Ukr.Biochem.J. 2015; Volume 87, Issue 5, Sep-Oct, pp. 133-140

doi: https://doi.org/10.15407/ubj87.05.133

New conformational properties of SH2 domain binding pocket

V. V. Hurmach1, M. O. Platonov2, Yu. I. Prylutskyy1

1Taras Shevchenko National University of Kyiv, Ukraine;
2Institute of Molecular Biology and Genetics,
National Academy of Sciences of Ukraine, Kyiv;
e-mail: gyrmach@gmail.com

The conformational changes of proteins play an important role in biological functioning such as ligand-protein and protein-protein interactions. The aim of the work was to investigate the conformational movement of most represented SH2 domains. It was found that SH2 domain binding pocket includes both flexible and not flexible regions: the central area of the binding pocket is the most unflexible, whereas the pTyr-binding and hydrophobic zones are the most flexible. Results of the computer analysis revealed new conformational properties of SH2 domain, which are important for drug design.

Keywords: , ,


References:

  1. Silva CM. Role of STATs as downstream signal transducers in Src family kinase-mediated tumorigenesis. Oncogene. 2004 Oct 18;23(48):8017-23. Review. PubMed, CrossRef
  2. Hurmach VV, Balinskyi OM, Platonov MO, Boyko AN, Borysko PO, Prylutskyy YuI. Design of potentially active ligands for SH2 domains by molecular modeling methods. Biopolym Cell. 2014;30(4):321-325. CrossRef
  3. Hurmach VV, Platonov MO, Boyko OM, Prylutskyy YuI. Comparative analysis of SH2 domain structures. Studia Biologica. 2015;9:5-14.
  4. Hurmach VV, Balinskyi OM, Platonov MO, Boyko OM, Prylutskyy YI. Application of the methods of molecular modeling to the search for new biologically active substances. Ukr Biochem J. 2015 Jan-Feb;87(1):109-20. Ukrainian. PubMed, CrossRef
  5. Pawson T, Gish GD, Nash P. SH2 domains, interaction modules and cellular wiring. Trends Cell Biol. 2001 Dec;11(12):504-11. Review. PubMed, CrossRef
  6. Liu BA, Jablonowski K, Raina M, Arcé M, Pawson T, Nash PD. The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell. 2006 Jun 23;22(6):851-68. PubMed, CrossRef
  7. Andreichenko KS, Prylutska SV, Medynska KO, Bogutska KI, Nurishchenko NE, Prylutskyy YuI, Ritter U, Scharff P. Effect of fullerene C60 on ATPase activity and superprecipitation of skeletal muscle actomyosin. Ukr Biokhim Zhurn. 2013 Mar-Apr;85(2):20-6. PubMed, CrossRef
  8. Corbeil CR, Williams CI, Labute P. Variability in docking success rates due to dataset preparation. J Comput Aided Mol Des. 2012 Jun;26(6):775-86. PubMed, PubMedCentral, CrossRef

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License.