title: Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase.
abstract: With consumers growing increasingly aware of environmental issues, industries find enzymes as a reasonable alternative over physical conditions and chemical catalysts. Amylases are important hydrolase enzymes, which have been widely used in variety of industrial process such as pharmaceutical, food, and fermentation industries. Among amylases α-Amylase is in maximum demand due to its wide range of applications. The homology modeling study on Schwanniomyces occidentalis amylase (AMY1, UniProt identifier number: P19269) was performed by Modeller using Aspergillus oryzae (6TAA) as the template. The resulting structure was analyzed for validity and subjected to 14 ns of molecular dynamics (MD) simulation trough GROMACS. The validity of obtained model may represent that utilized OPLS force field is suitable for calcium-containing enzymes. DSSP secondary structure and contact map analysis represent the conservation of domain A TIM barrel feature together with calcium ion coordination sphere. Investigating the covariance matrix followed by principle component analyses for the first five eigenvectors of both trajectories indicate a little more flexibility for AMY1 structure. The electrostatic calculation for the final structures shows similar isoelectric point and superimposed buffering zone in the 5-8 pH range.
authors.affiliation: a Protein Research Center, Shahid Beheshti University , G.C., Velenjak, Tehran , Iran.|b Biological Engineering Laboratories (BEL), Faculty of New Technologies and Energy Engineering, Biotechnology Department , Shahid Beheshti University , Velenjak, Tehran , Iran.
authors.forename: Yahya
authors.initials: Y
authors.lastname: Sefidbakht
authors.affiliation: a Protein Research Center, Shahid Beheshti University , G.C., Velenjak, Tehran , Iran.|b Biological Engineering Laboratories (BEL), Faculty of New Technologies and Energy Engineering, Biotechnology Department , Shahid Beheshti University , Velenjak, Tehran , Iran.
authors.forename: Omid
authors.initials: O
authors.lastname: Ranaei Siadat
authors.affiliation: a Protein Research Center, Shahid Beheshti University , G.C., Velenjak, Tehran , Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Taheri
mesh_terms: D000595:Amino Acid Sequence; D006863:Hydrogen-Ion Concentration; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D000072417:Protein Domains; D054730:Protein Interaction Domains and Motifs; D004718:Saccharomycetales / Q000201:enzymology*; D000516:alpha-Amylases / Q000737:chemistry*
chemical_list: D000516:alpha-Amylases
keywords: Schwanniomyces occidentalis; alpha-amylase; homology modeling; molecular dynamics