Coarse-grained potential for hydrogen bond interactions.
Coarse grain methods
Hydrogen bond
Mean field force filed
Protein modeling
Journal
Journal of molecular graphics & modelling
ISSN: 1873-4243
Titre abrégé: J Mol Graph Model
Pays: United States
ID NLM: 9716237
Informations de publication
Date de publication:
11 2023
11 2023
Historique:
received:
23
01
2023
revised:
12
04
2023
accepted:
18
04
2023
medline:
14
8
2023
pubmed:
10
6
2023
entrez:
9
6
2023
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 37295157
pii: S1093-3263(23)00105-5
doi: 10.1016/j.jmgm.2023.108507
pii:
doi:
Substances chimiques
Amyloid beta-Peptides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
108507Informations de copyright
Copyright © 2023 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.