publication . Article . Other literature type . 2016

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

Benjamin R Jack; Austin G Meyer; Julian Echave; Claus O Wilke;
Open Access English
  • Published: 01 May 2016
  • Publisher: Public Library of Science
  • Country: Argentina
Abstract
Author Summary The basic biochemical functions of life are carried out by large molecules called enzymes. Enzymes consist of long chains of amino acids folded into a three-dimensional structure. Within that structure, a specific cluster of amino acids, known as the active site, performs the biochemical function. Substituting one amino acid for another in the active site typically results in a defective, non-functional enzyme, and therefore mutations at or near enzyme active sites are often lethal. Moreover, even mutations far from the active site have been found to disrupt function. Nonetheless, as organisms evolve, enzymes accumulate random mutations. Where in ...
Subjects
free text keywords: Protein, Evolution, Functional, Constraints, Otras Ciencias Biológicas, Ciencias Biológicas, CIENCIAS NATURALES Y EXACTAS, Otras Ciencias Químicas, Ciencias Químicas, General Biochemistry, Genetics and Molecular Biology, General Immunology and Microbiology, General Neuroscience, General Agricultural and Biological Sciences, Biophysics, Protein structure prediction, Conserved sequence, Sequence alignment, Enzyme structure, Peptide sequence, Active site, biology.protein, biology, Biochemistry, Molecular evolution, Genetics, Protein structure, Research Article, Biology and Life Sciences, Enzymology, Evolutionary Biology, Evolutionary Processes, Evolutionary Rate, Enzymes, Proteins, Molecular Biology, Macromolecular Structure Analysis, Research and Analysis Methods, Database and Informatics Methods, Biological Databases, Protein Structure Databases, Molecular Biology Techniques, Sequencing Techniques, Sequence Analysis, Biology (General), QH301-705.5
Funded by
NSF| BEACON: An NSF Center for the Study of Evolution in Action
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939454
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NIH| The biophysical basis of translational selection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM088344-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
61 references, page 1 of 5

1 Bloom JD, Labthavikul ST, Otey CR, Arnold FH. Protein stability promotes evolvability. Proc Natl Acad Sci USA. 2006;103:5869–5874. 16581913 [OpenAIRE] [PubMed]

2 Bloom JD, Gong LI, Baltimore D. Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science. 2010;328:1272–1275. 10.1126/science.1187816 20522774 [OpenAIRE] [PubMed] [DOI]

3 Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the e volution of an influenza protein. eLife. 2013;2:e00631 10.7554/eLife.00631 23682315 [OpenAIRE] [PubMed] [DOI]

4 Shakhnovich E, Abkevich V, Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature. 1996;379:96–98. 8538750 [OpenAIRE] [PubMed]

5 Tokuriki N, Tawfik DS. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol. 2009;19:596–604. 10.1016/j.sbi.2009.08.003 19765975 [OpenAIRE] [PubMed] [DOI]

6 Gerlt JA. Relationships between enzymatic catalysis and active site structure revealed by applications of site-directed mutagenesis. Chem Rev. 1987;87:1079–1105.

7 Kanaya S, Kohara A, Miura Y, Sekiguchi A, Iwai S, Inoue H, et al Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis. J Biol Chem. 1990;265:4615–4621. 1689729 [PubMed]

8 Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996;257:342–358. 8609628 [OpenAIRE] [PubMed]

9 Mihalek I, RešI, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol. 2004;336:1265–1282. 15037084 [OpenAIRE] [PubMed]

10 Huang YW, Chang CM, Lee CW, Hwang JK. The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein. Proteins. 2015;83:1407–1413. 10.1002/prot.24809 25846748 [OpenAIRE] [PubMed] [DOI]

11 Romero PA, Tran TM, Abate AR. Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci USA. 2015;112:7159–7164. 10.1073/pnas.1422285112 26040002 [OpenAIRE] [PubMed] [DOI]

12 Abriata LA, Palzkill T, Dal Peraro M. How structural and physicochemical determinants shape sequence constraints in a functional enzyme. PLoS ONE. 2015;10:e0118684 10.1371/journal.pone.0118684 25706742 [OpenAIRE] [PubMed] [DOI]

13 Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat Commun. 2014;5:4395 10.1038/ncomms5395 25022223 [OpenAIRE] [PubMed] [DOI]

14 Dean AM, Neuhauser C, Grenier E, Golding GB. The pattern of amino acid replacements in alpha/beta-barrels. Mol Biol Evol. 2002;19:1846–1864. 12411594 [PubMed]

15 Shih CH, Chang CM, Lin YS, Lo WC, Hwang JK. Evolutionary information hidden in a single protein structure. Proteins. 2012;80:1647–1657. 10.1002/prot.24058 22454236 [OpenAIRE] [PubMed] [DOI]

