Conformational stability and order of Hoogsteen base pair induced by protein binding.
Conformational thermodynamics
DNA-protein interaction
Hoogsteen DNA
Watson-crick DNA
Journal
Biophysical chemistry
ISSN: 1873-4200
Titre abrégé: Biophys Chem
Pays: Netherlands
ID NLM: 0403171
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
received:
19
05
2023
revised:
18
07
2023
accepted:
24
07
2023
medline:
6
9
2023
pubmed:
1
8
2023
entrez:
31
7
2023
Statut:
ppublish
Résumé
Several experimental studies have shown that Hoogsteen (HG) base pair (bp) stabilizes in the presence of proteins. The molecular mechanism underlying this stabilization is not well known. This leads us to examine the stability of the HG bp in duplex DNA using all-atom molecular dynamics simulation in both the absence and presence of proteins. We use conformational thermodynamics to investigate the stability of a HG bp in duplex DNA at the molecular level. We compute the changes in the conformational free energy and entropy of DNA when DNA adopts a HG bp in its bp sequence rather than a Watson-Crick (WC) bp in both naked DNA and protein-bound DNA complex. We observe that the presence of proteins stabilizes and organizes the HG bp and the entire DNA duplex. Sugar-phosphate, sugar-base, and sugar-pucker torsion angles play key roles in stabilizing and ordering the HG bp in the protein-bound DNA complex.
Identifiants
pubmed: 37523944
pii: S0301-4622(23)00130-8
doi: 10.1016/j.bpc.2023.107079
pii:
doi:
Substances chimiques
DNA
9007-49-2
Sugars
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
107079Informations de copyright
Copyright © 2023 Elsevier B.V. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare no conflicts of interest.