ArticleBioinformatics (Oxford, England)2020
Census of halide-binding sites in protein structures.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 22 citations in OpenAlex.
- Peptidic Catalysts Conformationally Tuned for Fluoride Binding and Delivery.Journal of the American Chemical Society · 2026Article
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- Structural mechanisms of human sodium-coupled high-affinity choline transporter CHT1.Cell discovery · 2024Article
- Cryo-EM structures of the human band 3 transporter indicate a transport mechanism involving the coupled movement of chloride and bicarbonate ions.PLoS biology · 2024Article
- Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues.The Journal of organic chemistry · 2024Article
- Human Saposin B Ligand Binding and Presentation to α-Galactosidase A.bioRxiv : the preprint server for biology · 2024Article
- Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin.Biophysical journal · 2023Article
- A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion.Biology · 2022Article
- Siderophore Synthesis Ability of the Nitrogen-Fixing Bacterium (NFB) GXGL-4A is Regulated at the Transcriptional Level by a Transcriptional Factor (trX) and an Aminomethyltransferase-Encoding Gene (amt).Current microbiology · 2022Article
- Forchlorfenuron and Novel Analogs Cause Cytotoxic Effects in Untreated and Cisplatin-Resistant Malignant Mesothelioma-Derived Cells.International journal of molecular sciences · 2022Article
- Article
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationHalides 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.
resultsWe 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. AVAILABILITY AND IMPLEMENTATION: 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 INFORMATION: Supplementary data are available at Bioinformatics online.
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