{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Lan PD"],"funding":["National Science Centre Poland","National Science Foundation Division of Molecular and Cellular Biosciences","NIGMS NIH HHS"],"pagination":["168487"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11260358"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["436(6)"],"pubmed_abstract":["Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding substantially without changing the protein's amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease's dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-transla"],"journal":["Journal of molecular biology"],"pubmed_title":["Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements."],"pmcid":["PMC11260358"],"funding_grant_id":["DP2 GM140926","R35 GM124818"],"pubmed_authors":["Jiang Y","Xia Y","Lan PD","Sitarik I","Li MS","Vu QV","Fried SD","O'Brien EP","To P","Nissley DA"],"additional_accession":[]},"is_claimable":false,"name":"Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements.","description":"Synonymous mutations in messenger RNAs (mRNAs) can reduce protein-protein binding substantially without changing the protein's amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease's dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-transla","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Mar","modification":"2026-06-01T06:42:34.199Z","creation":"2025-05-18T13:26:13.297Z"},"accession":"S-EPMC11260358","cross_references":{"pubmed":["38341172"],"doi":["10.1016/j.jmb.2024.168487"]}}