An Experimental Tool to Estimate the Probability of a Nucleotide Presence in the Crystal Structures of the Nucleotide–Protein Complexes View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2017-06

AUTHORS

Maria Nemchinova, Vitaly Balobanov, Ekaterina Nikonova, Natalia Lekontseva, Alisa Mikhaylina, Svetlana Tishchenko, Alexey Nikulin

ABSTRACT

A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide-protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide-protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant <10 μM. At KD of 20-40 μM, long incubation of the protein crystals in the nucleotide solution is required to obtain the structures of the complexes. The complexes with KD value higher than 50 μM are not stable enough to survive in crystallization conditions. More... »

PAGES

157-165

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s10930-017-9709-y

DOI

http://dx.doi.org/10.1007/s10930-017-9709-y

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1084504003

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28317076


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s10930-017-9709-y'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s10930-017-9709-y'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s10930-017-9709-y'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s10930-017-9709-y'


 

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