A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds

In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—which can be determined exactly in the model. Simulating the model on a computer, we consistent...

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Main Authors:	Zeldovich, Konstantin B, Chen, Peiqiu, Shakhnovich, Boris E, Shakhnovich, Eugene I
Format:	Online
Language:	English
Published:	Public Library of Science 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914367/

id	pubmed-1914367
recordtype	oai_dc
spelling	pubmed-19143672007-07-26 A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds Zeldovich, Konstantin B Chen, Peiqiu Shakhnovich, Boris E Shakhnovich, Eugene I Research Article In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—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 soon as favorable sequence–structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales 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 timescales 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. On the population level we observe emergence of species—subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution. Public Library of Science 2007-07 2007-07-13 /pmc/articles/PMC1914367/ /pubmed/17630830 http://dx.doi.org/10.1371/journal.pcbi.0030139 Text en © 2007 Zeldovich et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Zeldovich, Konstantin B Chen, Peiqiu Shakhnovich, Boris E Shakhnovich, Eugene I
spellingShingle	Zeldovich, Konstantin B Chen, Peiqiu Shakhnovich, Boris E Shakhnovich, Eugene I A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
author_facet	Zeldovich, Konstantin B Chen, Peiqiu Shakhnovich, Boris E Shakhnovich, Eugene I
author_sort	Zeldovich, Konstantin B
title	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
title_short	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
title_full	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
title_fullStr	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
title_full_unstemmed	A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
title_sort	first-principles model of early evolution: emergence of gene families, species, and preferred protein folds
description	In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—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 soon as favorable sequence–structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales 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 timescales 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. On the population level we observe emergence of species—subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.
publisher	Public Library of Science
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914367/
_version_	1611398157582729216

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds

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