Molecular modeling, docking and dynamics studies of fenugreek (<i>Trigonella foenum-graecum</i>) α-amylase
Creators: name: Kumar, Avinash
name: Singh, Vinay Kumar
name: Kayastha, Arvind M.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: α-Amylase catalyses the hydrolysis of glucosidic bonds in polysaccharides such as starch, glycogen and their degradation products. In the present study, the three-dimensional structure of fenugreek (<i>Trigonella foenum-graecum</i>) α-amylase was determined using a homology modeling-based technique. The best predicted model was deposited in PMDB server with PMDB ID PM0084364. The phylogenetic tree was created using the UPGMA method with 8 homologous protein sequences, <i>Trigonella foenum-graecum</i> was utilized as the target protein. Alignment of the phylogenetic tree identified two primary functional groupings (A and B). α-Amylase from the target genome <i>Trigonella foenum-graecum</i> (Acc. No: GHNA01022531.1) was clustered with <i>Medicago truncatula</i> (Acc. No: XP003589186.1), <i>Cicer arietinum</i> (Acc. No: XP004499059.1), <i>Cajanus cajan</i> (Acc. No: XP020231823.1), <i>Vigna angularis</i> (Acc. No: NP001316768.1) and <i>Vigna mungo</i> (Acc. No: P17859.1), in group A cluster, while <i>Hordeum vulgare</i> (Acc. No: Q40015) and <i>Oryza sativa</i> (PDB ID: 3WN6) were in cluster B. The molecular dynamics simulations were performed to understand the molecular basis and mode of action of <i>Trigonella foenum-graecum</i> α-amylase. Additionally, a geometry-based molecular docking technique was used to evaluate potential binding interactions between the modeled structure of α-amylase and maltose. The results show that Trp<sup>228</sup>, Glu<sup>226</sup>, Arg<sup>199</sup>, His<sup>308</sup>, Tyr<sup>165</sup>, Asp<sup>309</sup>, Phe<sup>202</sup> and Asp<sup>201</sup> from <i>Trigonella foenum-graecum</i> α-amylase enzyme is involved in the binding to the substrate maltose. Our study provides a 3D model of <i>Trigonella foenum-graecum</i> α-amylase and aids in understanding the atomic level molecular underpinnings of the mechanism of α-amylase interaction with substrate maltose. Ca<sup>2+</sup> are essential for the stability of domain B since they are connected to it. Ca<sup>2+</sup> site ligands are Asp<sup>139</sup>, Glu<sup>130</sup>, Thr<sup>133</sup>, Asp<sup>135</sup> and Gly<sup>131</sup> residues.
HIGHLIGHTSIn <i>silico</i> analysis, gene prediction of α-amylase was carried from <i>Trigonella foenum-graecum</i>.Analysis of the structure of α-amylase was carried out using homology modelling.Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019.The molecular interaction between <i>Trigonella foenum-graecum</i> α-amylase and maltose was studied in <i>silico</i> using a molecular docking-based method.To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019. In <i>silico</i> analysis, gene prediction of α-amylase was carried from <i>Trigonella foenum-graecum</i>. Analysis of the structure of α-amylase was carried out using homology modelling. Calcium binding sites and their interactions with α-amylase were visualised using BIOVIA DISCOVERY STUDIO 2019. The molecular interaction between <i>Trigonella foenum-graecum</i> α-amylase and maltose was studied in <i>silico</i> using a molecular docking-based method. To give the required simulation parameters, RMSD, RMSF, and Total Energy were calculated using BIOVIA DISCOVERY STUDIO 2019. Communicated by Ramaswamy H. Sarma