Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects

Proteins: Structure, Function and Genetics

Volumn 51, Issue 3, 2003, Pages 470-483

  Das, Bedamati ^a   Meirovitch, Hagai ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE; ANTIBODY; CYCLOPEPTIDE; MYOGLOBIN; PEPTIDASE; PROTEIN; PROTEINASE; RIBONUCLEASE A;

ARTICLE; DIELECTRIC CONSTANT; ENTROPY; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLVATION; THERMODYNAMICS; X RAY ANALYSIS;

AMINO ACID SEQUENCE; ENTROPY; MODELS, CHEMICAL; PROTEIN CONFORMATION; PROTEINS; SOLUBILITY; SOLVENTS; THERMODYNAMICS;

EID: 0038300292     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10356     Document Type: Article

References (96)

1. Karplus PA, Schulz GE. Prediction of chain flexibility in proteins. Naturwissenschaften 1985;72:212-213.
2. Getzoff ED, Geysen HM, Rodda SJ, Alexander H, Tainer JA, Lerner RA. Mechanisms of antibody binding to a protein. Science 1987;235:1191-1196.
3. Rini JM, Schulze-Gahmen U, Wilson IA. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 1992;255:959-965.
4. Constantine KL, Friedrichs MS, Wittekind M, Jamil H, Chu CH, Parker RA, Goldfarb V, Mueller L, Farmer BT. Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins. Biochemistry 1998;37:7965-7980.
5. Nicholson LK, Yamazaki T, Torchia DA, Grzesiek S, Bax A, Stahl SJ, Kaufman JD, Wingfield PT, Lam PYS, Jadhav PK, Hodge CN, Domaille PJ, Chang C-H. Flexibility and function in HIV-1 protease. Struct Biol 1995;2:274-280.
6. Collins JR, Burt SK, Erickson JW. Flap opening in HIV-1 protease simulated by "activated" molecular dynamics. Struct Biol 1995;2:334-338.
7. Wagner G. The importance of being floppy. Struct Biol 1995;2:255-257.
8. Fetrow JS. Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J 1995;9:708-717.
9. Crasto CJ, Feng J. Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins. Proteins 2001;42:399-413.
10. Leszcynski JF, Rose GD. Loops in globular proteins: a novel category of secondary structure. Science 1986;234:849-855.
11. Donate LE, Rufino SD, Canard LH, Blundell TL. Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996;5:2600-2616.
12. Fechteler T, Dengler U, Schomburg D. Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria. J Mol Biol 1995;253:114-131.
13. Kwasigroch JM, Chomilier J, Mornon JP. A global taxonomy of loops in globular proteins. J Mol Biol 1996;259:855-872.
14. Martin AC, Toda K, Stirk HJ, Thornton JM. Long loops in proteins. Protein Eng 1995;8:1093-1101.
15. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. An automated classification of the structure of protein loops. J Mol Biol 1997;266:814-830.
16. Ring CS, Kneller DG, Langridge R, Cohen FE. Taxonomy and conformational analysis of loops in proteins. J Mol Biol 1992;224:685-699.
17. Bates PA, Sternberg MJ. Model building by comparison at CASP3: using expert knowledge and computer automation. Proteins 1999;Suppl 3:47-54.
18. Mosimann S, Meleshko R, James MN. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 1995;23:301-317.
19. Sali A. Modeling mutations and homologous proteins. Curr Opin Biotechnol 1995;6:437-451.
20. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 1987;196:901-917.
21. Chothia C, Lesk AM, Tramontano A, Levitt M, Smith-Gill SJ, Air G, Sheriff S, Padlan EA, Davies D, Tulip WR. Conformations of immunoglobulin hypervariable regions. Nature 1989;342:877-883.
22. Fidelis K, Stern PS, Bacon D, Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994;7:953-960.
23. Sudarsanam S, DuBose RF, March CJ, Srinivasan S. Modeling protein loops using a phi i + 1, psi i dimer database. Protein Sci 1995;4:1412-1420.
24. Summers NL, Karplus M. Modeling of globular proteins: a distancebased data search procedure for the construction of insertion/deletion regions and Pro - non-Pro mutations. J Mol Biol 1990;216:991-1016.
25. Tappura K. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations. Proteins 2001;44:167-179.
26. Deane CM, Blundell TL. A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins 2000;40:135-144.
27. Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987;26:137-168.
28. Moult J, James MN. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1986;1:146-163.
29. van Vlijmèn HW, Karplus M. PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 1997;267:975-1001.
30. Wojcik J, Mornon JP, Chomilier J. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 1999;289:1469-1490.
