Theoretical investigation of the role of clay edges in prebiotic peptide bond formation

1988 ◽  
Vol 18 (1-2) ◽  
pp. 107-119 ◽  
Author(s):  
Jack R. Collins ◽  
Gilda H. Loew ◽  
Brian T. Luke ◽  
David H. White
Keyword(s):  
Theoretical Investigation ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

2021 ◽  
Author(s):  
Sofie Dekimpe ◽  
Joleen Masschelein
Keyword(s):  
Natural Product ◽  
Bond Formation ◽  
Peptide Bond ◽  
Chemical Diversity ◽  
Peptide Bond Formation ◽  
Natural Product Biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.

ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation

2012 ◽  
Vol 90 (6) ◽  
pp. 691-700 ◽  
Author(s):  
Hadieh Monajemi ◽  
Mohammad Noh Daud ◽  
Sharifuddin Mohd. Zain ◽  
Wan Ahmad Tajuddin Wan Abdullah
Keyword(s):  
Amino Acids ◽  
Bond Formation ◽  
Computational Cost ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Initiator Trna ◽  
Reduced Rate ◽  
Surface Scan ◽  
A Site

Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNAimet and elongator tRNAphe are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNAimet in the absence of ribosomal bases. The misacylated elongator tRNAphe, however, did not show any difference in its PES compared with that for the phe-tRNAphe. This demonstrates the structural specification of initiator tRNAimet for the amino acids side chain.

Mechanism of peptide bond formation on the ribosome

2006 ◽  
Vol 39 (3) ◽  
pp. 203-225 ◽  
Author(s):  
Marina V. Rodnina ◽  
Malte Beringer ◽  
Wolfgang Wintermeyer
Keyword(s):  
Active Site ◽  
Electrostatic Interactions ◽  
Ph Dependence ◽  
Bond Formation ◽  
Peptide Bond ◽  
Hydroxyl Groups ◽  
Peptide Bond Formation ◽  
Uncatalyzed Reaction ◽  
Proton Shuttling

1. The ribosome 2042. Peptide bond formation is catalyzed by RNA 2053. Characteristics of the uncatalyzed reaction 2074. Potential catalytic strategies of the ribosome 2075. Experimental systems 2086. Substrate binding in the PT center 2107. Induced fit in the active site 2118. pH dependence of peptide bond formation 2129. Reaction with full-length aa-tRNA 21410. Role of active-site residues 21511. pH-dependent structural changes of the active site 21612. Entropic catalysis 21713. Role of 2′-OH of A76 in P-site tRNA 21814. Catalysis by proton shuttling 21915. Plasticity of the active site 22016. Conclusions 22117. Acknowledgments 22218. References 222Peptide bond formation is the fundamental reaction of ribosomal protein synthesis. The ribosome's active site – the peptidyl transferase center – is composed of rRNA, and thus the ribosome is the largest known RNA catalyst. The ribosome accelerates peptide bond formation by 107-fold relative to the uncatalyzed reaction. Recent progress of structural, biochemical and computational approaches has provided a fairly detailed picture of the catalytic mechanisms employed by the ribosome. Energetically, catalysis is entirely entropic, indicating an important role of solvent reorganization, substrate positioning, and/or orientation of the reacting groups within the active site. The ribosome provides a pre-organized network of electrostatic interactions that stabilize the transition state and facilitate proton shuttling involving ribose hydroxyl groups of tRNA. The catalytic mechanism employed by the ribosome suggests how ancient RNA-world enzymes may have functioned.

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