulations of non-diffusive systems. Mol. Phys. 51:1011-1028, 1984.
72. Karplus, M., Kushick, J.N. Method for estimating the configurational entropy of macromolecules. Macromolecules 14:325-332, 1981.
73. Levy, R.M., Karplus, M., Kushick, J., Perahia, D. Evaluation of the configurational entropy for proteins: Application to molecular dynamics simulations of an α helix. Macromolecules 17:1370-1374, 1984.
74. Gō, N. Conformational entropy of ring polymers. Macromolecules 19:2054-2058, 1984.
75. Meirovitch, H. Statistical properties of the scanning simulation method for polymer chains. J. Chem. Phys. 89:2514-2522, 1988.
76. Meirovitch, H., Vásquez, M., Scheraga, H.A. Stability of polypeptides conformational states: II. The Free Energy of the statistical coil obtained by the scanning simulation method. Biopolymers, 27:1189-1204, 1988.