Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice

Proteins: Structure, Function and Bioinformatics

Volumn 80, Issue 6, 2012, Pages 1683-1693

  Moreno Hernández, Sergio ^a,b   Levitt, Michael ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Hydrophobicity; Lattice models; Protein like; Protein universe; Residue composition; Self avoiding walk

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPARATIVE MODELING; ENERGY; HYDROPHOBIC POLAR LATTICE MODEL; HYDROPHOBICITY; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 84860645205     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24067     Document Type: Article

References (81)

1. Petrone PM, Snow CD, Lucent D, Pande VS. Side-chain recognition and gating in the ribosome exit tunnel. Proc Natl Acad Sci USA 2008; 105: 16549-16554.
2. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-level characterization of the structural dynamics of proteins. Science 2010; 330: 341-346.
3. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995; 4: 561-602.
4. Kolinski A, Skolnick J. Reduced models of proteins and their applications. Polymer 2004; 45: 511-524.
5. Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987; 193: 775-791.
6. Park BH, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 1995; 249: 493-507.
7. Unger R, Harel D, Wherland S, Sussman JL. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989; 5: 355-373.
8. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
9. Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol 2002; 323: 297-307.
10. Levitt M. Simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976; 104: 59-107.
11. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
12. Skolnick J, Kolinski A. Simulations of the folding of a globular protein. Science 1990; 250: 1121-1125.
13. Klimov DK, Thirumalai D. Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold Des 1998; 3: 127-139.
14. Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 2000; 7: 336-342.
15. Yue K, Fiebig K, Thomas P, Chan H, Shakhnovich E, Dill K. A test of lattice protein folding algorithms. Proc Natl Acad Sci USA 1995; 92: 325-329.
16. Klimov D, Thirumalai D. Factors governing the foldability of proteins. Proteins 1996; 26: 411-441.
17. Li H, Helling R, Tang C, Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science 1996; 273: 666-669.
18. Mirny LA, Abkevich VI, Shakhnovich EI. How evolution makes proteins fold quickly. Proc Natl Acad Sci USA 1998; 95: 4976-4981.
19. Cejtin H, Edler J, Gottlieb A, Helling R, Li H, Philbin J, Wingreen N, Tang C. Fast tree search for enumeration of a lattice model of protein folding. J Chem Phys 2002; 116: 352-359.
20. Lau K, Dill K. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules 1989; 22: 3986-3997.
21. Miller R, Danko C, Fasolka M, Balazs A, Chan H, Dill K. Folding kinetics of proteins and copolymers. J Chem Phys 1992; 96: 768-780.
22. Unger R, Moult J. Genetic algorithms for protein folding simulations. J Mol Biol 1993; 231: 75-81.
23. Bornberg-Bauer E, Chan HS. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci USA 1999; 96: 10689-10694.
24. Xia Y, Levitt M. Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution. Proteins 2004; 55: 107-114.
25. Skolnick J, Kolinski A. Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins. J Mol Biol 1990; 212: 787-817.
26. Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994; 243: 668-682.
27. Blackburne B, Hirst J. Three-dimensional functional model proteins: structure function and evolution. J Chem Phys 2003; 119: 3453-3460.
28. Chan HS, Dill KA. Comparing folding codes for proteins and polymers. Proteins 1996; 24: 335-344.
29. Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133-7155.
30. Wingreen N, Li H, Tang C. Designability and thermal stability of protein structures. Polymer 2004; 45: 699-705.
31. Chan HS, Dill KA. Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 1994: 9238-9257.
32. Li H, Tang C, Wingreen NS. Are protein folds atypical? Proc Natl Acad Sci USA 1998; 95: 4987-4990.
33. Abkevich VI, Gutin AM, Shakhnovich EI. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 1994;33: 10026-10036.
34. Li H, Tang C, Wingreen N. Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix. Proteins 2002; 49: 403-412.
35. Zeldovich KB, Berezovsky IN, Shakhnovich EI. Physical origins of protein superfamilies. J Mol Biol 2006; 357: 1335-1343.
36. Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985; 18: 534-552.
37. Unger R, Moult J. Local interactions dominate folding in a simple protein model. J Mol Biol 1996; 259: 988-994.
38. Noivirt-Brik O, Unger R, Horovitz A. Analysing the origin of long-range interactions in proteins using lattice models. BMC Struct Biol 2009; 9: 4.
39. Noivirt-Brik O, Horovitz A, Unger R. Trade-off between positive and negative design of protein stability: from lattice models to real proteins. PLoS Comput Biol 2009; 5: e1000592.
40. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536-540.
41. Orengo CA, Bray JE, Buchan DWA, Harrison A, Lee D, Pearl FMG, Sillitoe I, Todd AE, Thornton JM. The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics 2002; 2: 11-21.
42. Holm L, Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res 1996; 24: 206-209.
43. Unger R, Uliel S, Havlin S. Scaling law in sizes of protein sequence families: from super-families to orphan genes. Proteins 2003; 51: 569-576.
44. Chan HS, Bornberg-Bauer E. Perspectives on protein evolution from simple exact models. Appl Bioinformatics 2002; 1: 121-144.
45. Wang T, Miller J, Wingreen N, Tang C, Dill K. Symmetry and designability for lattice protein models. J Chem Phys 2000; 113: 8329-8336.
46. Sali A, Shakhnovich EI, Karplus M. How does a protein fold? Nature 1994; 369: 248-251.
47. Klimov DK, Thirumalai D. Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism. J Mol Biol 1998; 282: 471-492.
48. Klimov DK, Thirumalai D. Multiple protein folding nuclei and the transition state ensemble in two-state proteins. Proteins 2001; 43: 465-475.
49. Onuchic J, Socci, Luthey-Schulten, Wolynes. Protein folding funnels: the nature of the transition state ensemble. Fold Des 1996; 1: 441-450.
50. Pande VS, Rokhsar DS. Folding pathway of a lattice model for proteins. Proc Natl Acad Sci USA 1999; 96: 1273-1278.
51. Camacho CJ, Thirumalai D. Kinetics and thermodynamics of folding in model proteins. Proc Natl Acad Sci USA 1993; 90: 6369-6372.
52. Melin R, Li H, Wingreen N, Tang C. Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study. J Chem Phys 1999; 110: 1252-1262.
53. Kolinski A, Galazka W, Skolnick J. On the origin of the cooperativity of protein folding: implications from model simulations. Proteins 1996; 26: 271-287.
54. Jewett AI, Pande VS, Plaxco KW. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J Mol Biol 2003; 326: 247-253.
55. Chan HS. Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Proteins 2000; 40: 543-571.
56. Chan HS, Zhang Z, Wallin S, Liu Z. Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annu Rev Phys Chem 2011; 62: 301-326.
57. Xia Y, Levitt M. Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 2004; 14: 202-207.
58. Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI. Imprint of evolution on protein structures. Proc Natl Acad Sci USA 2004; 101: 2846-2851.
59. Blackburne BP, Hirst JD. Population dynamics simulations of functional model proteins. J Chem Phys 2005; 123: 154907.
60. Xia Y, Levitt M. Roles of mutation and recombination in the evolution of protein thermodynamics. Proc Natl Acad Sci USA 2002; 99: 10382-10387.
61. Cui Y, Wong WH, Bornberg-Bauer E, Chan HS. Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc Natl Acad Sci USA 2002; 99: 809-814.
62. Tang C. Simple models of the protein folding problem. Phys A 2000; 288: 31-48.
63. Chan H, Dill K. "Sequence space soup"of proteins and copolymers. J Chem Phys 1991; 95: 3775-3787.
64. Irback A, Troein C. Enumerating designing sequences in the HP model. J Biol Phys 2002; 28: 1-15.
65. Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990; 29: 3287-3294.
66. Dill KA, Fiebig KM, Chan HS. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci USA 1993; 90: 1942-1946.
67. Yue K, Dill KA. Forces of tertiary structural organization in globular proteins. Proc Natl Acad Sci USA 1995; 92: 146-150.
68. Backofen R, Will S. A constraint-based approach to fast and exact structure prediction in three-dimensional protein models. Constraints 2006; 11: 5-30.
69. Chothia C. One thousand families for the molecular biologist. Nature 1992; 357: 543-544.
70. Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature 1994; 372: 631-634.
71. Brenner SE, Chothia C, Hubbard TJ. Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 1997; 7: 369-376.
72. Chan HS, Dill KA. Compact polymers. Macromolecules 1989; 22: 4559-4573.
73. Taverna D, Goldstein R. The distribution of structures in evolving protein populations. Biopolymers 2000; 53: 1-8.
74. Arteca G. Scaling behavior of some molecular shape descriptors of polymer chains and protein backbones. Phys Rev E 1994; 49: 2417-2428.
75. Ivankov DN, Bogatyreva NS, Lobanov MY, Galzitskaya OV. Coupling between properties of the protein shape and the rate of protein folding. PLoS ONE 2009; 4: e6476.
76. Hong L, Lei J. Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity. J Polym Sci Pol Phys 2009; 47: 207-214.
77. Irback A, Sandelin E. On hydrophobicity correlations in protein chains. Biophys J 2000; 79: 2252-2258.
78. Creighton TE. The biophysical chemistry of nucleic acids and proteins. Helvetian Press 2010; Table 7-6, p. 262.
79. Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins 2009; 77: 18-28.
80. Xu J, Li M. Assessment of RAPTOR's linear programming approach in CAFASP3. Proteins 2003; 53: 579-584.
81. Levitt M. Nature of the protein universe. Proc Natl Acad Sci USA 2009; 106: 11079-11084.