61 references, page 1 of 5
Abstract
Author Summary The basic biochemical functions of life are carried out by large molecules called enzymes. Enzymes consist of long chains of amino acids folded into a three-dimensional structure. Within that structure, a specific cluster of amino acids, known as the active site, performs the biochemical function. Substituting one amino acid for another in the active site typically results in a defective, non-functional enzyme, and therefore mutations at or near enzyme active sites are often lethal. Moreover, even mutations far from the active site have been found to disrupt function. Nonetheless, as organisms evolve, enzymes accumulate random mutations. Where in ...
Subjects
free text keywords: Protein, Evolution, Functional, Constraints, Otras Ciencias Biológicas, Ciencias Biológicas, CIENCIAS NATURALES Y EXACTAS, Otras Ciencias Químicas, Ciencias Químicas, General Biochemistry, Genetics and Molecular Biology, General Immunology and Microbiology, General Neuroscience, General Agricultural and Biological Sciences, Biophysics, Protein structure prediction, Conserved sequence, Sequence alignment, Enzyme structure, Peptide sequence, Active site, biology.protein, biology, Biochemistry, Molecular evolution, Genetics, Protein structure, Research Article, Biology and Life Sciences, Enzymology, Evolutionary Biology, Evolutionary Processes, Evolutionary Rate, Enzymes, Proteins, Molecular Biology, Macromolecular Structure Analysis, Research and Analysis Methods, Database and Informatics Methods, Biological Databases, Protein Structure Databases, Molecular Biology Techniques, Sequencing Techniques, Sequence Analysis, Biology (General), QH301-705.5
Funded by
NSF| BEACON: An NSF Center for the Study of Evolution in Action
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939454
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NIH| The biophysical basis of translational selection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM088344-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
61 references, page 1 of 5

1 Bloom JD, Labthavikul ST, Otey CR, Arnold FH. Protein stability promotes evolvability. Proc Natl Acad Sci USA. 2006;103:5869–5874. 16581913 [OpenAIRE] [PubMed]

2 Bloom JD, Gong LI, Baltimore D. Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science. 2010;328:1272–1275. 10.1126/science.1187816 20522774 [OpenAIRE] [PubMed] [DOI]

3 Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the e volution of an influenza protein. eLife. 2013;2:e00631 10.7554/eLife.00631 23682315 [OpenAIRE] [PubMed] [DOI]

4 Shakhnovich E, Abkevich V, Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature. 1996;379:96–98. 8538750 [OpenAIRE] [PubMed]

5 Tokuriki N, Tawfik DS. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol. 2009;19:596–604. 10.1016/j.sbi.2009.08.003 19765975 [OpenAIRE] [PubMed] [DOI]

6 Gerlt JA. Relationships between enzymatic catalysis and active site structure revealed by applications of site-directed mutagenesis. Chem Rev. 1987;87:1079–1105.

7 Kanaya S, Kohara A, Miura Y, Sekiguchi A, Iwai S, Inoue H, et al Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis. J Biol Chem. 1990;265:4615–4621. 1689729 [PubMed]

8 Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996;257:342–358. 8609628 [OpenAIRE] [PubMed]

9 Mihalek I, RešI, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol. 2004;336:1265–1282. 15037084 [OpenAIRE] [PubMed]

10 Huang YW, Chang CM, Lee CW, Hwang JK. The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein. Proteins. 2015;83:1407–1413. 10.1002/prot.24809 25846748 [OpenAIRE] [PubMed] [DOI]

11 Romero PA, Tran TM, Abate AR. Dissecting enzyme function with microfluidic-based deep mutational scanning. Proc Natl Acad Sci USA. 2015;112:7159–7164. 10.1073/pnas.1422285112 26040002 [OpenAIRE] [PubMed] [DOI]

12 Abriata LA, Palzkill T, Dal Peraro M. How structural and physicochemical determinants shape sequence constraints in a functional enzyme. PLoS ONE. 2015;10:e0118684 10.1371/journal.pone.0118684 25706742 [OpenAIRE] [PubMed] [DOI]

13 Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat Commun. 2014;5:4395 10.1038/ncomms5395 25022223 [OpenAIRE] [PubMed] [DOI]

14 Dean AM, Neuhauser C, Grenier E, Golding GB. The pattern of amino acid replacements in alpha/beta-barrels. Mol Biol Evol. 2002;19:1846–1864. 12411594 [PubMed]

15 Shih CH, Chang CM, Lin YS, Lo WC, Hwang JK. Evolutionary information hidden in a single protein structure. Proteins. 2012;80:1647–1657. 10.1002/prot.24058 22454236 [OpenAIRE] [PubMed] [DOI]

61 references, page 1 of 5
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publication . Article . Other literature type . 2016

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

Benjamin R Jack; Austin G Meyer; Julian Echave; Claus O Wilke;