Literature DB >> 33130957

About the Protein Space Vastness.

Jorge A Vila1.   

Abstract

An accurate estimation of the Protein Space size, in light of the factors that govern it, is a long-standing problem and of paramount importance in evolutionary biology, since it determines the nature of protein evolvability. A simple analysis will enable us to, firstly, reduce an unrealistic Protein Space size of ~ 10130 sequences, for a 100-residues polypeptide chain, to ~ 109 functional proteins and, secondly, estimate a robust average-mutation rate per amino acid (ξ ~ 1.23) and infer from it, in light of the protein marginal stability, that only a fraction of the sequence will be available at any one time for a functional protein to evolve. Although this result does not solve the Protein Space vastness problem frames it in a more rational one and illustrates the impact of the marginal stability on protein evolvability.

Keywords:  Anfinsen; Maynard Smith; Protein Evolution; Protein Marginal Stability; Protein Space

Mesh:

Substances:

Year:  2020        PMID: 33130957     DOI: 10.1007/s10930-020-09939-4

Source DB:  PubMed          Journal:  Protein J        ISSN: 1572-3887            Impact factor:   2.371


  29 in total

1.  Robustness, evolvability, and neutrality.

Authors:  Andreas Wagner
Journal:  FEBS Lett       Date:  2005-03-21       Impact factor: 4.124

Review 2.  Missense meanderings in sequence space: a biophysical view of protein evolution.

Authors:  Mark A DePristo; Daniel M Weinreich; Daniel L Hartl
Journal:  Nat Rev Genet       Date:  2005-09       Impact factor: 53.242

3.  Protein stability promotes evolvability.

Authors:  Jesse D Bloom; Sy T Labthavikul; Christopher R Otey; Frances H Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-31       Impact factor: 11.205

4.  Levinthal's paradox.

Authors:  R Zwanzig; A Szabo; B Bagchi
Journal:  Proc Natl Acad Sci U S A       Date:  1992-01-01       Impact factor: 11.205

5.  Protein stability imposes limits on organism complexity and speed of molecular evolution.

Authors:  Konstantin B Zeldovich; Peiqiu Chen; Eugene I Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-03       Impact factor: 11.205

Review 6.  Stability effects of mutations and protein evolvability.

Authors:  Nobuhiko Tokuriki; Dan S Tawfik
Journal:  Curr Opin Struct Biol       Date:  2009-09-16       Impact factor: 6.809

7.  Levinthal's question answered … again?

Authors:  Alexei V Finkelstein; Sergiy O Garbuzynskiy
Journal:  J Biomol Struct Dyn       Date:  2013-01-09

Review 8.  Exploring protein fitness landscapes by directed evolution.

Authors:  Philip A Romero; Frances H Arnold
Journal:  Nat Rev Mol Cell Biol       Date:  2009-12       Impact factor: 94.444

9.  Exact correspondence between walk in nucleotide and protein sequence spaces.

Authors:  Dmitry N Ivankov
Journal:  PLoS One       Date:  2017-08-11       Impact factor: 3.240

10.  How much of protein sequence space has been explored by life on Earth?

Authors:  David T F Dryden; Andrew R Thomson; John H White
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

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  1 in total

Review 1.  About the Protein Space Vastness.

Authors:  Jorge A Vila
Journal:  Protein J       Date:  2020-11-01       Impact factor: 2.371

  1 in total

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