dorsal/arxiv
View SchemaEmergence of the protein universe in organismal evolution
| Authors | Konstantin B. Zeldovich, Boris E. Shakhnovich, Eugene I. Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0605044 |
| URL | https://arxiv.org/abs/q-bio/0605044 |
Abstract
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the Big Bang scenario whereby exponential population growth ensues as favorable sequence-structure combinations (precursors of stable proteins) are discovered. After that, random diversity of the structural space abruptly collapses into a small set of preferred structural motifs. We observe that protein folds remain stable and abundant in the population at time scales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary time scales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. The network of structural similarities of the universe of evolved proteins has the same scale-free like character as the actual protein domain universe graph (PDUG). Further, the model predicts that ancient protein domains represent a highly connected and clustered subset of all protein domains, in complete agreement with reality. Together, these results provide a microscopic first principles picture of how protein structures and gene families evolved in the course of evolution.
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"abstract": "In this work we propose a physical model of organismal evolution, where\nphenotype, organism life expectancy, is directly related to genotype i.e. the\nstability of its proteins which can be determined exactly in the model.\nSimulating the model on a computer, we consistently observe the Big Bang\nscenario whereby exponential population growth ensues as favorable\nsequence-structure combinations (precursors of stable proteins) are discovered.\nAfter that, random diversity of the structural space abruptly collapses into a\nsmall set of preferred structural motifs. We observe that protein folds remain\nstable and abundant in the population at time scales much greater than mutation\nor organism lifetime, and the distribution of the lifetimes of dominant folds\nin a population approximately follows a power law. The separation of\nevolutionary time scales between discovery of new folds and generation of new\nsequences gives rise to emergence of protein families and superfamilies whose\nsizes are power-law distributed, closely matching the same distributions for\nreal proteins. The network of structural similarities of the universe of\nevolved proteins has the same scale-free like character as the actual protein\ndomain universe graph (PDUG). Further, the model predicts that ancient protein\ndomains represent a highly connected and clustered subset of all protein\ndomains, in complete agreement with reality. Together, these results provide a\nmicroscopic first principles picture of how protein structures and gene\nfamilies evolved in the course of evolution.",
"arxiv_id": "q-bio/0605044",
"authors": [
"Konstantin B. Zeldovich",
"Boris E. Shakhnovich",
"Eugene I. Shakhnovich"
],
"categories": [
"q-bio.PE",
"q-bio.BM"
],
"title": "Emergence of the protein universe in organismal evolution",
"url": "https://arxiv.org/abs/q-bio/0605044"
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