Study on binding modes between cellobiose and β-glucosidases from glycoside hydrolase family 1.
The hydrolysis of cellobiose by β-glucodisases is an important step of cellulose biodegradation. However, the interactive mechanism between cellobiose and β-glucosidases is still unclear until now. Thus, in this study, we explored the binding modes between cellobiose and three β-glucosidases from glycoside hydrolase family 1 by means of molecular docking. The three β-glucosidases were named as TmGH1 (from bacterium Thermotoga), SsGH1 (from archaea Sulfolobus solfataricus) and TrGH1 (from fungus Trichoderma reesei) respectively, according to the monophyletic groups they belong to. Molecular dockings were performed between cellobiose and the three β-glucosidases, resulting in three optimum docking complexes, that is TmGH1-cellobiose, SsGH1-cellobiose and TrGh1-cellobiose complexes. Our docking results indicated that there were non-bonded interactions between cellobiose and the three β-glucosidases. The binding affinities of the three complexes were -13.6669kJ/mol, -13.2973kJ/mol and -18.6492kJ/mol, respectively. Then the detailed interactions were investigated, which revealed the key amino acid residues interacted with cellobiose by hydrogen bonds (H-bonds) or hydrophobic interactions. It was observed that most of the key residues involved in the non-bonded interactions were equivalent and conserved for the three complexes, and these residues were a glutamine, a histidine, a tyrosine, a phenylalanine, three glutamics, and four tryptophans. This information is of great importance for designing β-glucosidase with higher cellobiose-hydrolyzing efficiency.
College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, China.
Lifeng
L
Liu
Zhuotong
Z
Zeng
Guangming
G
Zeng
Ming
M
Chen
Yu
Y
Zhang
Jiachao
J
Zhang
Xin
X
Fang
Min
M
Jiang
Lunhui
L
Lu
D000595:Amino Acid Sequence; D001665:Binding Sites; D002475:Cellobiose / Q000737:chemistry* / Q000378:metabolism; D044602:Cellulases / Q000737:chemistry* / Q000378:metabolism; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D016415:Sequence Alignment
D002475:Cellobiose; D044602:Cellulases; D006026:Glycoside Hydrolases