Simple models of protein folding and of non-conventional drug design

Journal of Physics Condensed Matter

Volumn 16, Issue 6, 2004, Pages

  Broglia, R A ^a,b,c   Tiana, G ^a,b   Provasi, D ^a,b  

^a UNIVERSITY OF MILAN   (Italy)

^b INFN SEZIONE DI MILANO   (Italy)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; INCIPIENT SECONDARY STRUCTURES; LOCAL ELEMENTARY STRUCTURES; PROTEIN FOLDING;

AMINO ACIDS; COMPUTER SIMULATION; CONFORMATIONS; DRUG PRODUCTS; ENZYMES; FREE ENERGY; HYDROPHOBICITY;

PROTEINS;

EID: 1442287069     PISSN: 09538984     EISSN: None     Source Type: Journal    
DOI: 10.1088/0953-8984/16/6/R02     Document Type: Review

References (51)

1. Shoemaker D D et al 2001 Experimental annotation of the human genome using microarray technology Nature 409 922
2. Venter J C et al 2001 The sequence of the human genome Science 291 1304
3. Fersht A 1999 Structure and Mechanism in Protein Science (New York: Freeman)
4. Service R F 2002 Tapping DNA structures produces a trickle, new focus Science 298 948
5. Broglia R A, Shakhnovich E I and Tiana G (ed) 2001 Protein folding, evolution and design Proc. Int. School of Physics ('E Fermi' Course CXLV) (Amsterdam: IOS Press)
6. Smith H and Williams H 1998 Introduction to the Principle Of Drug Design and Action (London: Dunizt Martin Ltd)
7. Broglia R A, Tiana G and Berera R 2003 Resistance proof, folding inhibitor drugs. J. Chem. Phys. 118 4754
8. Ishchenko A V and Shakhnovich E I 2002 Small molecules growth 2001: in improved knowledge-based scoring function for protein-ligand interactions J. Med. Chem. 45 2770
9. Eichinger M, Tavan P, Hutter J and Parrinello M 1999 A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields J. Chem. Phys. 110 10452
10. Anfinsen C B 1973 Principles that govern the folding of protein chains Science 181 223
11. Frauenfelder H, Parak F and Young R D 1988 Conformational substates in proteins Annu. Rev. Biophys. Biophys. Chem. 17 451
12. Shakhnovich E I and Karplus M 1992 Protein Folding ed T Creighton (New York: Freeman)
13. McAllister E, Alm E and Baker D 2000 Critical role of β-hairpin in protein G folding Nat. Struct. Biol. 7 669
14. Mezard M, Parisi G and Virasoro M 1988 Spin Glasses and Beyond (New York: World Scientific)
15. Rost B 1997 Protein structures sustain evolutionary drift Fold. Des. 2 S19
16. Mirny L and Shakhnovich E I 1999 Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function J. Mol. Biol. 291 177
17. Kramers H A 1940 Brownian motion in a field of force and the diffusion model of chemical reactions Physica 7 284
18. Hänggi P, Talkner P and Borkovec M 1990 Reaction-rate theory: fifty years after Kramers Rev. Mod. Phys. 62 251
19. Guerois R, Nielsen J E and Serrano L 2002 Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320 369
20. Lau K F and Dill K 1989 A lattice statistical mechanics model of the conformational and sequence space of proteins Macromolecules 22 3986
21. Go N 1975 Int. J. Pept. Protein Res. 7 313
22. Metropolis N, Rosenbluth A W, Rosenbluth M N, Teller A H and Teller E 1953 Equation of state calculations by fast computing machines J. Chem. Phys. 21 1087
23. Clementi C, Nymeyer H and Onuchic J N 2000 Topological and energetic factors: what determines the structural details of the transition state ensemble and 'en-route' intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 937
24. Shimada J, Kussel E and Shakhnovich E I 2001 The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation J. Mol. Biol. 308 79
25. Miyazawa S and Jernigan R 1985 Estimation of effective interresidue contact energies from protein crystal structures Macromolecules 18 534
26. Derrida B 1981 Random energy model, an exactly solvable model of disordered systems Phys. Rev. B 24 2613
27. Flory P J 1949 The configuration of real polymer chains J. Chem. Phys. 17 303
28. Orland H, Itzykson C and De Dominicis C 1985 An evaluation of the number of Hamiltonian paths J. Phys. Lett. 46 L353
29. Shakhnovich E I and Gutin A 1989 Enumeration of all compact conformations of copolymers with random sequence of links J. Chem. Phys. 93 5967
30. Bryngelson J D and Wolynes P G 1989 Intermediates and barrier crossing in a random energy model J. Phys. Chem. 93 6902
31. Shakhnovich E I 1994 Proteins with selected sequences fold into unique native conformation Phys. Rev. Lett. 72 3907
32. Abkkevich V I, Gutin A M and Shakhnovich E I 1994 Specific nucleus as the transition state for protein folding Biochemistry 33 10026
33. van Kampen N G 1981 Stochastics Processes in Physics and Chemistry (Amsterdam: North-Holland)
34. Berendsen H J C, van der Spoel D and van Drunen R 1995 GROMACS: a message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 91 43
35. Pearlman D A, Case D A, Caldwell J W, Ross W S, Cheatham T E III, DeBolt S, Ferguson D, Seibel G and Kollman P 1995 AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules Comput. Phys. Commun. 91 1
36. Brooks B R, Bruccoleri R E, Olafson B D, States D J, Swaminathan S and Karplus M 1983 CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 187
37. Duan Y and Kollman P A 1998 Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 282 740
38. Dinner A R and Karplus M 1999 Is protein unfolding the reverse of protein folding? J. Mol. Biol. 292 403
39. Lazaridis T and Karplus M 1997 'New view' of protein folding reconciled with the old through multiple unfolding simulations Science 278 1928
40. Itzhaki L S, Otzen D E and Fersht A The structure of the transition state for folding of Chymotrypsin inhibitor 2 analyzed by protein engineering methods J. Mol. Biol. 254 260
41. Park R H and Levitt M 1995 The complexity and accuracy of discrete state models of protein structure J. Mol. Biol. 249 493
42. Toulouse G 1997 Theory of the frustration effect in spin glasses Commun. Phys. 2 115
43. Bryngelson J D and Wolynes P D 1987 Spin glasses and the statistical mechanisms of protein folding Proc. Natl Acad. Sci. USA 84 7524
44. Broglia R A, Tiana G, Pasquali S, Roman H E and Vigezzi E 1998 Folding and aggregation of designed protein chains Proc. Natl Acad. Sci. USA 95 12930
45. Broglia R A and Tiana G 2001 Hierarchy of events in the folding of model proteins J. Chem. Phys. 114 7267
46. Tiana G, Broglia R A, Roman H E, Vigezzi E and Shakhnovich E I 1998 Folding and misfolding of designed protein-like chains with mutations J. Chem. Phys. 108 757
47. Broglia R A and Tiana G 2001 Reading the three-dimensional structure of a protein from its amino acid sequence Proteins 45 421
48. Abkevich V I, Gutin A M and Shakhnovich E I 1998 Theory of kinetic partitioning in protein folding with possible applications to prions Proteins 31 335
49. Tomasselli A G and Heinrikson R L 2000 Targeting the HIV-protease in AIDS therapy: a current clinical perspective Biochem. Biophys. Acta 1477 189
50. Rey A and Skolnick J 1991 Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins Chem. Phys. 158 199
51. Kikuchi K, Yoshida M, Maekawa T and Watanabe H 1991 Metropolis Monte Carlo method as a numerical technique to solve Fokker-Planck equation Chem. Phys. Lett. 185 335