Biophysical and structural considerations for protein sequence evolution

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Grahnen, Johan A ^a   Nandakumar, Priyanka ^a,b   Kubelka, Jan ^c   Liberles, David A ^a  

^a UNIVERSITY OF WYOMING   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

^c UNIVERSITY OF WYOMING   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPHYSICS; CHEMICAL BINDING; EVOLUTIONARY BIOLOGY; HYDROPHOBICITY; MODEL VALIDATION; PHYLOGENETICS; PROTEIN; SAMPLING; THERMODYNAMICS;

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOPHYSICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

AMINO ACID SEQUENCE; BIOPHYSICS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 83455238341     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-361     Document Type: Article

References (74)

1. The Protein Folding Problem. Dill KA, Ozkan SB, Shell MS, Weikl TR, Annu Rev Biophys 2008 37 289 316 10.1146/annurev.biophys.37.092707.153558 18573083
2. INDELible: A Flexible Simulator of Biological Sequence Evolution. Fletcher W, Yang Z, Mol Biol Evol 2009 26 1879 1888 10.1093/molbev/msp098 19423664
3. Protein Folding Thermodynamics and Dynamics: Where Physics, Chemistry and Biology Meet. Shakhnovich E, Chem Rev 2006 106 1559 1588 10.1021/cr040425u 16683745 (Pubitemid 43792772)
4. Physics of protein folding. Finkelstein AV, Galzitskaya OV, Phys Life Rev 2004 1 23 56 10.1016/j.plrev.2004.03.001 (Pubitemid 38808598)
5. The evolution and evolutionary consequences of marginal thermostability in proteins. Goldstein RA, Proteins 2011 79 1396 1407 10.1002/prot.22964 21337623
6. Spin glasses and the statistical mechanics of protein folding. Bryngelson JD, Wolynes PG, PNAS 1987 84 7524 7528 10.1073/pnas.84.21.7524 3478708
7. Potentials "R" Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. Feng Y, Kloczkowski A, Jernigan RL, BMC Bioinformatics 2010 11 92 10.1186/1471-2105-11-92 20163737
8. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Miyazawa S, Jernigan RL, Macromolecules 1985 18 534 552 10.1021/ma00145a039
9. How to guarantee optimal stability for most representative structures in the protein data bank. Bastolla U, Farwer J, Knapp EW, Vendruscolo M, Proteins 2001 44 79 96 10.1002/prot.1075 11391771 (Pubitemid 32612103)
10. Challenges in protein folding simulations: Timescale, representation, and analysis. Freddolino PL, Harrison CB, Liu Y, Schulten K, Nat Phys 2010 6 751 758 10.1038/nphys1713 21297873
11. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Rastogi S, Reuter N, Liberles DA, Biophys Chem 2006 124 134 144 10.1016/j.bpc.2006.06.008 16837122 (Pubitemid 44602326)
12. Knowledge-based potentials for proteins. Sippl MJ, Curr Opin Struct Biol 1995 5 229 235 10.1016/0959-440X(95)80081-6 7648326
13. Optimizing potentials for the inverse protein folding problem. Chiu TL, Goldstein RA, Protein Eng 1998 11 749 752 10.1093/protein/11.9.749 9796822 (Pubitemid 28434483)
14. Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy. Liberles DA, Tisdell MDM, Grahnen JA, Proc R Soc B 2011 278 1930 1935 10.1098/rspb.2010.2637 21490020
15. Structure is three to ten times more conserved than sequence - a study of structural response in protein cores. Illergård K, Ardell DH, Elofsson A, Proteins 2009 77 499 508 10.1002/prot.22458 19507241
16. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Pamilo P, Bianchi NO, Mol Biol Evol 1993 10 271 281 8487630 (Pubitemid 23103001)
17. Among-site rate variation and its impact on phylogenetic analyses. Yang Z, TREE 1996 11 367 372 21237881 (Pubitemid 126381530)
18. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Yang Z, Mol Biol Evol 1993 10 1396 1401 8277861 (Pubitemid 23352619)
19. Predicting functional divergence in protein evolution by site-specific rate shifts. Gaucher EA, Gu X, Miyamoto MM, Benner SA, Trends Biochem Sci 2002 27 315 321 10.1016/S0968-0004(02)02094-7 12069792 (Pubitemid 34628672)
20. Principles that govern the folding of protein chains. Anfinsen CB, Science 1973 181 223 230 10.1126/science.181.4096.223 4124164
21. Evolution of structurally disordered proteins promotes neostructuralization. Siltberg-Liberles J, Mol Biol Evol 2011 28 59 62 10.1093/molbev/msq291 21037204
22. Development of Neutral and Nearly Neutral Theories. Ohta, Gillespie, Theor Popul Biol 1996 49 128 142 10.1006/tpbi.1996.0007 8813019
23. Missense meanderings in sequence space: a biophysical view of protein evolution. DePristo MA, Weinreich DM, Hartl DL, Nat Rev Genet 2005 6 678 687 10.1038/nrg1672 16074985 (Pubitemid 41192319)
24. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). Voelz VA, Bowman GR, Beauchamp K, Pande VS, J Am Chem Soc 2010 132 1526 1528 10.1021/ja9090353 20070076
25. Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition. Poy F, Yaffe MB, Sayos J, Saxena K, Morra M, Sumegi J, Cantley LC, Terhorst C, Eck MJ, Mol Cell 1999 4 555 561 10.1016/S1097-2765(00)80206-3 10549287 (Pubitemid 29531135)
26. Protein stability imposes limits on organism complexity and speed of molecular evolution. Zeldovich KB, Chen P, Shakhnovich EI, PNAS 2007 104 16152 16157 10.1073/pnas.0705366104 17913881 (Pubitemid 350099377)
27. Heterotachy, an important process of protein evolution. Lopez P, Casane D, Philippe H, Mol Biol Evol 2002 19 1 7 10.1093/oxfordjournals.molbev.a003973 11752184 (Pubitemid 34008041)
28. Heterotachy and Functional Shift in Protein Evolution. Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J, IUBMB Life 2003 55 257 265 10.1080/1521654031000123330 12880207 (Pubitemid 36842257)
29. Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution. Zhang J, Gu X, Genetics 1998 149 1615 1625 9649548 (Pubitemid 28334551)
30. The Pfam protein families database. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Nucleic Acids Res 2009 38 211 D222 19920124
31. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Ramsey DC, Scherrer MP, Zhou T, Wilke CO, Genetics 2011 188 479 488 10.1534/genetics.111.128025 21467571
32. A helix propensity scale based on experimental studies of peptides and proteins. Pace CN, Scholtz JM, Biophys J 1998 75 422 427 10.1016/S0006-3495(98) 77529-0 9649402 (Pubitemid 28311831)
33. Comparative Assessment of Scoring Functions on a Diverse Test Set. Cheng T, Li X, Li Y, Liu Z, Wang R, J Chem Inf Model 2009 49 1079 1093 10.1021/ci9000053 19358517
34. A Residue-Pairwise Generalized Born Scheme Suitable for Protein Design Calculations. Archontis G, Simonson T, J Chem Phys B 2005 109 22667 22673 10.1021/jp055282+ (Pubitemid 41796748)
35. Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution. Grahnen JA, Kubelka J, Liberles DA, J Mol Evol 2011 73 23 33 10.1007/s00239-011-9454-3 21800121
36. Simulating protein evolution in sequence and structure space. Xia Y, Levitt M, Curr Opin Struct Biol 2004 14 202 207 10.1016/j.sbi.2004.03.001 15093835 (Pubitemid 38490787)
37. Multiscale coarse-graining of the protein energy landscape. Hills RD, Lu L, Voth GA, PLoS Comput Biol 2010 6 1000827 10.1371/journal.pcbi.1000827 20585614
38. Current Status of the AMOEBA Polarizable Force Field. Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T, J Phys Chem B 2010 114 2549 2564 10.1021/jp910674d 20136072
39. A coarse-grained protein force field for folding and structure prediction. Maupetit J, Tuffery P, Derreumaux P, Proteins 2007 69 394 408 10.1002/prot.21505 17600832 (Pubitemid 47429300)
40. Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches. Gilis D, Biot C, Buisine E, Dehouck Y, Rooman M, J Chem Inf Model 2006 46 884 893 10.1021/ci050395b 16563020
41. Mutational effects and the evolution of new protein functions. Soskine M, Tawfik DS, Nat Rev Genet 2010 11 572 582 20634811
42. Optimization of specificity in a cellular protein interaction network by negative selection. Zarrinpar A, Park S-H, Lim WA, Nature 2003 426 676 680 10.1038/nature02178 14668868 (Pubitemid 38009377)
43. Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase. Dultz E, Ellenberg J, J Cell Biol 2010 191 15 22 10.1083/jcb.201007076 20876277
44. The Activation of RalGDS Can Be Achieved Independently of Its Ras Binding Domain. Linnemann T, Kiel C, Herter P, Herrmann C, J Biol Chem 2002 277 7831 7837 10.1074/jbc.M110800200 11748241 (Pubitemid 34968231)
45. The SH2 Domains of Inositol Polyphosphate 5-Phosphatases SHIP1 and SHIP2 Have Similar Ligand Specificity but Different Binding Kinetics. Zhang Y, Wavreille A-S, Kunys AR, Pei D, Biochemistry 2009 48 11075 11083 10.1021/bi9012462 19839650
46. Actin turnover-dependent fast dissociation of capping protein in the dendritic nucleation actin network: evidence of frequent filament severing. Miyoshi T, Tsuji T, Higashida C, Hertzog M, Fujita A, Narumiya S, Scita G, Watanabe N, J Cell Biol 2006 175 947 955 10.1083/jcb.200604176 17178911 (Pubitemid 44969200)
47. Maps of protein structure space reveal a fundamental relationship between protein structure and function. Osadchy M, Kolodny R, PNAS 2011 108 12301 12306 10.1073/pnas.1102727108 21737750
48. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Murzin AG, Brenner SE, Hubbard T, Chothia C, J Mol Biol 1995 247 536 540 7723011
49. Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding). Scalco R, Caflisch A, J Phys Chem B 2011 115 6358 6365 10.1021/jp2014918 21517045
50. What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. Lakner C, Holder MT, Goldman N, Naylor GJP, Syst Biol 2011 60 161 174 10.1093/sysbio/syq088 21233085
51. Statistical potentials for improved structurally constrained evolutionary models. Kleinman CL, Rodrigue N, Lartillot N, Philippe H, Mol Biol Evol 2010 27 1546 1560 10.1093/molbev/msq047 20159780
52. Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference. Nasrallah CA, Mathews DH, Huelsenbeck JP, Syst Biol 2011 60 60 73 10.1093/sysbio/syq074 21081481
53. A simplified representation of protein conformations for rapid simulation of protein folding. Levitt M, J Mol Biol 1976 104 59 107 10.1016/0022-2836(76) 90004-8 957439
54. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36. Mukherjee A, Bagchi B, J Chem Phys 2003 118 4733 4747 10.1063/1.1542599
55. Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide. Kim CA, Berg JM, Nature 1993 362 267 270 10.1038/362267a0 8459852 (Pubitemid 23093636)
56. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Bahar I, Kaplan M, Jernigan RL, Proteins 1997 29 292 308 10.1002/(SICI)1097-0134(199711)29: 3<292::AID-PROT4>3.0.CO;2-D 9365985 (Pubitemid 27484221)
57. Calculation of the dielectric properties of a protein and its solvent: theory and a case study. Löffler G, Schreiber H, Steinhauser O, J Mol Biol 1997 270 520 534 10.1006/jmbi.1997.1130 9237916 (Pubitemid 27326689)
58. Recent advances in implicit solvent-based methods for biomolecular simulations. Chen J, Brooks CL, Khandogin J, Curr Opin Struct Biol 2008 18 140 148 10.1016/j.sbi.2008.01.003 18304802
59. Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J, J Mol Model 2009 15 1093 1108 10.1007/s00894-009-0454-9 19234730
60. MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. Dani VS, Ramakrishnan C, Varadarajan R, Protein Eng 2003 16 187 193 10.1093/proeng/gzg024 12702798 (Pubitemid 36565633)
61. A graph-theory algorithm for rapid protein side-chain prediction. Canutescu AA, Shelenkov AA, Dunbrack RL, Protein Sci 2003 12 2001 2014 10.1110/ps.03154503 12930999 (Pubitemid 37022822)
62. Understanding hierarchical protein evolution from first principles. Dokholyan NV, Shakhnovich EI, J Mol Biol 2001 312 289 307 10.1006/jmbi.2001.4949 11545603 (Pubitemid 32835693)
63. Energy Landscape Theory, Funnels, Specificity, and Optimal Criterion of Biomolecular Binding. Wang J, Verkhivker GM, Phys Rev Lett 2003 90 188101 12786043
64. Protein Sequence Randomization: Efficient Estimation of Protein Stability Using Knowledge-based Potentials. Wiederstein M, Sippl MJ, J Mol Biol 2005 345 1199 1212 10.1016/j.jmb.2004.11.012 15644215 (Pubitemid 40092234)
65. Evaluating and optimizing computational protein design force fields using fixed composition-based negative design. Alvizo O, Mayo SL, PNAS 2008 105 12242 12247 10.1073/pnas.0805858105 18708527
66. Equation of State Calculations by Fast Computing Machines. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E, J Chem Phys 1953 21 1087 1092 10.1063/1.1699114
67. Monte Carlo Sampling Methods Using Markov Chains and Their Applications. Hastings WK, Biometrika 1970 57 97 109 10.1093/biomet/57.1.97
68. The structure of protein evolution and the evolution of protein structure. Goldstein RA, Curr Opin Struct Biol 2008 18 170 177 10.1016/j.sbi.2008.01.006 18328690
69. Theoretical and Computational Protein Design. Samish I, MacDermaid CM, Perez-Aguilar JM, Saven JG, Annu Rev Phys Chem 2011 62 129 149 10.1146/annurev-physchem-032210-103509 21128762
70. A new method for analyzing protein sequence relationships based on Sammon maps. Agrafiotis DK, Protein Sci 1997 6 287 293 9041629 (Pubitemid 27079919)
71. WebLogo: A Sequence Logo Generator. Crooks GE, Hon G, Chandonia J-M, Brenner SE, Genome Res 2004 14 1188 1190 10.1101/gr.849004 15173120 (Pubitemid 38811555)
72. PepX: a structural database of non-redundant protein-peptide complexes. Vanhee P, Reumers J, Stricher F, Baeten L, Serrano L, Schymkowitz J, Rousseau F, Nucleic Acids Res 2009 38 545 D551 19880386
73. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Li W-H, Wu C-I, Luo C-C, Mol Biol Evol 1985 2 150 174 3916709
74. ProtTest: selection of best-fit models of protein evolution. Abascal F, Zardoya R, Posada D, Bioinformatics 2005 21 2104 2105 10.1093/bioinformatics/ bti263 15647292 (Pubitemid 40668057)