Coils to β-sheets transitions and simulated structural interactions in human SOX4 and syntenin protein: An in silico insight into the cytological regulation: Computational approach for determination of the cell fate in humans

Abstract

SOX4; a crucial human protein acts as a transcriptional regulator for accurately determining the cytological regulations in human beginning from the embryonic development. It thus is aided by its only binding protein partner; human syntenin who binds to the C-terminal domain of SOX4 protein. Wet laboratory documentation well documents the interaction of proteins on this regard but the residual level analysis via optimization and simulation operation remains yet undisclosed. So, for the purpose, the essential responsible domain sequence of SOX4 protein was extracted thus the protein was modeled via the satisfaction of its several stereo-chemical properties. The human syntenin protein structure was there-after extracted from its experimentally validated crystal structure. Docking simulations of the two proteins further formed the essential protein complex, which then underwent necessary optimization and molecular dynamics simulation. Residual involvement from the pre optimized and post simulated protein-protein complex was evaluated and compared individually, with a focus on the pattern of binding. The doubling up of the predominant ionic interactions and side chain-side chain interactions poses the final simulated complex to be greatly interactive one. Mainly, polar positively charged; His14 from syntenin and Ser8 from the C-terminal protein domain of SOX4 protein aided in the stronger interactions, with His14 forming three predominant interactions solely. Furthermore, Asp10 from syntenin and Glu11 from SOX4 C-terminal domain also remained for increasing the strength of the duo protein complex. Statistically significant evaluations from free energy of folding, net area available for solvent accessibility along-with the conformational shifts from coils to β-sheets in the protein complex additionally affirms the simulated complex structure to increase its stability and conformational strength post optimization and simulation. Therefore, this current molecular level optimized exploration provides a novel scope to scrutinize the residual interactive pattern and the most stable interactive protein structure dependable for the proper cytological regulation in humans. For the upcoming research, it thereby instigates the clinical and biomedical field for cell fate determinations and neurogeny.