Study On The Three Dimensional Structure Of Cyclodextrins Interact With Coffee-bean ?-Galactosidase

In order to further understand the structure of coffee-bean ?-galactosidase,this thesis carried on the theoretical analysis and the forecast of physical and chemical properties,secondary structure and three-dimensional structures.The three-dimensional structures of coffee-bean ?-galactosidase were constructed by homology modeling.Analysis of the primary structure found that its main peptide chain is composed of 378 amino acids,molecular weight is 41.31 kDa,total number of atoms is 5708,isoelectric point is 5.60.The coffee-bean ?-galactosidase is hydrophilic,water,and stable.N-terminal is M(Met).In all of the amino acids composed of coffee-bean ?-galactosidase,maximum content is Serine for 9.5%,minimum value is Cysteine and Histidine for 1.6%.Hydrophobic amino acid residues of the enzyme is 124,hydrophilic amino acid residues of the enzyme is 254,no transmembrane region,all 378 amino acid residues are within the cell membrane,and there is no signal peptide.Secondary structure analysis found that the coffee-bean ?-galactosidase was dominated by ?-helices and random coils,the ?-helices and random coils exist alternately.This distribution is helpful for the stability of coffee-bean ?-galactosidase.Through sequence search and comparison,the three-dimensional structures of coffee-bean ?-galactosidase were constructed based on the template of rice ?-galactosidase by homology modeling because their spatial structures were similarity.After homology modeling the three-dimensional structure shows that the coffee-bean ?-galactosidase contains 8 ?-helices and 16 ?-turns,8 ?-helices is located in one side of the structure,forming a globular structure,8 ?-turns parallel to each other inside the sphere structure,and the other 8 ?-turns in the other side of the structure.Comprehensive evaluation shows that it conforms to the rules of stereochemistry,modeling structure is reasonable.This structure model can serve as the basis of molecular docking,at it can also provided the theoretical basis for the study on the spatial structure and catalytic site of coffee-bean ?-galactosidase.The molecular mechanisms of interactions between coffee-bean ?-galactosidase and three cyclodextrins,including alpha-cyclodextrin,beta-cyclodextrin and gamma-cyclodextrin,were studied in detail by molecular docking.To analyze the calculating results,?-cyclodextrin has covered the active cavity of coffee-bean ?-galactosidase,formed two hydrogen bonds of coffee-bean ?-galactosidase,one is Trp31 with methylene in ?-galactosidase,another is Asp200 with methylene in ?-galactosidase;part of ?-cyclodextrin has entered the active cavity of coffee-bean ?-galactosidase,formed three hydrogen bonds of coffee-bean ?-galactosidase,one is Trp179 with methane in ?-cyclodextrin,the other two is Asp200 with methane in ?-cyclodextrin;?-cyclodextrin has covered the active cavity of coffee-bean ?-galactosidase,formed two hydrogen bonds of coffee-bean ?-galactosidase,one is Trp31 with methylene in ?-galactosidase,another is Asp200 with methylene in ?-galactosidase.Calculating results showed that Trp31,Trp179,and Asp200 in coffee-bean ?-galactosidase were the key amino acid residues in the active pocket.Hydroxyls of the methylene and the methane in cyclodextrins were the key groups.Cyclodextrins inhibit coffee-bean ?-galactosidase through hydrophilic interactions.Beta-cyclodextrin is the most potent inhibitor of ?-galactosidase among the three cyclodextrins.The molecular docking results provide a theoretical basis for the research about enzymatic inhibitor interaction ?-galactopyranosyl-cyclodextrin.