Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations

Proteins: Structure, Function and Genetics

Volumn 37, Issue 3, 1999, Pages 454-464

  Kurt, Neşe ^a   Haliloǧlu, Türkan ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Dynamic Monte Carlo; Fluctuations; Knowledge based potentials; Low resolution model; Orientational and conformational correlations; Virtual bond rotations

Indexed keywords

CHYMOTRYPSIN INHIBITOR; DEUTERIUM; HYDROGEN; PROTEIN;

ARTICLE; CHEMICAL BOND; CRYSTALLOGRAPHY; ENERGY; GEOMETRY; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; ROTATION; SIMULATION;

MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDES; PLANT PROTEINS; PROTEIN CONFORMATION;

EID: 0345281586     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991115)37:3<454::AID-PROT12>3.0.CO;2-V     Document Type: Article

References (43)

1. Tanaka S, Scheraga HI. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976;9:945-950.
2. Miyazawa S, Jernigan RL. Estimation of effective inter-residue contact energies from protein crystal structures: quasichemical approximation. Macromolecules 1985;18:534-552.
3. Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
4. Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
5. Singh J, Thornton JM. SIRIUS: an automated method of analysis of preferred packing arrangements between protein groups. J Mol Biol 1990;211:595-615.
6. Vriend G, Sander C. Quality control of protein models: directional atomic contact analysis. J Appl Crystallogr 1993;26:47-60.
7. Bahar I, Jernigan RL. Coordination geometry of non-bonded residues in globular proteins. Folding Design 1996;1:357-370.
8. De Witte RS, Shakhnovich EI. Pseudodihedrals: simplified protein backbone representation with knowledge-based energy. Protein Sci 1994;2:1570-1581.
9. Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997;29:292-308.
10. Hendlich M, Lackner P, Weitckus S, et al. Identification of native protein folds amongst a large number of incorrect models: the calculation of low-energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
11. Kocher JPA, Rooman MJ, Wodak S. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994;235:1598-1613.
12. Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
13. Miyazawa S, Jernigan RL. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng 1994;7:1209-1220.
14. Altuvia Y, Schueler O, Margalit H. Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 1995;249:244-250.
15. Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975;253:694-698.
16. Ueda Y, Taketomi H, Go N. Studies on protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model for lyzosyme. Biopolymers 1978;17:1531-1548.
17. Skolnick J, Kolinski A. Dynamic Monte Carlo simulation of globular protein folding/unfolding pathway. I. Six member, Greek key β barrel proteins. J Mol Biol 1990;212:787-817.
18. Covell DG. Lattice model simulation of polypeptide chain folding. J Mol Biol 1994;235:1032-1043.
19. Kolinski A, Skolnick J. Monte Carlo simulation of protein folding. I. Lattice model and interaction scheme. Proteins 1994;18:338-352.
20. Sali A, Shakhnovich E, Karplus M. Kinetics of protein folding: a lattice model study of the requirements for folding to the native state. J Mol Biol 1994;235:1614-1636.
21. Vieth M, Kolinski A, Brooks ICL, Skolnick J. Prediction of the folding pathways and structure of GCN4 leucine zipper. J Mol Biol 1994;237:361-367.
22. Elofsson A, LeGrand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins 1995;23:73-82.
23. Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 1995;5:58-73.
24. Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993;2:762-785.
25. Park BH, Levitt M. The complexity of accuracy of discrete state models of protein structure. J Mol Biol 1995;249:493-507.
26. Sun S, Thomas PD, Dill KA. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 1995;8:769-778.
27. Park BH, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constrained decoys. J Mol Biol 1996; 258:367-392.
28. Haliloǧlu T. Characterization of internal motions of Escherichia coli ribonuclease H by Monte Carlo simulation. Proteins 1999;34: 533-539.
29. Haliloǧlu T. Coarse-grained simulations of conformational dynamics of proteins. Theor Computat Polymer Sci 1999;9:255-260.
30. Haliloǧlu T, Bahar I. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins 1998;31:271-281.
31. Ladurner AG, Itzhaki LS, de Prat Gay G, Fersht AR. Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. J Mol Biol 1997;273:317-329.
32. Jackson SE, Moracci M, elMasry N, Johnson CM, Fersht AR. Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. Biochemistry 1993;32:11259-11269.
33. Daggett V, Li A, Itzhaki LS, Otzen DE, Fersht AR. Structure of the transition state for folding of a protein derived from experiment and simulation. J Mol Biol 1996;257:430-440.
34. McPhalen CA, James MNG. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry 1987;26:261-269.
35. Flory PJ. Statistical mechanics of chain molecules. New York: Hanser Publishers; 1998.
36. Li A, Daggett V. Investigation of the solution structure of CI2 using MD: comparison to x-ray crystallographic and NMR data. Protein Eng 1995;8:1117-1128.
37. Ludvigsen S, Shen H, Kjaer M, Madsen JC, Poulsen FM. Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals. J Mol Biol 1991;222:621-635.
38. Otzen DE. The structure of the transition state for the folding/ unfolding of the barley chymotrypsin inhibitor-2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci USA 1994;91:10422-10425.
39. Itzhaki LS, Otzen DE, Fersht AR. The structure of the transition state for folding of CI2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 1995;254:260-288.
40. Neira JL, Itzhaki LS, Otzen DE, Davis B, Fersht AR. Hydrogen exchange in CI2 probed by mutagenesis. J Mol Biol 1997;270:99-110.
41. Shaw GL, Davis B, Keeler J, Fersht AR. Backbone dynamics of CI2: effect of breaking the active site bond and its implications for the mechanism of inhibition of serine proteases. Biochemistry 1995;34:2225-2233.
42. Haliloǧlu T, Bahar I, Erman B, Kim EG, Mattice WL. A dynamic rotational isomeric state approach for extension of the time scale of the local dynamics observed in fully atomistic molecular dynamics simulations: application to polybutadiene. J Chem Phys 1996;104:4828-4834.
43. Clarage JB, Romo T, Andrews BK, Pettitt BM, Philips GA. Sampling problem in molecular dynamics simulations of macromolecules. Proc Natl Acad Sci USA 1995;92:3288-3292.