Computational protocol: Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis

Similar protocols

Protocol publication

[…] The initial structure used for equilibrium simulations was the crystal structure of the C. glutamicum PafA/Pup complex (pdb: 4BJR) (). Alanine and phenylalanine mutants at S126 were generated using VMD (). Force-field parameters for covalent attachment of AEBSF to the hydroxyl group of serine were generated using CGenFF (, ) and the initial structure of the modified protein was generated using VMD. All proteins were solvated in TIP3 water in 0.15 M NaCl and minimized and equilibrated using VMD/NAMD and the CHARMM 27 force field (, ). The particle mesh Ewald algorithm was employed to treat electrostatic interactions, and van der Waal interactions were treated with a cut-off of 12 Å. Langevin dynamics were employed to maintain a constant temperature of 310 K and a Nose-Hoover Langevin piston was used to maintain a constant pressure of 1 atm. The integration step was set to 2 fs. Extended simulations (35 ns) were performed for each complex. In the movies of the simulations, adjacent frames of the 80 ps/frame simulations were smoothed to facilitate understanding of the conformational changes. […]

Pipeline specifications

Software tools VMD, CGenFF, NAMD
Applications Protein structure analysis, Membrane protein analysis
Organisms Mycolicibacterium smegmatis, Mycobacterium tuberculosis, Mus musculus
Diseases Tuberculosis, Mastocytosis, Systemic
Chemicals Amino Acids