Combination of multiple methods and views for recognition, transportation, and structure-guided modification of lysine-specific demethylase phenylcyclopropylamine inhibitor

Abstract

Lysine-Specific Demethylase 1 (LSD1) is a typical histone specific demethylase, which plays an important role in protein methylation modification. It is a member of the amine oxidase family (MAO) that...

Atomistic insight into the binding mode and self-regulation mechanism of IsPETase towards PET substrates with different polymerization degrees

“…In the long-term MD simulation, the SHAKE 45 algorithm is used to constrain all hydrogen bonds with a tolerance of 10 À5 , and the van der Waals and electrostatic interactions are set to 12 Å. [46][47][48][49] The simulation of polymers may be particularly difficult. Therefore, to obtain a satisfactory sampling of the PETase in the bound state, we applied restraint forces during 100 ns MD simulation (Fig.…”

Histone demethylases in the regulation of immunity and inflammation

“…The LSDs family were currently constituted by two members only, LSD1/KDM1A and LSD2/KDM1B [ 18 , 19 ]. KDM1 had a C-terminal amine oxidase-like domain that contained the substrate and flavin adenine dinucleotide binding sites, which process the removal of monomethylated and dimethylated markers [ 20 , 21 ]. KDM1 cannot remove trimethyl groups [ 22 ].…”

Molecular dynamic simulations identifying the mechanism of holoenzyme formation byO-GlcNAc transferase and active p38α

“…The molecular mechanics generalized Born surface area (MM/GBSA) method is a common method for calculating the binding free energy, and it has been successfully applied to various systems including protein–ligand, protein–protein, and protein–peptide. 40–43…”

“…The molecular mechanics generalized Born surface area (MM/ GBSA) method is a common method for calculating the binding free energy, and it has been successfully applied to various systems including protein-ligand, protein-protein, and proteinpeptide. [40][41][42][43] In this method, the total binding free energy DG binding is calculated using the following equation. 44 DG binding = DG complex À (DG pro1 + DG pro2 )…”