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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
36
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pubmed:dateCreated |
2006-9-6
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pubmed:abstractText |
Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-12535524,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-12787020,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-14669983,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-15141076,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-15163407,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-15475967,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-15916549,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16114867,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16116099,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16164408,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16258236,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16373492,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16407993,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16522067,
http://linkedlifedata.com/resource/pubmed/commentcorrection/16938893-16569023
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Sep
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pubmed:issn |
0027-8424
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:day |
5
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pubmed:volume |
103
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
13327-32
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:16938893-Crystallography, X-Ray,
pubmed-meshheading:16938893-Hydrogen Bonding,
pubmed-meshheading:16938893-Models, Chemical,
pubmed-meshheading:16938893-Models, Molecular,
pubmed-meshheading:16938893-Peptides,
pubmed-meshheading:16938893-Peptidyl Transferases,
pubmed-meshheading:16938893-Protein Binding,
pubmed-meshheading:16938893-Protein Conformation,
pubmed-meshheading:16938893-Quantum Theory,
pubmed-meshheading:16938893-RNA, Transfer,
pubmed-meshheading:16938893-Ribosomes,
pubmed-meshheading:16938893-Rotation
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pubmed:year |
2006
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pubmed:articleTitle |
The transition state for formation of the peptide bond in the ribosome.
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pubmed:affiliation |
Hunter College and the Graduate School, City University of New York, New York, NY 10021, USA.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't,
Research Support, N.I.H., Extramural
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