Ab-Initio Computational Study : The Activation Energy Changes and Steric Effects In Peptide Synthesis Of Ac-AA-NH2 and Ac-AP-NH2

Indah Pratiwi,Parsaoran Siahaan,Bambang Cahyono

doi:10.20884/1.jm.2021.16.2.723

Abstract

Ab-Initio computational method can be used for simulating reaction mechanisms, such as concerted reaction mechanism on peptide synthesis. The concerted reaction is one of many possible pathways on how peptide can be synthesized. The purpose of this study are probing the concerted reaction mechanism and comparing the steric effect to the reaction, given by different side-chain of alanine (A) and proline (P). Two dipeptides formed from alanine and proline were computed at HF-SCF/6-31G** theory level: Ac-AA-NH2 and Ac-AP-NH2. The res.lts show the activation energy of Ac-AA-NH2 and Ac-AP-NH2 forming via concerted pathway are 167.541 kJ/mol and 161.044 kJ/mol, respectively. The steric difference in side-chain affects the dihedral angle of the structure, and also gives difference to the entropy value of reaction.

Highlights

Condensation of amino acids is a crucial reaction in protein chemistry as it represents a key reaction for all life processes
The detailed knowledge of the peptide bond formation mechanism is vital for understanding of various biological processes, and it is a subject of intensive investigations as such
A peptide formation reaction is a reaction between two active groups: the amine (-NH2) group and the carboxylic group (-COOH) from two different amino acids

Summary

Introduction

Condensation of amino acids is a crucial reaction in protein chemistry as it represents a key reaction for all life processes. An essential structural element of all proteins is a peptide bond (C–N), which is formed because of the conjugation between the α-amino group of one amino acid and the α-carboxylic group of another amino acid (Santos et al, 2014). Concerted reaction mechanism is one of possible mechanism propose It has been studied using molecular dynamics approach by Trobro and Aqvist (2005) and further by Wallin and Aqvist (2010), as a process of peptides synthesis occurring at cell level. A peptide formation reaction is a reaction between two active groups: the amine (-NH2) group and the carboxylic group (-COOH) from two different amino acids.

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