The Protein Journal

, Volume 36, Issue 3, pp 157–165 | Cite as

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

  • Maria Nemchinova
  • Vitaly Balobanov
  • Ekaterina Nikonova
  • Natalia Lekontseva
  • Alisa Mikhaylina
  • Svetlana Tishchenko
  • Alexey NikulinEmail author


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.


Nucleotide–protein interactions RNA–protein interactions Equilibrium dissociation constant Fluorescence anisotropy Protein crystallography Transcription factors 



Single-stranded RNA










Equilibrium dissociation constants


Sm-like archaeal protein


Sm-like archaeal protein from Sulfolobus solfataricus


Sm-like archaeal protein from Methanococcus jannaschii


Protein Hfq from Escherichia coli


Protein Hfq from Pseudomonas aeruginosa


Gamma subunit of archaeal initiation factor aIF2γ from S. solfataricus


Sm-like proteins



This work was supported by RSF grant #14-14-00496.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Institute of Protein Research RASPushchinoRussian Federation

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