Computational protocol: Understanding Lignin-Degrading Reactions of Ligninolytic Enzymes: Binding Affinity and Interactional Profile

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Protocol publication

[…] The crystal structures of Lac, LiP and MnP were downloaded from the Protein Data Bank (PDB) (http://www.pdb.org/pdb/home/home.do) . Their PDB IDs and resolution (R) are 1GYC (R = 1.90 Å) , 1LLP (R = 1.70 Å) and 3M5Q (R = 0.93 Å) , respectively. The bound ligands of each analyzed enzyme were deleted. The chemical 2D structure of lignin derivative in SDF format with ID 167333 was obtained from PubChem (http://pubchem.ncbi.nlm.nih.gov/) , and was used as a lignin model substrate for exploring the interactions of ligninolytic enzymes with lignin. Its 3D conformation was further generated and optimized as docking ligand.MVD, a graphical-automatic docking software, was utilized to perform docking of lignin into the binding pockets of ligninolytic enzymes . This tool has been reported to have high accuracy and versatility . Each enzyme was analyzed separately. The bond order and the atom types of ligninolytic enzymes and lignin structures were automatically corrected with the correct charges assigned during the preparation process. Potential binding pockets (also named cavities or active sites) were detected by use of the cavity detection algorithm of MVD. Docking was performed using the MolDock scoring function (MolDock Score) together with the Moldock SE algorithm. This algorithm applied a maximum population size of 50 individuals. Maximum interactions, number of runs, energy threshold, maximum steps, and neighbour distance factor were set to 1500, 10, 100.00, 300, and 1.00, respectively. The best conformations with the lowest docked energy were chosen from all generated conformations. For each best conformation, we used the LPC/CSU server to analyze ligand–protein contacts, including hydrogen bonding (Hb) contact, hydrophobic (Ph) contact, aromatic-aromatic (Ar) contact, hydrophilic-hydrophobic (HH) contact, and acceptor-acceptor (AA) contact .MD simulations for the obtained complexes of lignin with Lac, LiP and MnP were performed using the standard GROMOS96 force field, implemented in GROMACS 4.0.7 software package –. The topology file was built using PRODRG program . We neutralized the charges of each complex with Na+ ions. The SPC216 water model was used for the solvation of all complexes. The Particle Mech Ewald (PME) method was applied to the treatment of long-range electrostatic interactions . A steepest descents minimization was used to release bad van der Waals contacts. Subsequently, three 3000 ps MD simulations at 300 K and 1 bar pressure were carried out. […]

Pipeline specifications

Software tools GROMACS, PRODRG
Application Drug design
Diseases Genetic Diseases, Inborn
Chemicals Lignin, Manganese