31. Das B, Meirovitch H. Optimization of solvation models for predicting the structure of surface loops in proteins. Proteins 2001;43:303-314.
32. Fine RM, Wang H, Shenkin PS, Yarmush DL, Levinthal C. Predicting antibody hypervariable loop conformations. II. Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins 1986;1:342-362.
33. Higo J, Collura V, Garnier J. Development of an extended simulated annealing method: application to the modeling of complementary determining regions of immunoglobulins. Biopolymers 1992;32:33-43.
34. Rosenfeld R, Zheng Q, Vajda S, DeLisi C. Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors. J Mol Biol 1993;234:515-521.
35. Shenkin PS, Yarmush DL, Fine RM, Wang HJ, Levinthal C. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers 1987;26:2053-2085.
36. Caralacci L, Englander SW. Loop problem in proteins: developments on the Monte Carlo simulated annealing approach. J Comput Chem 1996;17:1002-1012.
37. Dudek MJ, Scheraga HA. Protein structure prediction using a combination of sequence homology and global energy minimization. I. Global energy minimization of surface loops. J Comput Chem 1990;11:121-151.
38. Gõ N, Scheraga HA. Ring closure and local conformational deformations of chain molecules. Macromolecules 1970;3:178-187.
39. Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Loop closure via bond scaling and relaxation. J Comput Chem 1993;14:556-565.
40. Mas MT, Smith KC, Yarmush DL, Aisaka K, Fine RM, Modeling the anti-CEA antibody combining site by homology and conformational search. Proteins 1992;14:483-498.
41. Smith KC, Honig B. Evaluation of the conformational free energies of loops in proteins. Proteins 1994;18:119-132.
42. Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
43. Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem 1997;101:3005-3014.
44. Rapp CS, Friesner RA. Prediction of loop geometries using generalized Born model of solvation effects. Proteins 1999;35:173-183.
45. Bruccoleri RE, Haber E, Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 1988;335:564-568.
46. Baysal C, Meirovitch H. Determination of the stable microstates of a peptide from NOE distance constraints and optimization of atomic solvation parameter. J Am Chem Soc 1998;120:800-812.
47. Baysal C, Meirovitch H. Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data. Biopolymers 1999;50:329-344.
48. Meirovitch H, Meirovitch E, Lee J. New theoretical methodology for elucidating the solution structure of peptides from NMR data. I. The relative contribution of low energy microstates to the partition function. J Phys Chem 1995;99:4847-4854.
49. Meirovitch H, Meirovitch E. New theoretical methodology for elucidating the solution structure of peptides from NMR data. 3. Solvation effects. J Phys Chem 1996;100:5123-5133.
50. Baysal C, Meirovitch H. On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO. Biopolymers 2000;54:416-428.
51. Baysal C, Meirovitch H. Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model. Biopolymers 2000;53:423-433.
52. Baysal C, Meirovitch H. Efficiency of the local torsional deformations method for identifying the stable structures of cyclic molecules. J Phys Chem 1997;101:2185-2191.
53. Baysal C, Meirovitch H. Efficiency of simulated annealing for peptides with increasing geometrical constraints. J Comput Chem 1999;20:1659-1670.
54. Meirovitch H. Calculation of entropy with computer simulation methods. Chem Phys Lett 1977;45:389-392.
55. Meirovitch H, Koerber SC, Rivier JE, Hagler AT. 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 1994;34:815-839.
56. Ponder JW. TINKER-software tools for molecular design. St. Louis:Washington University 1999; Version 3.7.
57. Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-11236.
58. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnik S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamic studies of proteins. J Phys Chem 1998;102:3586-3616.
59. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
60. Santoro J, Gonzalez C, Bruix M, Neira JL, Nieto JL, Herranz J, Rico M. High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy. J Mol Biol 1993;229:722-734.
61. Kuriyan J, Osapay K, Burley SK, Brunger AT, Hendrickson WA, Karplus M. Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins 1991;10:340-358.
62. Svenson LA, Sjolin L, Dill J, Gilliand GL. The conformation flexibility of surface residues of bovine pancreatic ribonuclease A at 1.1Å. In: Cuchillo CM, de Llorens R, Nogues MV, Pares X, editors. Proceedings of the 2nd International Meeting, Universitat Autonoma de Barcelona, Barcelona 1991;31-38.
