Evolutionary Divergence and Convergence in Proteins

Zuckerkandl, Emile; Pauling, Linus

doi:10.1016/b978-1-4832-2734-4.50017-6

Cited by 2,358 publications

(1,526 citation statements)

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“…For ␤ ‫ס‬ 1, Equation (25) transforms to u ‫ס‬ e −d , which is a Poisson-correction formula (Zuckerkandl and Pauling 1965). This equation relates the fraction of unchanged residues to the distance for the case of amino acid-independent and siteindependent substitution rates.…”

Section: Distance and Identity Fraction: Empirical Formulamentioning

confidence: 99%

“…Thus a variety of models to estimate distance d ij from the fraction of different residues p ij are proposed (Zuckerkandl and Pauling 1965;Dayhoff et al 1972Dayhoff et al , 1978Uzzel and Corbin, 1971;Holmquist et al 1983;Wilbur 1985;Barry and Hartigan 1987;Ota and Nei 1994;Zharkikh 1994;Tajima and Takezaki 1994;Grishin 1995). Analysis of alignments (Dayhoff et al 1978) used for estimation of relation between distance d ij and fraction of identical residues q ij ‫ס‬ 1 − p ij misses some back substitutions for the case of lower similarity between sequences.…”

Section: Introductionmentioning

confidence: 99%

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Estimation of evolutionary distances from protein spatial structures

Grishin

1997

J Mol Evol

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Abstract. 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.

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Section: Distance and Identity Fraction: Empirical Formulamentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Estimation of evolutionary distances from protein spatial structures

Grishin

1997

J Mol Evol

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“…We assessed monophyly of the S. marina species group using multiple Indo-west Pacific (IWP) species of Strongylura and the belonid genera, Tylosurus, Ablennes, and Belone, as outgroups. Our temporal analysis used molecular markers representing two linkage groups to provide independent estimates of genetic distances and time, based on the concept of a molecular clock (Zuckerkandl and Pauling, 1965).…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogenetics and biogeography of transisthmian and amphi-Atlantic needlefishes (Belonidae: Strongylura and Tylosurus): perspectives on New World marine speciation

Banford¹,

Bermingham²,

Collette³

2004

Molecular Phylogenetics and Evolution

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“…The idea of representing these hypotheses as trees probably dates back to Darwin, but the numerical calculation of trees using quantitative methods is relatively recent [1], and their application to molecular data even more so [2]. In the age of rapid and rampant gene sequencing, molecular phylogeny has truly come into its own, emerging as a major tool for making sense of a sometimes overwhelming amount information.…”

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confidence: 99%