title: Altered dynamics upon oligomerization corresponds to key functional sites.
abstract: It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422-1434. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.|Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011.
authors.forename: Sambit Kumar
authors.initials: SK
authors.lastname: Mishra
authors.affiliation: Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.|Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011.
authors.forename: Kannan
authors.initials: K
authors.lastname: Sankar
authors.affiliation: Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.|Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011.
authors.forename: Robert L
authors.identifier: http://orcid.org/0000-0003-0996-8360
authors.initials: RL
authors.lastname: Jernigan
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001119:Arginase / Q000737:chemistry*; D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003605:D-Amino-Acid Oxidase / Q000737:chemistry*; D005969:Glutamate Dehydrogenase / Q000737:chemistry*; D050938:Glycine N-Methyltransferase / Q000737:chemistry*; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D013379:Substrate Specificity; D013816:Thermodynamics; D014305:Triose-Phosphate Isomerase / Q000737:chemistry*
chemical_list: D005969:Glutamate Dehydrogenase; C485958:Dao1 protein, mouse; D003605:D-Amino-Acid Oxidase; D050938:Glycine N-Methyltransferase; C574619:ARG1 protein, human; D001119:Arginase; D014305:Triose-Phosphate Isomerase
keywords: elastic network models; homooligomers; oligomerization; protein dynamics; residue communities