scholarly journals Amino Acids and Peptides. I. Novel Peptide Bond Formation Catalyzed by Metal Ions. I. Formation of Glycine Peptide Esters

1971 ◽  
Vol 19 (11) ◽  
pp. 2380-2388 ◽  
Author(s):  
SHUNICHI YAMADA ◽  
MITSUYOSHI WAGATSUMA ◽  
YOSHIO TAKEUCHI ◽  
SHIRO TERASHIMA
Keyword(s):  
Amino Acids ◽  
Metal Ions ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Peptide Esters

scholarly journals Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site

2018 ◽  
Vol 47 (4) ◽  
pp. 2089-2100 ◽  
Author(s):  
Sergey V Melnikov ◽  
Nelli F Khabibullina ◽  
Elisabeth Mairhofer ◽  
Oscar Vargas-Rodriguez ◽  
Noah M Reynolds ◽  
...  
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation

scholarly journals Unwanted hydrolysis or α/β-peptide bond formation: how long should the rate-limiting coupling step take?

RSC Advances ◽  
2019 ◽  
Vol 9 (53) ◽  
pp. 30720-30728 ◽  
Author(s):  
Viktória Goldschmidt Gőz ◽  
Adrienn Nagy ◽  
Viktor Farkas ◽  
Ernő Keszei ◽  
András Perczel
Keyword(s):  
Amino Acids ◽  
Bond Formation ◽  
Side Reaction ◽  
Peptide Bond ◽  
Amide Bond ◽  
Peptide Bond Formation ◽  
Active Esters ◽  
Amide Bond Formation ◽  
Rate Limiting ◽  
Hydrolysis Of

Parallel to the amide bond formation, the hydrolysis of the active esters of α/β-amino acids, as an unwanted side reaction limiting coupling efficacy, is studied.

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.

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