上位性在蛋白质进化中的作用。 - Suppr

Suppr

超能文献

The role of epistasis in protein evolution.

作者信息

McCandlish David M, Rajon Etienne, Shah Premal, Ding Yang, Plotkin Joshua B

机构信息

Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

出版信息

Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. doi: 10.1038/nature12219.

DOI:10.1038/nature12219

PMID:23719465

Abstract

摘要

相似文献

The role of epistasis in protein evolution.

Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. doi: 10.1038/nature12219.

The evolution of epistasis and its links with genetic robustness, complexity and drift in a phenotypic model of adaptation.

Genetics. 2009 May;182(1):277-93. doi: 10.1534/genetics.108.099127. Epub 2009 Mar 11.

Epistasis as the primary factor in molecular evolution.

Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.

Genetics: The inner life of proteins.

Nature. 2012 Oct 25;490(7421):493-4. doi: 10.1038/490493a.

Global epistasis emerges from a generic model of a complex trait.

Elife. 2021 Mar 29;10:e64740. doi: 10.7554/eLife.64740.

High-order epistasis shapes evolutionary trajectories.

PLoS Comput Biol. 2017 May 15;13(5):e1005541. doi: 10.1371/journal.pcbi.1005541. eCollection 2017 May.

Negative Epistasis in Experimental RNA Fitness Landscapes.

J Mol Evol. 2017 Dec;85(5-6):159-168. doi: 10.1007/s00239-017-9817-5. Epub 2017 Nov 10.

Growth of novel epistatic interactions by gene duplication.

Genome Biol Evol. 2011;3:295-301. doi: 10.1093/gbe/evr016. Epub 2011 Mar 14.

Epistasis constrains mutational pathways of hemoglobin adaptation in high-altitude pikas.

Mol Biol Evol. 2015 Feb;32(2):287-98. doi: 10.1093/molbev/msu311. Epub 2014 Nov 18.

Estimating the contribution of folding stability to nonspecific epistasis in protein evolution.

Proteins. 2018 Dec;86(12):1242-1250. doi: 10.1002/prot.25588. Epub 2018 Nov 9.

引用本文的文献

Effect of Mutations on the Evolution of Extended Spectrum β-lactamases (ESBL).

Protein J. 2025 Aug 19. doi: 10.1007/s10930-025-10284-7.

Epistasis facilitates functional evolution in an ancient transcription factor.

Elife. 2024 May 20;12:RP88737. doi: 10.7554/eLife.88737.

Intragenic compensation through the lens of deep mutational scanning.

Biophys Rev. 2022 Oct 26;14(5):1161-1182. doi: 10.1007/s12551-022-01005-w. eCollection 2022 Oct.

Design of a Protein with Improved Thermal Stability by an Evolution-Based Generative Model.

Angew Chem Int Ed Engl. 2022 Dec 12;61(50):e202202711. doi: 10.1002/anie.202202711. Epub 2022 Nov 16.

Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.

Nat Commun. 2022 Jul 12;13(1):4030. doi: 10.1038/s41467-022-31643-3.

Complex fitness landscape shapes variation in a hyperpolymorphic species.

Elife. 2022 May 9;11:e76073. doi: 10.7554/eLife.76073.

Senescence and entrenchment in evolution of amino acid sites.

Nat Commun. 2020 Sep 14;11(1):4603. doi: 10.1038/s41467-020-18366-z.

Harnessing Conformational Plasticity to Generate Designer Enzymes.

J Am Chem Soc. 2020 Jul 1;142(26):11324-11342. doi: 10.1021/jacs.0c04924. Epub 2020 Jun 17.

How Often Do Protein Genes Navigate Valleys of Low Fitness?

Genes (Basel). 2019 Apr 8;10(4):283. doi: 10.3390/genes10040283.

Pervasive contingency and entrenchment in a billion years of Hsp90 evolution.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4453-4458. doi: 10.1073/pnas.1718133115. Epub 2018 Apr 6.

本文引用的文献

Epistasis as the primary factor in molecular evolution.

Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.

Genetics. 2012 Mar;190(3):1101-15. doi: 10.1534/genetics.111.136432. Epub 2011 Dec 29.

Initial mutations direct alternative pathways of protein evolution.

PLoS Genet. 2011 Mar;7(3):e1001321. doi: 10.1371/journal.pgen.1001321. Epub 2011 Mar 3.

Prevalence of epistasis in the evolution of influenza A surface proteins.

PLoS Genet. 2011 Feb;7(2):e1001301. doi: 10.1371/journal.pgen.1001301. Epub 2011 Feb 17.

High-resolution mapping of protein sequence-function relationships.

Nat Methods. 2010 Sep;7(9):741-6. doi: 10.1038/nmeth.1492. Epub 2010 Aug 15.

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4629-34. doi: 10.1073/pnas.0910915107. Epub 2010 Feb 22.

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3931-9. doi: 10.1098/rstb.2008.0167.

PAML 4: phylogenetic analysis by maximum likelihood.

Mol Biol Evol. 2007 Aug;24(8):1586-91. doi: 10.1093/molbev/msm088. Epub 2007 May 4.

Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1.

Genetics. 2006 Nov;174(3):1689-94. doi: 10.1534/genetics.106.062885. Epub 2006 Jul 18.

