Census of halide-binding sites in protein structures

Rostislav K Skitchenko, Dmitrii Usoltsev, Maya Uspenskaya, Andrey V Kajava, Albert Guskov*

*Corresponding author voor dit werk

OnderzoeksoutputAcademicpeer review

16 Citaten (Scopus)
152 Downloads (Pure)

Samenvatting

Motivation: 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.

Results: 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.

Originele taal-2English
Pagina's (van-tot)3064-3071
Aantal pagina's8
TijdschriftBioinformatics (Oxford, England)
Volume36
Nummer van het tijdschrift10
Vroegere onlinedatum5-feb.-2020
DOI's
StatusPublished - 15-mei-2020

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