SARS-CoV-2 remains life-threatening human pathogen witnessed in the present world. Purpose. The key objective of this research was to incorporate a bioinformatics technique forecast molecular docking ACE2-associated SARS-CoVs nucleocapsid protein. Methods. Different tools were used study order compare chemical structures with their biological behaviour at levels atoms and ligand-binding affinit...

We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the disco...

Biological systems are often exposed to mechanical perturbations, which may modulate many biochemical processes. Ligand binding involves a wide range of structural changes in the receptor protein, from hinge movement entire domains minor sidechain rearrangements pocket residues. Hydrophobic ligand protein alters system’s vibrational free energy, allowing different conformational states alloster...

Title: The computational design of ligand binding is not a solved problem

Allostery, the coupling between ligand binding and protein conformational change, is the heart of biological network and it has often been explained by two representative models, the induced-fit and the population-shift models. Here, we clarified for what systems one model fits better than the other by performing molecular simulations of coupled binding and conformational change. Based on the d...

Ligand binding to receptors is the initial event in many signaling processes, and a quantitative understanding of this interaction is important for modeling cell behavior. In this paper, we study the kinetics of reversible ligand binding to receptors on a spherical cell surface using a self-consistent stochastic theory. Binding, dissociation, diffusion and rebinding of ligands are incorporated ...

Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting wit...