Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins.
Journal
ACS omega
ISSN: 2470-1343
Titre abrégé: ACS Omega
Pays: United States
ID NLM: 101691658
Informations de publication
Date de publication:
30 Jun 2020
30 Jun 2020
Historique:
received:
25
03
2020
accepted:
13
05
2020
entrez:
9
7
2020
pubmed:
9
7
2020
medline:
9
7
2020
Statut:
epublish
Résumé
We developed a novel force field in the context of AMBER parameterization for glutamate and aspartate zinc(II)-binding residues. The interaction between the zinc ion and the coordinating atoms is represented by a spherical nonbonded parameterization. The polarization effect due to the zinc ion has been taken into account by redefining the atomic charges on the residues through accurate quantum mechanical calculations. The new zinc-binding ASP and GLU residues, along with the CYS and HIS zinc-binding residues, parameterized in a recent work [Macchiagodena M.;J. Chem. Inf. Model.2019, 59, 3803-3816], allow users to reliably simulate 96% of the Zn-proteins available in the Protein Data Bank. The upgraded force field for zinc(II)-bound residues has been tested performing molecular dynamics simulations with an explicit solvent and comparing the structural information with experimental data for five different proteins binding zinc(II) with GLU, ASP, HIS, and CYS. We further validated our approach by evaluating the binding free energy of (
Identifiants
pubmed: 32637803
doi: 10.1021/acsomega.0c01337
pmc: PMC7331063
doi:
Types de publication
Journal Article
Langues
eng
Pagination
15301-15310Informations de copyright
Copyright © 2020 American Chemical Society.
Déclaration de conflit d'intérêts
The authors declare no competing financial interest.
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