Evaluation of models for the evolution of protein sequences and functions under structural constraint

Biophysical Chemistry

Volumn 124, Issue 2, 2006, Pages 134-144

  Rastogi, Shruti ^a,b   Reuter, Nathalie ^b   Liberles, David A ^a,b  

^a UNIVERSITY OF WYOMING   (United States)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

Binding; Coarse grained models; Folding; Molecular evolution; Population dynamics; Structural genomics

Indexed keywords

FLAVODOXIN; GLOBIN; PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; ENERGY; EVALUATION; GENOME ANALYSIS; KNOWLEDGE BASE; LIGAND BINDING; MODEL; MOLECULAR EVOLUTION; PHYSICAL PARAMETERS; POPULATION DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; STATISTICAL ANALYSIS; STRUCTURAL GENOMICS; VELOCITY;

COMPUTATIONAL BIOLOGY; DIRECTED MOLECULAR EVOLUTION; FLAVODOXIN; MODELS, BIOLOGICAL; PROTEIN FOLDING; SRC HOMOLOGY DOMAINS;

EID: 33750180978     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.06.008     Document Type: Article

References (35)

1. Gerstein M. A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J. Mol. Biol. 274 (1997) 562-576
2. Lynch M., and Conery J.S. On the origins of genome complexity. Science 302 (2003) 1401-1404
3. Braun F.N., and Liberles D.A. Retention of enzyme gene duplicates by subfunctionalization. Int. J. Biol. Macromol. 33 (2003) 19-22
4. Braun F.N., and Liberles D.A. Repeat modulated population genetic effects in fungal proteins. J. Mol. Evol. 59 (2004) 97-102
5. Bastolla U., Porto M., Roman H.E., and Vendruscolo M. Statistical properties of neutral evolution. J. Mol. Evol. 57S1 (2003) 103-119
6. Lynch M. Simple evolutionary pathways to complex proteins. Protein Sci. 14 (2005) 2217-2225
7. Govindarajan S., and Goldstein R.A. Evolution of model proteins on a foldability landscape. Proteins Struct. Funct. Genet. 29 (1997) 461-466
8. Williams P.D., Pollock D.D., and Goldstein R.A. Evolution of functionality in lattice proteins. J. Mol. Graph. Model. 19 (2001) 150-156
9. Tiana G., Dokholyan N.V., Broglia R.A., and Shakhnovich E.I. The evolution dynamics of model proteins. J. Chem. Phys. 121 (2004) 2381-2389
10. Rastogi S., and Liberles D.A. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol. Biol. 5 (2005) 28
11. Chan H.S., and Dill K.A. Origins of structure in globular proteins. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 6388-6392
12. Vendruscolo M., and Domany E. Pairwise contact potentials are unsuitable for protein folding. J. Chem. Phys. 109 (1998) 11101-11108
13. Suzuki Y. Three dimensional window analysis for detecting positive selection at structural regions of proteins. Mol. Biol. Evol. 21 (2004) 2352-2359
14. Berglund A.C., Wallner B., Elofsson A., and Liberles D.A. Tertiary windowing to detect positive diversifying selection. J. Mol. Evol. 60 (2005) 499-504
15. Miyazawa S., and Jernigan R.L. Estimation of effective inter-residue contact energies from protein crystal structures-quasi-chemical approximation. Macromolecules 18 (1985) 534-552
16. Taverna D.M., and Goldstein R.A. Why are proteins marginally stable?. Proteins Struct. Funct. Genet. 46 (2002) 105-109
17. Taverna D.M., and Goldstein R.A. Why are proteins so robust to site mutations?. J. Mol. Biol. 315 3 (2002) 479-484
18. Shakhnovich B.E., Deeds E., Delisi C., and Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res. 15 (2005) 385-392
19. Bahar I., and Jernigan R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266 (1997) 195-214
20. Bahar I., Kaplan M., and Jernigan R.L. Short-range conformational energies, secondary structure propensities and recognition of correct sequence-structure matches. Proteins Struct. Funct. Genet. 29 (1997) 292-308
21. Bastolla U., Farwer J., Knapp E.W., and Vendruscolo M. How to guarantee optimal stability for most representative structures in the protein data bank. Proteins Struct. Funct. Genet. 44 (2001) 79-96
22. Koehl P., and Levitt M. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 1280-1285
23. Canutescu A.A., Shelenkov A.A., and Dunbrack R.L. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci. 12 (2003) 2001-2014
24. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shinyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
25. Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., and Gibson T.J. 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 (1994) 4673-4680
26. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 6 (2004) 1188-1190
27. Mukherjee A., and Bagchi B. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36. J. Chem. Phys. 118 (2003) 4733-4747
28. Kim A., and Berg M.J. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature 362 (1993) 267-270
29. Kurt N., Haliloglu T., and Schiffer C.A. Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. Biophys. J. 85 (2003) 853-863
30. Wiederstein M., and Sippl M.J. Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. J. Mol. Biol. 345 (2005) 1199-1212
31. Samudrala R., and Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275 (1998) 895-916
32. Pawson T., Gish G.D., and Nash P. SH2 domains, interaction modules, and cellular wiring. Trends Cell Biol. 12 (2001) 504-510
33. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 19 (1998) 1639-1662
34. Rocchia W., Sridharan S., Nicholls A., Alexov E., Chiabrera A., and Honig B. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J. Comput. Chem. 23 (2002) 128-137
35. Vendruscolo M., Najmanovich R., and Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?. Proteins Struct. Funct. Bioinform. 38 (2000) 134-147