Census of halide-binding sites in protein structures.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 05 2020
01 05 2020
Historique:
received:
24
10
2019
revised:
24
01
2020
accepted:
29
01
2020
pubmed:
6
2
2020
medline:
30
10
2020
entrez:
6
2
2020
Statut:
ppublish
Résumé
Halides are negatively charged ions of halogens, forming fluorides (F-), chlorides (Cl-), bromides (Br-) and iodides (I-). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide-protein interactions, based on the entries in the Protein Data Bank. We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide-protein interactions and assist phasing experiments relying on halides as anomalous scatters. All data described in this article can be reproduced via complied pipeline published at https://github.com/rostkick/Halide_sites/blob/master/README.md. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32022861
pii: 5727755
doi: 10.1093/bioinformatics/btaa079
pmc: PMC7214031
doi:
Substances chimiques
Bromides
0
Iodides
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3064-3071Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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