The Structure Analysis Of Pinellia Ternata Agglutinin And Molecular Simulation Study

The current research on Pinellia ternata agglutinin (PTA) was concentrated in geneexpression, protein purification and identification of biological activity. However, the studiesabout structural analysis of PTA and molecular simulation were relatively less. In this paper, weanalyzed the sequence information, constructed homology model and prepared moleculardocking to study the structural characteristics of PTA.Firstly, retrieved PTA protein sequence information from the NCBI protein database, usingExpasy, SMART, CBS and other bioinformatics prediction software to comprehensivelyanalyzed the protein primary structure, senior structure and biological function of agglutinin. Thesecondary Structural information analysis told us PTAs contained16α-helices,91β-strands and150random coils. The domain-containing analysis indicated that there were two representativeB-type lectin domains in PTA, and each domain contained conserved mannose binding sites.These protein binding sites were almost located outside of the space configuration.We took Remusatia vivipara as a template to build PTA homology model on Swiss-modelby homology modeling procedures and used QMEAN and PROCHECK tools to optimize thestructure of the model. Surface properties of structural showed that the three-dimensional surfaceelectrostatic potential was low, and solvent accessibility was very highly.The molecule docking experiment between PTA and ligand illustrated molecule bindingmechanism. Experimental results showed that the binding force of non-mannose typeD-glucose, N-acetylglucosamine combinated with PTA were lower than D-mannose. And thecapacity of α1,3glycosidic bond or α1,6glycosidic linkage polysaccharide mannose bindingPTA increased with the number of glycoside. This result showed that the impact of thepolysaccharide mannose binding PTA through glycosidic bond form and the number ofglycosidic bonds. PTA can connect with28s rRNA, Thyroglobulin, Methyltransferase enzymecomplex protein50, HIV viral capsid protein to form stable complexes. The N-terminal domainof PTA binding position in the major groove of28s rRNA single-stranded, blocking thereplication of RNA. PTA’ N-terminal domain had the capable of specifically binding TYR213~ASP298domain on MEP50protein, inhibiting MEP50methyl transferase activity. HIV viruscapsid protein connected with PTA’ N-terminal domain to form stable complexes, the compositeblocks HIV virus capsid assembly, thereby inhibiting the replication of HIV.In this article, we simulated and analyzed the structure characteristics of PTA by homology modeling and molecular docking. It made a beneficial reference to elucidate molecularinteraction mechanisms between functional molecular and PTA, and validate the biologicalfunction of PTA.