Peptide Bond Formation of Amino Acids by Transient Masking with Silylating Reagents

2021 ◽  
Author(s):  
Wataru Muramatsu ◽  
Hisashi Yamamoto
Keyword(s):  
Amino Acids ◽  
Bond Formation ◽  
Peptide Bond ◽  
Peptide Bond Formation

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.

scholarly journals Mechanochemical Prebiotic Peptide Bond Formation

2020 ◽  
Author(s):  
Tomislav Stolar ◽  
Saša Grubešić ◽  
Nikola Cindro ◽  
Ernest Meštrović ◽  
Krunoslav Užarević ◽  
...  
Keyword(s):  
Amino Acids ◽  
Bond Formation ◽  
Thermal Conditions ◽  
Peptide Bond ◽  
Bulk Water ◽  
Degree Of Polymerization ◽  
Bulk Liquid ◽  
Peptide Bond Formation ◽  
Alternative Hypotheses ◽  
Synthetic Approaches

<p>The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. In contrast, prebiotically plausible pathways to achieve peptides from unactivated amino acids are still unclear since most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Alternative hypotheses such as the prebiotic impact scenario postulate that the mechanical impacts from meteorites and geochemical phenomena played an important role in delivering exogenous material to Earth, thus providing the geochemical, mechanical, and thermal conditions to synthesize small prebiotic organic compounds in the absence of bulk liquid media. In this context, here we evaluate the applicability of mechanochemistry by ball milling for peptide bond formation under a prebiotic impact scenario. We found that the combination of mechanical forces and prebiotically plausible and ubiquitous minerals as activators enable the oligomerization of amino acids such as glycine in the absence of bulk water (or solvents) and at ambient temperature. Increasing the mechanochemical reactor’s temperature is shown to favor the degree of polymerization concomitantly with the formation of cyclic glycine dimer [cyclo(Gly<sub>2</sub>) or DKP], a product commonly considered as a dead-end in solution peptide bond formation. However, our study shows that DKP can be mechanochemically activated and used as a source for glycine oligomers. The findings of this research provide alternative mechanochemical routes towards oligopeptides and establish new synthetic approaches for prebiotic chemistry that are not limited by poor diffusion of the reactants, thus complementing the current alternating wetting and drying prebiotic environment strategy.</p>

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