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Literature DB >> 23719465

The role of epistasis in protein evolution.

David M McCandlish¹, Etienne Rajon, Premal Shah, Yang Ding, Joshua B Plotkin.

Abstract

Mesh：

Year: 2013 PMID： 23719465 DOI： 10.1038/nature12219

Source DB: PubMed Journal: Nature ISSN： 0028-0836 Impact factor: 49.962

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14 in total

1. Modeling genetic architecture: a multilinear theory of gene interaction.

Authors: T F Hansen; G P Wagner
Journal: Theor Popul Biol Date: 2001-02 Impact factor: 1.570

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. PAML 4: phylogenetic analysis by maximum likelihood.

Authors: Ziheng Yang
Journal: Mol Biol Evol Date: 2007-05-04 Impact factor: 16.240

4. Synonymous and nonsynonymous rate variation in nuclear genes of mammals.

Authors: Z Yang; R Nielsen
Journal: J Mol Evol Date: 1998-04 Impact factor: 2.395

5. Dobzhansky-Muller incompatibilities in protein evolution.

Authors: Alexey S Kondrashov; Shamil Sunyaev; Fyodor A Kondrashov
Journal: Proc Natl Acad Sci U S A Date: 2002-10-28 Impact factor: 11.205

6. Epistasis as the primary factor in molecular evolution.

Authors: Michael S Breen; Carsten Kemena; Peter K Vlasov; Cedric Notredame; Fyodor A Kondrashov
Journal: Nature Date: 2012-10-14 Impact factor: 49.962

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

Authors: Jack da Silva
Journal: Genetics Date: 2006-07-18 Impact factor: 4.562

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

Authors: Sergey Kryazhimskiy; Jonathan Dushoff; Georgii A Bazykin; Joshua B Plotkin
Journal: PLoS Genet Date: 2011-02-17 Impact factor: 5.917

9. Initial mutations direct alternative pathways of protein evolution.

Authors: Merijn L M Salverda; Eynat Dellus; Florien A Gorter; Alfons J M Debets; John van der Oost; Rolf F Hoekstra; Dan S Tawfik; J Arjan G M de Visser
Journal: PLoS Genet Date: 2011-03-03 Impact factor: 5.917

10. High-resolution mapping of protein sequence-function relationships.

Authors: Douglas M Fowler; Carlos L Araya; Sarel J Fleishman; Elizabeth H Kellogg; Jason J Stephany; David Baker; Stanley Fields
Journal: Nat Methods Date: 2010-08-15 Impact factor: 28.547

25 in total

Review 1. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.

Authors: Georgii A Bazykin
Journal: Biol Lett Date: 2015-10 Impact factor: 3.703

Review 2. Epistasis in protein evolution.

Authors: Tyler N Starr; Joseph W Thornton
Journal: Protein Sci Date: 2016-02-28 Impact factor: 6.725

The role of epistasis in protein evolution.

1. Modeling genetic architecture: a multilinear theory of gene interaction.

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

3. PAML 4: phylogenetic analysis by maximum likelihood.

4. Synonymous and nonsynonymous rate variation in nuclear genes of mammals.

5. Dobzhansky-Muller incompatibilities in protein evolution.

6. Epistasis as the primary factor in molecular evolution.

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

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

9. Initial mutations direct alternative pathways of protein evolution.

10. High-resolution mapping of protein sequence-function relationships.

Review 1. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.

Review 2. Epistasis in protein evolution.

3. Reverse evolution leads to genotypic incompatibility despite functional and active site convergence.

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

5. Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

6. Contingency and entrenchment in protein evolution under purifying selection.

7. Quantitative Description of a Protein Fitness Landscape Based on Molecular Features.

8. A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation.

9. Epistasis and the Dynamics of Reversion in Molecular Evolution.

10. Evolutionary history of a complex adaptation: tetrodotoxin resistance in salamanders.