Hydrophilic Aromatic Residue and in silico Structure for Carbohydrate Binding Module

Wei-Yao Chou,Wei-I Chou,Tun-Wen Pai,Margaret Dah-Tsyr Chang,Chuan-Yi Tang,Ting-Ying Jiang,Andreas Hofmann

doi:10.1371/journal.pone.0024814

Wei-Yao Chou, Wei-I Chou + Show 5 more

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https://doi.org/10.1371/journal.pone.0024814

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Abstract

Carbohydrate binding modules (CBMs) are found in polysaccharide-targeting enzymes and increase catalytic efficiency. Because only a relatively small number of CBM structures have been solved, computational modeling represents an alternative approach in conjunction with experimental assessment of CBM functionality and ligand-binding properties. An accurate target-template sequence alignment is the crucial step during homology modeling. However, low sequence identities between target/template sequences can be a major bottleneck. We therefore incorporated the predicted hydrophilic aromatic residues (HARs) and secondary structure elements into our feature-incorporated alignment (FIA) algorithm to increase CBM alignment accuracy. An alignment performance comparison for FIA and six others was made, and the greatest average sequence identities and similarities were achieved by FIA. In addition, structure models were built for 817 representative CBMs. Our models possessed the smallest average surface-potential z scores. Besides, a large true positive value for liagnd-binding aromatic residue prediction was obtained by HAR identification. Finally, the pre-simulated CBM structures have been deposited in the Database of Simulated CBM structures (DS-CBMs). The web service is publicly available at http://dscbm.life.nthu.edu.tw/ and http://dscbm.cs.ntou.edu.tw/.

Highlights

Carbohydrate-binding modules (CBMs) are structural domains found within polysaccharide-targeting enzymes but do not contain the active sites
When the positions of the conserved hydrophilic aromatic residues (HARs) and the secondary structure elements of CBMs were integrated into a feature-incorporated alignment (FIA) algorithm [21], we found an,5% improvement in the average sequence similarity and identity compared with target-template alignments obtained using six leading alignment algorithms
Functional correlation The goal of this work reported was to establish reliable in silico structures for CBMs by improving the target-template sequence alignment procedure and template filter steps

Summary

Introduction

Carbohydrate-binding modules (CBMs) are structural domains found within polysaccharide-targeting enzymes but do not contain the active sites. Regardless of the three types, aromatic residues contribute to stacking interactions with the sugar rings leading to van der Waals interactions and the side chain of polar residues may provide hydrogen bonds with the sugar ligand [10]. Despite of their low sequence identity, CBMs are structurally characterized by a b-sandwich fold and seven fold types have been observed: b-sandwich, b-trefoil, cysteine knot, unique, OB fold, hevein fold and hevein-like fold [7]. Bsandwich and b-trefoil foldings are found in most CBM families

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