Peng Sang

TL;DR: The physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized.

TL;DR: The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein’s dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.

TL;DR: This study provides insight into the possible role of structural flexibility during interactions between SARS HCoV 3CL Pro and inhibitors and sheds light on structure-based design of anti-COVID-19 drugs targeting SARS-CoV-2 3CLpro.

TL;DR: Insight is provided into molecular basis of thermostability of homologous serine proteases adapted to different temperatures and the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area.

TL;DR: Comparison between the large concerted motions derived from essential dynamics analyses indicated that the degree of motion and direction of some regions in psychrophilic proteinase K could enlarge the substrate-binding pocket, thereby favoring catalytic efficiency and cold-adaptation.