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Cited by 35Evolution and Genetic DynamicsProtein Structure and DynamicsRNA and protein synthesis mechanisms

Lack of Self-Averaging in Neutral Evolution of Proteins

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Bastolla, Ugo, Porto, Markus, Roman, H. Eduardo, Vendruscolo, Michele·2002·Physical Review Letters
DOI 10.1103/physrevlett.89.208101
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Abstract

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.

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  • The three-dimensional structure assumed by proteins has an important effect on the patterns of substitutions.

    “The three-dimensional structure assumed by proteins has an important effect on the patterns of substitutions, as modelled by a structurally constrained neutral model 15 : although many sequences can fold to the same three-dimensional structure, different sequences have different numbers of 'neighbours' that they can mutate to and still maintain thermodynamic stability.”

    From The modern molecular clock (2003) · cites this paper as [15]

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Authors
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M.
Affiliations
  • Consejo Superior de Investigaciones Científicas (ES)
  • Max Planck Society (DE)
  • University of Cambridge (GB)
ORCID
Venue
Physical Review Letters
Publisher
American Physical Society (APS)
Published
2002-10-24
Volume
89
Issue
20
Pages
208101-208101
ISSN
  • 0031-9007 (ISSN-L)
  • 1079-7114
DOI
10.1103/physrevlett.89.208101
OpenAlex
W2040401984
Cited by
35
References
35
Citations by year
2024: 1 · 2021: 1 · 2019: 1 · 2016: 2 · 2014: 1
FWCI
2.65
Type
journal article
Language
en
Open access
Licence
link.aps.org/licenses/aps-default-license (vor)
Locations
  • Physical Review Letters (publishedVersion)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • BOA (University of Milano-Bicocca) (submittedVersion)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Max Planck Digital Library (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
  • arXiv (Cornell University)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
neutral evolution, protein folding, thermodynamic stability, neutral mutations, sequence spaces, self-averaging, evolutionary trajectories
MeSH terms
Cytochrome c Group, Models, Genetic, Muramidase, Mutation, Myoglobin, Proteins, Ribonucleases, Rubredoxins, Thermodynamics, Protein Folding, Evolution, Molecular

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