Molecular Modelling of Oryza sativa Starch-branching Enzyme 1

Abstract

Starch-branching enzymes (SBE) serves as the only enzyme generating glucan branches in green plants and consequently plays a significant role on the resulting starch final structure. Research on rice (Oryza sativa) SBE1 (OsSBE1) structural biology remain untapped. Therefore, there is a necessity for research on the enzyme molecular structure which could lead to the protein function annotation, starch production and energy booster drug design. Analysis of OsSBE1 secondary structure, domains and their interactions, enzyme 3D structure prediction and validation based on C-score were carried out. The OsSBE1 primary sequence was retrieved from GenBank and its secondary structure was predicted to be; α-helix (27.68%), extended strand (22.78%) and higher random coil (949.54%). Enzyme domains were found to be carbohydrate-binding module (CBM) 48 (isoamylase N-terminal domain), α-amylase catalytic domain and α-amylase C-terminal all-beta domain with active sites important amino acids asparagine and glutamic acid. From the five 3D models generated, model 3 displayed best prediction. The Ramachandran refinement has 97.3 amino acids residues in favoured region and 0.4 C-score. This bioinformatics study has elucidated on the OsSBE1 molecular model and first to report on its domain interaction.

Prediction and Validation of 3-Dimensional Structure of Rice OsTHIC Abiotic Stress Responsive Gene

“…The OsTHIC protein full-length sequences from the GeneBank were analyzed using BLASTp algorithm. Then, later translated the protein sequence to nucleotides using ExPASy [http://web.expasy.org/translate/] as earlier described by Mohammed, Ndejiko [9].…”

“…Moreover, the I-TASSER server was discovered to provide more quality models and good viewing, albeit, a complex formulation used in the last two CASP experiments. The server is an integrated program for automated protein 3-dimensional modelling, prediction and determinant of their functions based on the sequence-to-structure to function paradigm [9,18]. The 3D model is used to determine the biological function of protein building blocks, as well as describe the interaction of proteinligand or protein-protein.…”

“…A Similar was reported by Rabbani, Maruyama [8] who demonstrated the overlap between abiotic stresses during gene expression. In recent years, cellular and molecular mechanisms have attracted more attention in providing more details information on any biological activity [9,10].…”