Characterization of surface binding sites in glycoside hydrolases: A computational study. Issue 9 (15th March 2017)

• Record Type: Journal Article
• Authors: Samaei‐Daryan, Samaneh; Goliaei, Bahram; Ebrahim‐Habibi, Azadeh
• Is Part Of: Journal of molecular recognition. Volume 30:Issue 9(2017)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2017-03-15
• Subjects: glycoside hydrolases -- non catalytic binding sites -- secondary binding sites; Molecular recognition -- Periodicals; Models, Molecular -- Periodicals; Molecular Conformation -- Periodicals; Molecular Sequence Data -- Periodicals; Molecular Structure -- Periodicals; Carrier Proteins -- Periodicals; 572.8
• DOI: 10.1002/jmr.2624
• Languages: English
• ISSNs: 0952-3499

Abstract

Abstract: Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty‐five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut‐off differences in each SBSs with different ligand size, molecular docking were performed. Molecular docking results were used to refine SBSs classification and binding sites cut‐off. Docking results predicted putative ligands positions and displayed dependence of the ligands binding mode to the structural type of SBSs. Physicochemical properties of SBSs were calculated for all docking results with YASARA Structure. The results showed that all SBSs are hydrophilic, while their charges could vary and depended to ligand size and defined cut‐off. Surface binding sites type B had highest average values of solvent accessible surface area. Analysis of interactions showed that hydrophobic interactions occur more than hydrogen bonds, which is related to the presence of aromatic residues and carbohydrates interactions. Abstract : A dataset was prepared with the PDB IDs of glycoside hydrolyses bound to carbohydrates on their surface‐binding sites (SBSs). Surface‐binding sites were categorized in 3 groups on the basis of their shapes: flat surfaces, clefts, and small cavities. Physicochemical properties were computed for each category. Molecular docking was used to refine SBSs classification and binding sites cut‐off. Docking results predicted putative ligands positions and showed dependence of the ligands binding mode to the structural type of SBSs.