Molecular Dynamics Modeling of Potential Osteoarthritic Biomarkers

Osteoarthritis (OA) is one of the most common forms of arthritis and is commonly characterized by the breakdown of the hyaline cartilage and synovial fluid in joints. The body naturally responds by releasing proteins with specific functions to combat the degradation of the joint. The objective of the research undertaken in this study was to simulate a selection of these proteins from previous work in the literature to gather data on their energies. This was accomplished using the molecular dynamics software NAMD and VMD, in which each protein was simulated for 5 ps in water at three different temperatures. The simulations showed that at body temperature, orosomucoid-1 and complement component 4B had energies that stabilized significantly faster than the other proteins simulated, and alpha-2-macroglobulin had energies that stabilized significantly slower than the others. These outliers were further investigated by simulating them for 1 ns to reveal their molecular dynamics. Based on the data collected, it was proposed that the proteins that had faster stabilization times would be more stable biomarkers overall. Despite any limitations of the research performed, the novel work performed here provides a foundation for future work that could give clinical insight into the diagnosis and prognosis of individuals experiencing symptoms associated with osteoarthritis.