publication . Other literature type . Article . 2016

Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins.

Nelson, Erik D.; Grishin, Nick V.;
  • Published: 21 Nov 2016
Abstract
Recent analyses of amino acid mutations in proteins reveal that mutations at many pairs of sites are epistatic—i.e., their effects on fitness are non—additive—the combined effect of two mutations being significantly larger or smaller than the sum of their effects considered independently. Interestingly, epistatic sites are not necessarily near each other in the folded structure of a protein, and may even be located on opposite sides of a molecule. However, the mechanistic reasons for long–range epistasis remain obscure. Here, we study long–range epistasis in proteins using a previously developed model in which off–lattice polymers are evolved under ligand bindin...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology and Life Sciences, Heredity, Physical Sciences, Polymer Chemistry, Macromolecules, Polymers, Materials Science, Materials by Structure, Molecular Biology, Molecular Biology Techniques, Sequencing Techniques, Protein Sequencing, Research and Analysis Methods, Mutation, Deletion Mutation, Fitness Epistasis, Macromolecular Structure Analysis, Protein Structure, Biochemistry, Proteins, Sequence Analysis, Sequence Alignment, Amino Acid Sequence Analysis, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Structural change, Ligand (biochemistry), Computational biology, Epistasis, Chemistry, Genetics
Funded by
NIH| Computational methods for structural-functional studies of protein
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM094575-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
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30 references, page 1 of 2

1 Starr TN, Thornton JW. Epistasis in protein evolution. Prot Sci. 2016;25:1204–1218. 10.1002/pro.2897 [OpenAIRE] [DOI]

2 Olson CA, Wu NC, Sun R. A Comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol. 2014;24:2643–2651. 10.1016/j.cub.2014.09.072 25455030 [OpenAIRE] [PubMed] [DOI]

3 L M, Golding GB, Dean AM. Pervasive Cryptic Epistasis in Molecular Evolution. PLoS Genet. 2010;6:e1001162 10.1371/journal.pgen.1001162 20975933 [OpenAIRE] [PubMed] [DOI]

4 Poon AF, Chao L. The rate of compensatory mutation in the DNA bacteriophage φ X174. Genetics. 2005;170:989–999. 10.1534/genetics.104.039438 15911582 [OpenAIRE] [PubMed] [DOI]

5 Poon AF, Chao L. Functional origins of fitness effect–sizes of compensatory mutations in the DNA bacteriophage φ X174. Evolution. 2006;60:2032–2043. 17133860 [PubMed]

6 Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: Evolution by conformational epistasis. Science. 2007;317:1544–1548. 10.1126/science.1142819 17702911 [OpenAIRE] [PubMed] [DOI]

7 Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature. 2009;461:515–519. 10.1038/nature08249 19779450 [OpenAIRE] [PubMed] [DOI]

8 Breen MS, Kremena C, Vlasov PK, Notredame C, Kondrashov FA. Epistasis as the primary factor in molecular evolution. Nature. 2012;490:535–538. 10.1038/nature11510 23064225 [OpenAIRE] [PubMed] [DOI]

9 McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature. 2013;497:E1–E2. 10.1038/nature12219 23719465 [OpenAIRE] [PubMed] [DOI]

10 Breen MS, Kremena C, Vlasov PK, Notredame C, Kondrashov FA. Breen et al reply. Nature. 2013;497:E2–E3.

11 Pollock DD, Thiltgen G, Goldstein RA. Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci USA. 2012;109:E1352–E1359. 10.1073/pnas.1120084109 22547823 [OpenAIRE] [PubMed] [DOI]

12 Ashenberg O, Gong LI, Bloom JD. Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci USA. 2013;110:21071–21076. 10.1073/pnas.1314781111 24324165 [OpenAIRE] [PubMed] [DOI]

13 Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci USA. 2014;111:E1450 10.1073/pnas.1401112111 24706894 [OpenAIRE] [PubMed] [DOI]

14 Nelson ED, Grishin NV. Evolution of off–lattice model proteins under ligand binding constraints. Phys Rev E. 2016;94:022410 10.1103/PhysRevE.94.022410 27627338 [OpenAIRE] [PubMed] [DOI]

15 Hormoz S. Amino acid composition of proteins reduces deleterious impact of mutations. Sci Rep. 2013;3:2919 10.1038/srep02919 24108121 [OpenAIRE] [PubMed] [DOI]

