Coarse-grained potential for hydrogen bond interactions

Justyna D Kryś; Dominik Gront

doi:10.1016/j.jmgm.2023.108507

Coarse-grained potential for hydrogen bond interactions

J Mol Graph Model. 2023 Nov:124:108507. doi: 10.1016/j.jmgm.2023.108507. Epub 2023 May 23.

Authors

Justyna D Kryś¹, Dominik Gront²

Affiliations

¹ Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland. Electronic address: jkrys@chem.uw.edu.pl.
² Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.

PMID: 37295157
DOI: 10.1016/j.jmgm.2023.108507

Abstract

Understanding protein structure and dynamics is crucial for investigating numerous biological processes. This however requires proper description of molecular interactions, most notably hydrogen bonds, which are the driving force behind the folding of protein sequences into working molecules. Due to the multi-body character of this interaction, proper mathematical formulation has been a matter of long debate in the literature. This description becomes even more complex in reduced protein models. In this contribution, we propose a novel hydrogen bond energy function definition that is based only on Cα positions and used for coarse-grained simulations. We show that this new method has the capability to recognize hydrogen bonds with over 80% accuracy and can successfully identify β-sheet in β-amyloid peptide simulations.

Keywords: Coarse grain methods; Hydrogen bond; Mean field force filed; Protein modeling.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amyloid beta-Peptides* / chemistry
Hydrogen Bonding
Molecular Dynamics Simulation*

Substances

Amyloid beta-Peptides