Statistical Properties of Neutral Evolution

Journal of Molecular Evolution

Volumn 57, Issue SUPPL. 1, 2003, Pages

  Bastolla, Ugo ^a   Porto, Markus ^b   Eduardo Roman, H ^c   Vendruscolo, Michele ^d  

^a CENTRO DE ASTROBIOLOGÍA CSIC INTA   (Spain)

^b MAX PLANCK INSTITUT FÜR PHYSIK KOMPLEXER SYSTEME   (Germany)

^c UNIVERSITY OF MILAN   (Italy)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Correlations; Neutral evolution; Non poissonian substitution process

Indexed keywords

CONFERENCE PAPER; EVOLUTION; MODEL; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NERVE CELL NETWORK; NEUTRAL EVOLUTION; PROTEIN FOLDING; PROTEIN STABILITY; STATISTICAL ANALYSIS; THERMODYNAMICS;

AMINO ACID SUBSTITUTION; EVOLUTION, MOLECULAR; GLOBINS; MATHEMATICAL COMPUTING; MODELS, GENETIC; MUTATION; POISSON DISTRIBUTION; PROTEINS; TIME FACTORS;

EID: 0346750651     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-0013-4     Document Type: Conference Paper

References (52)

1. Abkevich VI, Gutin AM, Shakhnovich El (1994) Free energy landscapes for protein folding kinetics - intermediates, traps and multiple pathways in theory and lattice model simulations. J Chem Phys 101:6052-6062
2. Babajide A, Hofacker IL, Sippl MJ, Stadler PF (1997) Neutral networks in protein space. Fol Des 2:261-269
3. Bastolla U, Farwer J, Knapp EW, Vendruscolo M (2001) How to guarantee optimal stability for most representative structures in the protein data bank. Proteins 44:79-96
4. Bastolla U, Roman HE, Vendruscolo M (1999) Neutral evolution of model proteins: Diffusion in sequence space and overdispersion. J Theor Biol 200:49-64
5. Bastolla U, Porto M, Roman HE, Vendruscolo M (2003) Connectivity of neutral networks, overdispersion and structural conservation in protein evolution. J Mol Evol 56:243-254
6. Bastolla U, Porto M, Roman HE, Vendruscolo M (2002) Lack of self-averaging in neutral evolution of proteins. Phys Rev Lett 89:20181/1-4
7. Bastolla U, Vendruscolo M, Roman HE (2000b) Structurally constrained protein evolution: Results from a lattice simulation. Eur Phys J B 15:385-397
8. Bastolla U, Vendruscolo M, Knapp EW (2000a) A statistical mechanical method to optimize energy functions for protein folding. Proc Natl Acad Sci USA 97:3977-3981
9. Bornberg-Bauer E (1997) How are model protein structures distributed in sequence space? Biophys J 73:2393-2403
10. Bornberg-Bauer E, Chan HS (1999) Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci USA 96:10689-10694
11. Bowie JU, Lüthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known 3-dimensional structure. Science 253:164-170
12. Britten RJ (1986) Rates of DNA sequence evolution differ between taxonomic groups. Science 231:1393-1398
13. Bussemaker HJ, Thirumalai D, Bhattacharjee JK (1997) Thermodynamic stability of folded proteins against mutations. Phys Rev Lett 79:3530-3533
14. Dokholyan NV, Shakhnovich EI (2001) Understanding hierarchical protein evolution from first principles. J Mol Biol 312:289-307
15. Fay JC, Wyckoff GJ, Wu C-I (2002) Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415:1024-1026
16. Fontana W, Schuster P (1998) Continuity in evolution: On the nature of transitions. Science 280:1451-1455
17. Gillespie JH (1991) The causes of molecular evolution. Oxford University Press, Oxford, UK
18. Gillespie JH (1989) Lineage effects and the index of dispersion of molecular evolution. Mol Biol Evol 6:636-647
19. Goldstein RA, Luthey-Schulten ZA, Wolynes PG (1992) Optimal protein-folding codes from spin-glass theory. Proc Natl Acad Sci USA 89:4918-4922
20. Govindarajan S, Goldstein RA (1997) The foldability landscape of model proteins. Biopolymers 42:427-438
21. Govindarajan S, Goldstein RA (1998) On the thermodynamic hypothesis of protein folding. Prod Natl Acad Sci USA 95:5545-5549
22. Gutin AM, Abkevich VI, Shakhnovich EI (1995) Proc Natl Acad Sci USA 92:1282-1286
23. Hobohm U, Sander C (1994) Enlarged representative set of protein structure. Protein Sci 3:522-524
24. Holm L, Sander C (1996) Mapping the protein universe. Science 273:595-602
25. Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: The role of neutrality in adaptation. Proc Natl Acad Sci USA 93:397-401
26. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624-626
27. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275-276
28. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press
29. King J-L, Jukes TH (1969) Non-Darwinian evolution. Science 164:788-798
30. Langley C-H, Fitch WM (1974) An estimation of the constancy of the rate of molecular evolution. J Mol Evol 3:161-177
31. Li WH, Tanimura M, Sharp PM (1987) An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25:330-342
32. Graur D, Li WH (2000) Fundamentals of molecular evolution. Sinauer, Sunderland, MA
33. McDonald J, Kreitman M (1991) Adaptive evolution at the Adh locus in Drosophila. Nature 351:652-654
34. Mirny LA, Shakhnovich EI (1996) How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 264:1164-1179
35. Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics, and function. J Mol Biol 291:177-196
36. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford, UK
37. Ohta T (1973) Slightly deleterious mutant substitutions in evolution. Nature 246:96-98
38. Ohta T (1976) Role of very slightly deleterious mutations in molecular evolution and polymorphism. Theor Pop Biol 10:254-275
39. Ohta T, Kimura M (1971) On the constancy of the evolutionary rate of cistrons. J Mol Evol 1:18-25
40. Perutz MF, Kendrew JC, Watson HC (1965) Structure and function of Haemoglobin: Some relations between polypeptide chain configuration and amino acid sequence. J Mol Biol 13:669-678
41. Ptitsyn OB, Ting KH (1999) Non-functional conserved residues in globins and their possible role as a folding nucleus. J Mol Biol 291:671-682
42. Rost B (1997) Protein structures sustain evolutionary drift. Fol Des 2:S19-S24
43. Saitou N, Nei M (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
44. Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415:1022-1024
45. Schuster P, Fontana W, Stadler PF, Hofacker IL (1994) From sequences to shapes and back - A case-study in RNA secondary structures. Proc R Soc Lond B 255:279-284
46. Shakhnovich E, Abkevich V, Ptitsyn O (1996) Conserved residues and the mechanism of protein folding. Nature 379:96-98
47. Takahata N (1987) On the overdispersed molecular clock. Genetics 116:169-179
48. Tiana G, Broglia RA, Roman HE, Vigezzi E, Shakhnovich EI (1998) Folding and misfolding of designed proteinlike chains with mutations. J Chem Phys 108:757-761
49. Thompson JD, Higgins DG, Gibson TJ, Clustal W (1994) 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
50. Uzzell T, Corbin K (1971) Fitting discrete probability distributions to evolutionary events. Science 172:1089-1096
51. Xia Y, Levitt M (2002) Roles of mutation and recombination in the evolution of protein thermodynamics. Proc Natl Acad Sci USA 99:10382-10387
52. Zuckerkandl E, Pauling L (1962) Molecular disease, evolution and genetic heterogenity. In: Kasha M, Pullman B (eds) Horizons in biochemistry. Academic Press, New York, pp 189-225