PREDICTION AND CHARACTERIZATION OF SUBSTRATE SPECIFICITY AND THERMAL STABILITY FOR THERMOSTABLE ALIPHATIC AMIDASES: AN IN-SILICO APPROCH

Abstract

Molecular modeling is a rapidly growing field that uses new data and techniques to control access for trading with computational biology. To decipher the structural integrity of thermophilic amidases, an in silico approach was studied for 14 thermostable amidases from selected different thermophiles to perform the homology modeling. Results of the sequence based characterization showed the presence of higher glutamate and histidine in thermophilic aliphatic amidases as compared to mesophilic aliphatic bacterial amidase and they are conserved at specific position of 205-283. Presence ofmasparagine, glutamine and histidine along with cysteine in a hydrophobic core region provide more stability. These amino acids were found to be higher in amidase from Geobacillus sp. Catalytic triad was found at various helix, which is present in both the aliphatic amidases. These developed models have been considered for the molecular docking simulations to identify the binding affinity of amidases with selected targets (substrates). Malonamide, lactamide and valeramide possessed the minimum binding energy with all the thermophilic targets, which were in the range of 3 to 5 kcal.mol-1 Malonamide demonstrated higher specificity as compared to rest of the docked substrates and was further used for molecular dynamics (MD) simulations to evaluate the binding stability and conformational changes. After 1 nano second (ns) MD study with pre-defined parameters, the structural arrangements of individual atoms have been survived at higher temperature specifically for the Geobacillus sp.