Estimation of evolutionary distances from protein spatial structures
- 70 Downloads
New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures.
Key wordsProtein structure RMS deviation Molecular evolution Evolutionary distance Substitution rates
Unable to display preview. Download preview PDF.
- Chotia C, Lesk A (1986) The relation between the divergence of sequence and structure in proteins. The EMBO J 5:823–826Google Scholar
- Dayhoff MO, Eck RV, Park CM (1972) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, 5. National Biomedical Research Foundation, Washington, DC, pp 89–99Google Scholar
- Dayhoff MO, Schwartz RM & Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, 5, Suppl 3. National Biomedical Research Foundation, Washington, DC, pp 345–352Google Scholar
- Gutin AM, Badretdinov AY (1994) Evolution of protein 3D structures as diffusion in multidimensional conformational space. J Mol Evol 39:206–209Google Scholar
- Rzhetsky A, Nei M. (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967Google Scholar
- Takacs L. (1966) Stochastic process. Methuen & Co LTD, London, John Wiley & Sons Inc., NYGoogle Scholar
- Zuckerkandl E, Pauling L. (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vodel HJ (eds) Evolving genes and proteins. Academic Press, NY, pp 97–166Google Scholar