Protein folding conformations take the form of networks, sets of conformations (vertices) joined together in pairs by links or edges. Protein folding conformation network is a complex network, and has scale-free property that many networks have in common. Understanding the scale-free property in the network of protein folding conformation, one can find the better conformation of protein folding...

We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in active site that mimic binding terminal carboxylates (l,l-SDAP) substrate. demonstrated inhibition DapE by (IC50 = 13.8 ±...

Infectious bursal disease virus (IBDV) is the causative agent of Gumboro disease, an infectious disease of global economic importance in poultry. Structural protein VP2 of IBDV is the most frequently studied protein due to its significant roles in virus attachment, protective immunity, and serotype specificity. The objective of the present study was to improve the expression of hypervariable re...

We investigate binding of linoleate and other potential ligands to the recently discovered fatty acid site in SARS-CoV-2 spike protein, using docking molecular dynamics simulations. Simulations suggest that dexamethasone stabilize locked conformation, thus reducing opportunity for ACE2 interaction. In contrast, cholesterol may expose receptor-binding domain by destabilizing closed structure, pr...