Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach

Year 2023, Volume: 12 Issue: 1, 10 - 16, 22.03.2023

Levent Songur , Oguzhan Orhan , Soner Ozgen

https://doi.org/10.17798/bitlisfen.1146682

Abstract

Accurate determination of the thermodynamic and molecular mechanical properties of amino acids will contribute to a better understanding of their folding mechanisms. In this study, the enthalpy values and molecular mechanics parameters of 17 amino acids were investigated by the classical molecular dynamics method. All calculations were performed using the force-field potential approach. As a result, the calculated solid formation enthalpy for ALA, ASN, ASP, CYS, LYS, and PHE are in good agreement with the experimental data. In addition, molecular mechanics parameters such as Coulomb, bond, angle, dihedral, and Van der Waals were calculated for all amino acids. It is seen that the Coulomb energy is quite low compared to the rest of the molecular mechanical energies. The molecular mechanical energies obtained from the study will contribute to protein-lipid modification studies for electronic interaction, ligand binding to the cell surface, and correct protein localization.

Keywords

Solid formation enthalpy, Molecular Mechanics Energies, Amino Acids, Molecular Dynamics Simulation

Supporting Institution

Management Unit of Scientific Research projects of Firat University (FÜBAP)

Project Number

FF.16.28

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