In-silico study: Kistomin as anti-coagulant (two-dimensional structure)

Abstract

Kistomin was metalloproteinase, homodimer structure and dominated α-helix residues. Kistomin interacts with several platelet receptors. The aim of the study is to determine the role of the secondary structure of kistomin to interact with reseptor platelet GPVI, GPIb-IX-V and Integrin αIIbβ3 by computation method. Protein collection of Kistomin, GPVI, GPIB-IX, and integrin αiibβ3 and abiciximab complexes was used RSCB PDB and UNIPROT database. Then, GPV squences was modeller with SwissProt modeller. Protein preparation was carried out with ligand and water molecule. Then, cutting Kistomin protein and integrin αiibβ3 with Abiciximab complex. Docking was started with the formation of the GPIB-IX and GPV complexes. Then continued docking between kistomin and abiciximab with the third receptor. Simulation docking was done with Hex 8.0 software, then changed correlation type to shape+electro with other parameter as default. Visualisation was used with Ligplot V.1.4.5. An α-helix and a turn of α-helix residues of kistomin bound with GPVI and Integrin αiibβ3 by hydrogen bond, hydrophobic bond and salt bridges. Abiciximab bound with GPVI, GPIb-IX-V and Integrin αiibβ3 by hydrogen bond, hydrophobic bond and salt bridges by β-sheet residues. The α-heliks residues in kistomin plays an important role to interact with platelet receptor. The target of kistomin was protein which have a few α-helix residues. In future studies, interaction kistomin with other protein can be investigated