63. Tilton RF Jr., Dewan JC, Petsko GA. Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry 1992;31:2469-2481.
64. Elber R, Karplus M. Multiple conformational states of proteins-a molecular dynamics analysis of myoglobin. Science 1987;235:318-321.
65. Karplus M, Kushik JN. Method for estimating configurational entropy of macromolecules. Macromolecules 1981;14:325-332.
66. Stillinger FH, Weber TA. Packing structures and transitions in liquids and solids. Science 1984;225:983-989.
67. Meirovitch H. Calculation of the free energy and entropy of macromolecular systems by computer simulation. In: Lipkowitz KB, Boyd DB, editors. Rev Comp Chem 1998;12:1-74.
68. Beveridge DL, DiCapua FM. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 1989;18:431-492.
69. Tanner JJ, Nell LJ, McCammon JA. Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent. Biopolymers 1992;32:23-32.
70. Ooi T, Oobatake M, Némethy G, Scheraga HA. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 1987;84:3086-3090.
71. Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. Protein structure prediction with a combined solvation free energymolecular mechanics force field. Mol Simul 1993;10:121-149.
72. Fraternali F, Van Gunsteren WF. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. J Mol Biol 1996;256:939-948.
73. Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J Comput Aided Mol Des 1991;5:5-20.
74. Najmanovich R, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 2000;39:261-268.
75. Zhao S, Goodsell DS, Olson AJ. Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation. Proteins 2001;43:271-279.
76. Wilson MA, Brunger AT. The 1.0 A crystal structure of Ca(2+)bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. J Mol Biol 2000;301:1237-1256.
77. Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L. The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol 2000;297:713-732.
78. Muller CW, Schulz GE. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. J Mol Biol 1992;224:159-177.
79. Flory PJ. Statistical mechanics of chain molecules. New York: Hasner; 1988.
80. Liu DC, Nocedal J. On the limited memory BFGS method for large scale optimization. Technical Report NAM03, Evanston, IL, Department of Electrical Engineering and Computer Science, North Western University; 1988.
81. Perrot G, Cheng B, Gibson KD, Palmer KA, Nayeem A, Maigret B, Scheraga HA. MSEED - a program for rapid analytical determination of of accessible surface area s and their derivatives. J Comput Chem 1992;13:1-11.
82. Collura V, Higo J, Garnier J. Modeling of protein loops by simulated annealing. Protein Sci 1993;2:1502-1510.
83. Zheng Q, Kyle DJ. Accuracy and reliability of the scalingrelaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings. Proteins 1996;24:209-217.
84. Xiang X, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002;99:7432-7437.
85. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1092.
86. Brady J, Karplus M. Conformational entropy of the alanine dipeptide in vacuum and in solution: a molecular dynamics study. J Am Chem Soc 1985;107:6103-6105.
87. Haukins GD, Liotard DA, Cramer CJ, Truhlar DG. OMNISOL: fast prediction of free energy of solvation and partition coeeficients. J Org Chem 1998;63:4305-4313.
88. Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins 2001;45:144-158.
89. Gallicchio E, Zhang LY, Levy RM. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem 2002;23:517-529.
90. Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 1996;100:1578-1599.
91. Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding: comparison of implicit solvent Poisson and surface generalized born models with explicit solvent simulations. J Comput Chem 2001;22:591-607.
92. Dominy BN, Brooks CI III. Development of a generalized Born model parametrization for proteins and nucleic acids. J Phys Chem 1999;103:3765-3773.
93. Hassan SA, Guarnieri F, Mehler EL. A general treatment of solvent effects based on screened Coulomb potentials. J Phys Chem B 2000;104:6478-6489.
94. Hassan SA, Mehler EL. A critical analysis of continuum electrostatics: the screened Coulomb potential-implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins. Proteins 2002;47:45-61.
95. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
96. Warshel A, Russell ST. Calculation of electrostatic interactions in biological systems and in solutions. Q Rev Biophys 1984;17:283-422.