Trade-off between positive and negative design of protein stability: From lattice models to real proteins

PLoS Computational Biology

Volumn 5, Issue 12, 2009, Pages

  Noivirt Brik, Orly ^a   Horovitz, Amnon ^a   Unger, Ron ^b  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; CRYSTAL LATTICES; ECONOMIC AND SOCIAL EFFECTS;

CONFORMATIONAL ENSEMBLE; CONTACT FREQUENCY; LATTICE MODELS; MODEL PROTEINS; NATIVE CONFORMATION; NATIVE STATE; NON-NATIVE; PROPERTY; PROTEIN STABILITY; TRADE OFF;

PROTEINS;

CHAPERONIN; PROTEIN;

ARTICLE; LATTICE MODEL; MODEL; PROTEIN CONFORMATION; PROTEIN STABILITY; BIOLOGICAL MODEL; CHEMISTRY; MUTATION; PROTEIN FOLDING;

MODELS, BIOLOGICAL; MUTATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEINS;

EID: 74549184107     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000592     Document Type: Article

References (36)

1. Hecht MH, Richardson JS, Richardson DC, Ogden RC (1990) De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence. Science 249: 884-891.
2. Hellinga HW (1997) Rational protein design: Combining theory and experiment. Proc Natl Acad Sci USA 94: 10015-10017.
3. Berezovsky IN, Zeldovich KB, Shakhnovich EI (2007) Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput Biol 3: 498-507.
4. Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277: 985-994.
5. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, et al. (1995) Principles of protein folding-a perspective from simple exact models. Protein Sci 4: 561-602.
6. Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369: 248-251.
7. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG (1996) Protein folding funnels: the nature of the transition state ensemble. Fold & Des 1: 441-450.
8. Unger R, Moult J (1996) Local interactions dominate folding in a simple protein model. J Mol Biol 259: 988-994.
9. Chan HS, Bornberg-Bauer E (2002) Perspectives on protein evolution from simple exact models. Appl Bioinformatics 1: 121-144.
10. Xia Y, Levitt M (2004) Simulating protein evolution in sequence and structure space. Curr Opin Struct Biol 14: 202-207.
11. Zeldovich KB, Shakhnovich EI (2008) Understanding protein evolution: from protein physics to Darwinian selection. Annu Rev Phys Chem 59: 105-127.
12. Horovitz A (1996) Double-mutant cycles: a powerful tool for analysing protein structure and function. Fold & Des 1: R121-R126.
13. Noivirt-Brik O, Unger R, Horovitz A (2009) Analysing the origin of long-range interactions in proteins using lattice models. BMC Struct Biol 9: 4.
14. Chan HS, Dill KA (1989) Intrachain loops in polymers: effects of excluded volume. J Chem Phys 90: 492-509.
15. Göbel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins: Struct Funct Genet 18: 309-317.
16. Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci USA 91: 98-102.
17. Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
18. Kass I, Horovitz A (2002) Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins: Struct Funct Genet 48: 611-617.
19. Pazos F, Valencia A (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Struct Funct Genet 47: 219-227.
20. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106: 67-72.
21. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, et al. (2005) Evolutionary information for specifying a protein fold. Nature 437: 512-518.
22. Wollenberg KR, Atchley WR (2000) Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. Proc Natl Acad Sci USA 97: 3288-3291.
23. Fodor AA, Aldrich RW (2004) Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins: Struct Funct Bioinf 56: 211-221.
24. Noivirt O, Eisenstein M, Horovitz A (2005) Detection and reduction of evolutionary noise in correlated mutation analysis. Protein Eng Des Sel 18: 247-253.
25. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122: 209-220.
26. Berezovsky IN, Shakhnovich EI (2005) Physics and evolution of thermophilic adaptation. Proc Natl Acad Sci USA 102: 12742-12747.
27. Puigbò P, Pasamontes A, Garcia-Vallve S (2007) Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genet 24: 10-14.
28. Wang J, Ma BG, Zhang HY, Chen LL, Zhang SC (2008) How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors. Gene 421: 32-36.
29. Zeldovich KB, Berezovsky IN, Shakhnovich EI (2007) Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 3: 62-72.
30. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21: 1087-1092.
31. Serrano L, Horovitz A, Avron B, Bycroft M, Fersht AR (1990) Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry 29: 9343-9352.
32. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, et al. (2007) DisProt: the Database of Disordered Proteins. Nucleic Acids Res 35: D786-D793.
33. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32: D115-D119.
34. Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res 34: 1-9.
35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
36. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.