Open AccessCOMPUTER SIMULATION OF GLICOPHORIN A AND 4-METHYL-2,6-DIISOBORNILFENOL INTERACTION BY AUTODOCK AND HEXSERVER PROGRAMS
Author(s) -
Ольга Ивановна Острикова
Publication year - 2014
Publication title -
bûlletenʹ sibirskoj mediciny
Language(s) - English
Resource type - Journals
eISSN - 1819-3684
pISSN - 1682-0363
DOI - 10.20538/1682-0363-2014-5-62-66
Subject(s) - glycophorin , autodock , chemistry , molecular dynamics , docking (animal) , interaction energy , computer science , molecular model , molecule , computational chemistry , stereochemistry , biochemistry , membrane , in silico , organic chemistry , medicine , nursing , gene
4-methyl-2,6-diisobornilphenol (dibornol) – a promising drug with a hemorheological activity. Glycophorin A is one of erythrocyte membrane proteins involved in the aggregation and possibly mediating rheological effects of dibornol. Objective: to conduct a modeling of the interaction dibornol and glycophorin A by AutoDock and HexServer programs. Material and methods. We used three-dimensional models of molecules dibornol and glycophorin A. Information on the three-dimensional model of glycophorin A was received from the database RCSB Protein Data Bank – 1AFO. Modeling the three-dimensional model of a dibornol (4-methyl-2,6- diisobornilfenol) was modeling by PRODRG Server. Results. This paper presents the results of computer modeling of interaction dibornol and glycophorin A by HexServer and AutoDock programs. We used the electrostatic properties of the molecule glycophorin A, site of interaction is position chain A VAL83, chain B – ALA82, GLY83, GLY86, THR87. The energy of binding was –6.73 kcal/mol by AutoDock program, HexServer – –2.89 kcal/mol. The charge of the molecular complex dibornol-glycophorin A decreased to –4.126 (the charge of the native molecule glycophorin A – –4.003). Conclusion. Integrated use of the program AutoDock and HexServer helps significantly reduce the time and computational resources in the modeling. The study identified the amino acids that may play a key role in the interaction with dibornol glycophorin A. This study has given us reason to believe that as a result of such interaction dibornol may prevent adhesion of red blood cells.