A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome
We report the feasible pathways of the quaternary model system for the ribosome-catalyzed PT reaction obtained by density functional calculations. Our results indicate that the step from the reactant complex to the first six-membered TS involving a proton shuttle via the 2'-OH of the P-site A76...
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| Veröffentlicht in: | Physical chemistry chemical physics : PCCP 2013-09, Vol.15 (36), p.14931-14935 |
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| container_title | Physical chemistry chemical physics : PCCP |
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| creator | Byun, Byung Jin Kang, Young Kee |
| description | We report the feasible pathways of the quaternary model system for the ribosome-catalyzed PT reaction obtained by density functional calculations. Our results indicate that the step from the reactant complex to the first six-membered TS involving a proton shuttle via the 2'-OH of the P-site A76 in the stepwise pathway is the most favored rate-limiting step in solution. It is found that the C-O3' bond-breaking of A76 is not significant but the C-N bond formation with a tetrahedral intermediate occurs in the rate-limiting step and that the fast breakdown of the C-O3' bond is followed in the second transition state. These are consistent with recent kinetic experiments. |
| doi_str_mv | 10.1039/c3cp51082d |
| format | Article |
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Our results indicate that the step from the reactant complex to the first six-membered TS involving a proton shuttle via the 2'-OH of the P-site A76 in the stepwise pathway is the most favored rate-limiting step in solution. It is found that the C-O3' bond-breaking of A76 is not significant but the C-N bond formation with a tetrahedral intermediate occurs in the rate-limiting step and that the fast breakdown of the C-O3' bond is followed in the second transition state. These are consistent with recent kinetic experiments.</description><identifier>ISSN: 1463-9076</identifier><identifier>EISSN: 1463-9084</identifier><identifier>DOI: 10.1039/c3cp51082d</identifier><identifier>PMID: 23900690</identifier><language>eng</language><publisher>Cambridge: Royal Society of Chemistry</publisher><subject>Bonding ; Breakdown ; Catalysis ; Chemistry ; Density ; Exact sciences and technology ; General and physical chemistry ; Kinetics ; Mathematical models ; Models, Molecular ; Molecular Conformation ; Pathways ; Peptides ; Peptides - chemical synthesis ; Peptides - chemistry ; Physical chemistry ; Quantum Theory ; Ribosomes - chemistry ; Theory of reactions, general kinetics. Catalysis. 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These are consistent with recent kinetic experiments.</description><subject>Bonding</subject><subject>Breakdown</subject><subject>Catalysis</subject><subject>Chemistry</subject><subject>Density</subject><subject>Exact sciences and technology</subject><subject>General and physical chemistry</subject><subject>Kinetics</subject><subject>Mathematical models</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Pathways</subject><subject>Peptides</subject><subject>Peptides - chemical synthesis</subject><subject>Peptides - chemistry</subject><subject>Physical chemistry</subject><subject>Quantum Theory</subject><subject>Ribosomes - chemistry</subject><subject>Theory of reactions, general kinetics. Catalysis. 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Nomenclature, chemical documentation, computer chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Byun, Byung Jin</creatorcontrib><creatorcontrib>Kang, Young Kee</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><jtitle>Physical chemistry chemical physics : PCCP</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Byun, Byung Jin</au><au>Kang, Young Kee</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome</atitle><jtitle>Physical chemistry chemical physics : PCCP</jtitle><addtitle>Phys Chem Chem Phys</addtitle><date>2013-09-28</date><risdate>2013</risdate><volume>15</volume><issue>36</issue><spage>14931</spage><epage>14935</epage><pages>14931-14935</pages><issn>1463-9076</issn><eissn>1463-9084</eissn><abstract>We report the feasible pathways of the quaternary model system for the ribosome-catalyzed PT reaction obtained by density functional calculations. 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| ispartof | Physical chemistry chemical physics : PCCP, 2013-09, Vol.15 (36), p.14931-14935 |
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| source | MEDLINE; Royal Society Of Chemistry Journals; Alma/SFX Local Collection |
| subjects | Bonding Breakdown Catalysis Chemistry Density Exact sciences and technology General and physical chemistry Kinetics Mathematical models Models, Molecular Molecular Conformation Pathways Peptides Peptides - chemical synthesis Peptides - chemistry Physical chemistry Quantum Theory Ribosomes - chemistry Theory of reactions, general kinetics. Catalysis. Nomenclature, chemical documentation, computer chemistry |
| title | A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome |
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