Open AccessMolecular dynamic simulations reveal suboptimal binding of salbutamol in T164I variant of β2 adrenergic receptor
Author(s) -
Srinivas Bandaru,
Mallika Alvala,
Anuraj Nayarisseri,
Saphy Sharda,
Himshikha Goud,
Hema Prasad Mundluru,
Sanjeev Kumar Singh
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0186666
Subject(s) - molecular dynamics , opls , docking (animal) , force field (fiction) , salbutamol , chemistry , ligand (biochemistry) , receptor , binding site , biophysics , stereochemistry , computational chemistry , biochemistry , biology , physics , medicine , nursing , quantum mechanics , water model , asthma , immunology
The natural variant C491T (rs1800088) in ADRB2 gene substitutes Threonine to Isoleucine at 164 th position in β2AR and results in receptor sequestration and altered binding of agonists. Present investigation pursues to identify the effect of T164I variation on function and structure of β2AR through systematic computational approaches. The study, in addition, addresses altered binding of salbutamol in T164I variant through molecular dynamic simulations. Methods involving changes in free energy, solvent accessibility surface area, root mean square deviations and analysis of binding cavity revealed structural perturbations in receptor to incur upon T164I substitution. For comprehensive understanding of receptor upon substitution, OPLS force field aided molecular dynamic simulations were performed for 10 ns. Simulations revealed massive structural departure for T164I β2AR variant from the native state along with considerably higher root mean square fluctuations of residues near the cavity. Affinity prediction by molecular docking showed two folds reduced affinity of salbutamol in T164I variant. To validate the credibility docking results, simulations for ligand-receptor complex were performed which demonstrated unstable salbutamol-T164I β2AR complex formation. Further, analysis of interactions in course of simulations revealed reduced ligand-receptor interactions of salbutamol in T164I variant. Taken together, studies herein provide structural rationales for suboptimal binding of salbutamol in T164I variant through integrated molecular modeling approaches.