What amino acid properties affect protein evolution?

Journal of Molecular Evolution

Volumn 47, Issue 5, 1998, Pages 557-564

  Xia, Xuhua ^a   Li, Wen Hsiung ^b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Aromaticity; Chemical composition; Genetic code; Hydropathy; Isoelectric point; Polarity; Protein evolution; Substitution rate; Volume

Indexed keywords

MITOCHONDRIAL DNA;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONFORMATIONAL TRANSITION; GENETIC CODE; MOLECULAR EVOLUTION; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN CONFORMATION;

AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY; PROTEINS;

EID: 0031766244     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006412     Document Type: Article

References (31)

1. Alff-Steinberger C (1969) The genetic code and error transmission. Proc Natl Acad Sci USA 64:584-591
2. Boissonnas RA, Guttmann S (1960) Synthèse d'analogues de l'oxytocine et de la lysine-vasopressine contenant de la phénylalanine ou de la tyrosine en positions 2 et 3. Helv Chim Acta 43:190-200
3. Cao Y, Adachi J, Janke A, Pääbo S, Hasegawa M (1994) Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J Mol Evol 39:519-527
4. Clarke B (1970) Selective constraints on amino-ucid substitutions during the evolution of proteins. Nature 228:159-160
5. Crick FHC (1968) The origin of the genetic code. J Mol Biol 38:367-379
6. Cummings M, Otto S, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12:814-822
7. Epstein CJ (1967) Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature 215:355-359
8. Felsenstein J (1992) Estimating effective population size from samples of sequences: Inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet Res 59:139-147
9. Goldberg AL, Wittes RE (1966) Genetic code: Aspects of organization. Science 153:420-424
10. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
11. Guttmann S, Boissonnas RA (1960) Synthèse de dix analogues de l'oxytocine et de la lysine-vasopressine contenant de la sérine, de l'histidine ou du tryptophane en position 2 ou 3. Helv Chim Acta 43:200-216
12. Haig D, Hurst LD (1991) A quantitative measure of error minimization in the genetic code. J Mol Evol 33:412-417
13. Janke A, Xu X, Arnason U (1997) The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proc Natl Acad Sci USA 94:1276-1281
14. 2-oxytocine. Helv Chim Acta 42:788-793
15. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
16. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132
17. Miller SL (1986) Current status of the prebiotic synthesis of small molecules. In: Baltscheffsky H, Jörnvall H, Rigler R (eds) Molecular evolution of life. Cambridge University Press, Cambridge, pp 5-11
18. Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitution in protein evolution. J Mol Evol 12:219-236
19. Nee S, Holmes EC, Rambaut A, Harvey PH (1996) Inferring population history from molecular phylogenies. In: Harvey PH, Brown AJL, Maynard Smith J, Nee S (eds) New uses for new phylogenies. Oxford University Press, Oxford, pp 66-80
20. Novacek MJ, Wyss AR, McKenna M (1988) The major groups of eutherian mammals. In: Benton MJ (ed) The phylogeny and classification of the tetrapods, Vol 2. Clarendon Press, Oxford, pp 31-71
21. Otto SP, Cummings MP, Wakeley J (1996) Inferring phylogenies from DNA sequence data: The effects of sampling. In: Harvey PH, Brown AJL, Maynard Smith J, Nee S (eds) New uses for new phylogenies. Oxford University Press, Oxford, pp 103-115
22. Sneath PHA (1966) Relations between chemical structure and biological activity. J Theor Biol 12:157-195
23. Sonneborn TM (1965) Degeneracy of the genetic code: Extent, nature and genetic implications. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 377-397
24. Vogel H, Zuckerkandl E (1972) The evolution of polarity relationships in globins. In: Neyman J (ed) Darwinian, neo-Darwinian, and Non-Darwinian evolution. Proc 6th Berkeley Symp Math Stat Prob. University of California Press, Berkeley, pp 155-176
25. Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC (1966) On the fundamental nature and evolution of the genetic code. Cold Spring Labor Symp Quant Biol 31:723-736
26. Xia X (1996) Maximizing transcription efficiency causes codon usage bias. Genetics 144:1309-1320
27. Xia X (1998) The rate heterogeneity of nonsynonymous substitutions in mammalian mitochondrial genes. Mol Biol Evol 15:336-344
28. Xia X, Hafner MS, Sudman PD (1996) On transition bias in mitochondrial genes of pocket gophers. J Mol Evol 43:32-40
29. Yang Z (1996) Phylogenetic analysis by maximum likelihood (PAML). Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park
30. Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650
31. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel J (eds) Evolving genes and proteins. Academic Press, New York, pp 97-166