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Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field
Version 1
: Received: 4 August 2024 / Approved: 4 August 2024 / Online: 6 August 2024 (05:56:38 CEST)
How to cite:
Burns, W. A.; Lovas, S.; Watts, C. R. Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field. Preprints2024, 2024080268. https://doi.org/10.20944/preprints202408.0268.v1
Burns, W. A.; Lovas, S.; Watts, C. R. Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field. Preprints 2024, 2024080268. https://doi.org/10.20944/preprints202408.0268.v1
Burns, W. A.; Lovas, S.; Watts, C. R. Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field. Preprints2024, 2024080268. https://doi.org/10.20944/preprints202408.0268.v1
APA Style
Burns, W. A., Lovas, S., & Watts, C. R. (2024). Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field. Preprints. https://doi.org/10.20944/preprints202408.0268.v1
Chicago/Turabian Style
Burns, W. A., Sándor Lovas and Charles R. Watts. 2024 "Dynamic Solvent Accessible Surface Areas of Proteogenic a-Amino Acids as a Function of Explored f,y Dihedral Angle Space Modelled using the Ac-Ala-Xaa-Ala-NH2 system and CHARMM36m Force Field" Preprints. https://doi.org/10.20944/preprints202408.0268.v1
Abstract
Solvent accessible surface area (SASA) of amino acid residues plays a significant role in inter-residue, protein-ligand, and protein-protein interactions. Affecting the exposure and interactions of hydrophobic and hydrophilic regions, driving protein folding. While previous SASA calculations are accurate with respect to the chosen parameters of simulation, they do not account for the dynamic behavior of peptides in solution under physiological conditions and cannot be used to compare populations within phi,psi dihedral angle space (phi,psi space). Molecular dynamics trajectories obtained at 310 K, 1 atm, and 150 mM NaCl for the Ac-Ala-Xaa-Ala-NH2 model peptides simulated using the CHARMM36m force field and TIP3Pm water as implemented in GROMACS 2022 were used to study SASA. The more balanced parametrization of CHARMM36m, resulted in increased sampling of beta region compared to alpha, alphaL, and epsilon regions were observed. There are statistically significant differences in SASA for the backbone and side chain comparing the beta, alpha, alphaL, epsilon and contiguous regions of phi,psi space. Differences occur in sampled phi,psi space particularly in the alphaL and epsilon regions of phi,psi space as a function of side chain size and chemical properties. The epsilon region of phi,psi space is not significantly sampled for multiple amino acids while the alphaL region is.
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
