Date of Publication
9-2022
Document Type
Bachelor's Thesis
Degree Name
Bachelor of Science in Premed Physics
Subject Categories
Physics
College
College of Science
Department/Unit
Physics
Thesis Advisor
Romeric F. Pobre
Glenn G. Oyong, co-adviser
Defense Panel Chair
Melanie Y. David
Defense Panel Member
Mariquit M. De Los Reyes
Ric John L. Ombid
Abstract/Summary
This study used an in-silico approach to investigate the molecular interaction between D-dimer and Glycoprotein VI (GPVI) in blood plasma as a potential biomarker for ischemic stroke. GPVI underwent structural validation through Ramachandran Plot, ERRAT, and Verify 3D. Preliminary results showed that GPVI attained a high-quality structural fidelity for molecular docking with high level of accuracy after validation. ClusPro 2.0 was used to dock D-dimer in GPVI whereas Discovery Studio 2021 Client was used to view the interactions between GPVI and D-dimer. It showed that the interactions of the amino acids between the two aforementioned molecules are mostly dominated by intermolecular forces from the Van der Waals and electrostatic forces arising from the hydrogen bonds and hydrophobic bonds. Moreover, to determine the stability of the GPVI - D-dimer bonding, molecular dynamics simulation was undertaken through CABS-Flex 2.0. Visual results with a time step size of 10 nanoseconds showed minimal fluctuations on the receptor-ligand complex with no significant difference (p = 0.54797) between the unbound GPVI and bound GPVI using statistical T-test analysis. Thus, computer simulation has demonstrated that GPVI's structural integrity remained invariant when bounded with D-dimer. This strongly suggests that the stable receptor- ligand complex formed by GPVI, and D-dimer is indicative of a potential biomarker candidate for ischemic stroke in blood plasma. For further in-silico studies, surface plasmon resonance (SPR) can also be considered to validate the results in addition to placing water solvent background in the receptor-ligand complex formed by GPVI and D-dimer.
Abstract Format
html
Language
English
Format
Electronic
Physical Description
xii, 102 leaves
Keywords
Protein-protein interactions; Glycoproteins; Blood plasma
Recommended Citation
de Ramos, B. R., & Ruivivar, K. B. (2022). In silico study on the protein-protein interaction of D-dimer and glycoprotein VI in blood plasma as potential biomarker of ischemic stroke. Retrieved from https://animorepository.dlsu.edu.ph/etdb_physics/15
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Embargo Period
9-23-2022
