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Examination of Molecular Dynamic Simulations for Glucokinase (GCK) Mutations in Type 2 Diabetes

An essential aspect of undergraduate biology includes visualization of the relationship between protein structure and function. Glucokinase (GCK) is significant to glucose homeostasis. When mutated, GCK has been demonstrated to play a role in Type II Diabetes, leading to diminished sensitivity to insulin detection. The focus of this project was to create a molecular dynamic simulation that could be used to visualize mutations at residues L25Q, L25R, R36P, V33E, E40K, G44D, M41T, and T49N on GCK and, in turn, illustrate how amino acid substitutions alter the structure and function of GCK. Glucokinase was selected because it is a common protein demonstrated to have mutations suspected of the Type II Diabetes phenotype when screened through Clinvar, Polyphen, Provean, and SIFT. Specific residues were determined as most prevalent and classifiable as “damageable” or “pathogenic” in the impact of affected cellular function upon comparing information from the aforementioned databases. Yet Another Scientific Alternate Reality Application (YASARA) and cloud computing were used to model selected mutations to asses structural changes compared to wild type. Such research and specific use of bioinformatics is important because it has the capacity to consolidate large masses of information from multiple sources and specify the focus for groups working on treatments of particular diseases. Modelling is further useful in communication of disease and amino acid level mutations to patients as it provides visuals to compare wild type and mutated phenotypes of affected proteins. Further research could be conducted on specific perturbations caused by selected GCK variants.