30 references, page 1 of 2
Abstract
Recent analyses of amino acid mutations in proteins reveal that mutations at many pairs of sites are epistatic—i.e., their effects on fitness are non—additive—the combined effect of two mutations being significantly larger or smaller than the sum of their effects considered independently. Interestingly, epistatic sites are not necessarily near each other in the folded structure of a protein, and may even be located on opposite sides of a molecule. However, the mechanistic reasons for long–range epistasis remain obscure. Here, we study long–range epistasis in proteins using a previously developed model in which off–lattice polymers are evolved under ligand bindin...
Subjects
free text keywords: Medicine, R, Science, Q, Research Article, Biology and Life Sciences, Heredity, Physical Sciences, Polymer Chemistry, Macromolecules, Polymers, Materials Science, Materials by Structure, Molecular Biology, Molecular Biology Techniques, Sequencing Techniques, Protein Sequencing, Research and Analysis Methods, Mutation, Deletion Mutation, Fitness Epistasis, Macromolecular Structure Analysis, Protein Structure, Biochemistry, Proteins, Sequence Analysis, Sequence Alignment, Amino Acid Sequence Analysis, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Structural change, Ligand (biochemistry), Computational biology, Epistasis, Chemistry, Genetics
Funded by
NIH| Computational methods for structural-functional studies of protein
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM094575-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
Download fromView all 5 versions
PLoS ONE
Article . 2016
PLoS ONE
Article . 2016
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
30 references, page 1 of 2

1 Starr TN, Thornton JW. Epistasis in protein evolution. Prot Sci. 2016;25:1204–1218. 10.1002/pro.2897 [OpenAIRE] [DOI]

2 Olson CA, Wu NC, Sun R. A Comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol. 2014;24:2643–2651. 10.1016/j.cub.2014.09.072 25455030 [OpenAIRE] [PubMed] [DOI]

3 L M, Golding GB, Dean AM. Pervasive Cryptic Epistasis in Molecular Evolution. PLoS Genet. 2010;6:e1001162 10.1371/journal.pgen.1001162 20975933 [OpenAIRE] [PubMed] [DOI]

4 Poon AF, Chao L. The rate of compensatory mutation in the DNA bacteriophage φ X174. Genetics. 2005;170:989–999. 10.1534/genetics.104.039438 15911582 [OpenAIRE] [PubMed] [DOI]

5 Poon AF, Chao L. Functional origins of fitness effect–sizes of compensatory mutations in the DNA bacteriophage φ X174. Evolution. 2006;60:2032–2043. 17133860 [PubMed]

6 Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: Evolution by conformational epistasis. Science. 2007;317:1544–1548. 10.1126/science.1142819 17702911 [OpenAIRE] [PubMed] [DOI]

7 Bridgham JT, Ortlund EA, Thornton JW. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature. 2009;461:515–519. 10.1038/nature08249 19779450 [OpenAIRE] [PubMed] [DOI]

8 Breen MS, Kremena C, Vlasov PK, Notredame C, Kondrashov FA. Epistasis as the primary factor in molecular evolution. Nature. 2012;490:535–538. 10.1038/nature11510 23064225 [OpenAIRE] [PubMed] [DOI]

9 McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature. 2013;497:E1–E2. 10.1038/nature12219 23719465 [OpenAIRE] [PubMed] [DOI]

10 Breen MS, Kremena C, Vlasov PK, Notredame C, Kondrashov FA. Breen et al reply. Nature. 2013;497:E2–E3.

11 Pollock DD, Thiltgen G, Goldstein RA. Amino acid coevolution induces an evolutionary Stokes shift. Proc Natl Acad Sci USA. 2012;109:E1352–E1359. 10.1073/pnas.1120084109 22547823 [OpenAIRE] [PubMed] [DOI]

12 Ashenberg O, Gong LI, Bloom JD. Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci USA. 2013;110:21071–21076. 10.1073/pnas.1314781111 24324165 [OpenAIRE] [PubMed] [DOI]

13 Pollock DD, Goldstein RA. Strong evidence for protein epistasis, weak evidence against it. Proc Natl Acad Sci USA. 2014;111:E1450 10.1073/pnas.1401112111 24706894 [OpenAIRE] [PubMed] [DOI]

14 Nelson ED, Grishin NV. Evolution of off–lattice model proteins under ligand binding constraints. Phys Rev E. 2016;94:022410 10.1103/PhysRevE.94.022410 27627338 [OpenAIRE] [PubMed] [DOI]

15 Hormoz S. Amino acid composition of proteins reduces deleterious impact of mutations. Sci Rep. 2013;3:2919 10.1038/srep02919 24108121 [OpenAIRE] [PubMed] [DOI]

30 references, page 1 of 2
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