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

Nat Rev Genet. 2005 Sep;6(9):678-87. doi: 10.1038/nrg1672.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验

相似文献

The role of epistasis in protein evolution.

Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. doi: 10.1038/nature12219.

The evolution of epistasis and its links with genetic robustness, complexity and drift in a phenotypic model of adaptation.

Genetics. 2009 May;182(1):277-93. doi: 10.1534/genetics.108.099127. Epub 2009 Mar 11.

Epistasis as the primary factor in molecular evolution.

Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.

Genetics: The inner life of proteins.

Nature. 2012 Oct 25;490(7421):493-4. doi: 10.1038/490493a.

Global epistasis emerges from a generic model of a complex trait.

Elife. 2021 Mar 29;10:e64740. doi: 10.7554/eLife.64740.

High-order epistasis shapes evolutionary trajectories.

PLoS Comput Biol. 2017 May 15;13(5):e1005541. doi: 10.1371/journal.pcbi.1005541. eCollection 2017 May.

Negative Epistasis in Experimental RNA Fitness Landscapes.

J Mol Evol. 2017 Dec;85(5-6):159-168. doi: 10.1007/s00239-017-9817-5. Epub 2017 Nov 10.

Growth of novel epistatic interactions by gene duplication.

Genome Biol Evol. 2011;3:295-301. doi: 10.1093/gbe/evr016. Epub 2011 Mar 14.

Epistasis constrains mutational pathways of hemoglobin adaptation in high-altitude pikas.

Mol Biol Evol. 2015 Feb;32(2):287-98. doi: 10.1093/molbev/msu311. Epub 2014 Nov 18.

Estimating the contribution of folding stability to nonspecific epistasis in protein evolution.

Proteins. 2018 Dec;86(12):1242-1250. doi: 10.1002/prot.25588. Epub 2018 Nov 9.

引用本文的文献

Effect of Mutations on the Evolution of Extended Spectrum β-lactamases (ESBL).

Protein J. 2025 Aug 19. doi: 10.1007/s10930-025-10284-7.

Epistasis facilitates functional evolution in an ancient transcription factor.

Elife. 2024 May 20;12:RP88737. doi: 10.7554/eLife.88737.

Intragenic compensation through the lens of deep mutational scanning.

Biophys Rev. 2022 Oct 26;14(5):1161-1182. doi: 10.1007/s12551-022-01005-w. eCollection 2022 Oct.

Design of a Protein with Improved Thermal Stability by an Evolution-Based Generative Model.

Angew Chem Int Ed Engl. 2022 Dec 12;61(50):e202202711. doi: 10.1002/anie.202202711. Epub 2022 Nov 16.

Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.

Nat Commun. 2022 Jul 12;13(1):4030. doi: 10.1038/s41467-022-31643-3.

Complex fitness landscape shapes variation in a hyperpolymorphic species.

Elife. 2022 May 9;11:e76073. doi: 10.7554/eLife.76073.

Senescence and entrenchment in evolution of amino acid sites.

Nat Commun. 2020 Sep 14;11(1):4603. doi: 10.1038/s41467-020-18366-z.

Harnessing Conformational Plasticity to Generate Designer Enzymes.

J Am Chem Soc. 2020 Jul 1;142(26):11324-11342. doi: 10.1021/jacs.0c04924. Epub 2020 Jun 17.

How Often Do Protein Genes Navigate Valleys of Low Fitness?

Genes (Basel). 2019 Apr 8;10(4):283. doi: 10.3390/genes10040283.

Pervasive contingency and entrenchment in a billion years of Hsp90 evolution.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4453-4458. doi: 10.1073/pnas.1718133115. Epub 2018 Apr 6.

本文引用的文献

Epistasis as the primary factor in molecular evolution.

Nature. 2012 Oct 25;490(7421):535-8. doi: 10.1038/nature11510. Epub 2012 Oct 14.

Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.

Genetics. 2012 Mar;190(3):1101-15. doi: 10.1534/genetics.111.136432. Epub 2011 Dec 29.

Initial mutations direct alternative pathways of protein evolution.

PLoS Genet. 2011 Mar;7(3):e1001321. doi: 10.1371/journal.pgen.1001321. Epub 2011 Mar 3.

Prevalence of epistasis in the evolution of influenza A surface proteins.

PLoS Genet. 2011 Feb;7(2):e1001301. doi: 10.1371/journal.pgen.1001301. Epub 2011 Feb 17.

High-resolution mapping of protein sequence-function relationships.

Nat Methods. 2010 Sep;7(9):741-6. doi: 10.1038/nmeth.1492. Epub 2010 Aug 15.

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4629-34. doi: 10.1073/pnas.0910915107. Epub 2010 Feb 22.

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3931-9. doi: 10.1098/rstb.2008.0167.

PAML 4: phylogenetic analysis by maximum likelihood.

Mol Biol Evol. 2007 Aug;24(8):1586-91. doi: 10.1093/molbev/msm088. Epub 2007 May 4.

Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1.

Genetics. 2006 Nov;174(3):1689-94. doi: 10.1534/genetics.106.062885. Epub 2006 Jul 18.

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

Nat Rev Genet. 2005 Sep;6(9):678-87. doi: 10.1038/nrg1672.