Abstract
Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b558, heme b595, and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber’s LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.
Highlights
Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field
Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning
Since it has the highest sequence identity to Mtb (36%) and we are interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations
Summary
The data provided in this article can be used for running molecular dynamics (MD) simulations of Escherichia coli (E. coli) cytochrome bd oxidase (Protein Data Bank ID number: 6RKO) [2]. The missing residues 240–248 and 334–339 in chain A were modelled using Maestro, and the missing atoms in the palmitoyl-oleoyl-phosphatidylcholine (POPC) lipids were added back using the CHARMMGUI membrane builder [4]. The Amber LEaP script that builds the initial dry and the solvated structures (tleap.in) is provided in this publication This script uses the Amber ff14SB force field [8] for the standard residues, TIP3P water molecules [6], Joung/Cheatham ion parameters [9] for the counterions (Na+, Cl−), Generalized Amber force field (GAFF) [10] for ubiquinone, Amber Lipid 14 force field [11] for the POPC lipids, and the force field parameters for non-standard residues taken from Ref. More details for the MCPB.py derivation will be provided
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have