Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field

Surl-Hee Ahn; Christian Seitz; Vinícius Wilian D Cruzeiro; J Andrew McCammon; Andreas W Götz

doi:10.1016/j.dib.2021.107401

Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field

Data Brief. 2021 Sep 23:38:107401. doi: 10.1016/j.dib.2021.107401. eCollection 2021 Oct.

Authors

Surl-Hee Ahn¹, Christian Seitz¹, Vinícius Wilian D Cruzeiro^{1

2}, J Andrew McCammon^{1

3}, Andreas W Götz²

Affiliations

¹ Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States.
² San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States.
³ Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States.

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 b $_{558}$ , heme b $_{595}$ , 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.

Keywords: Amber force field; Cytochrome bd oxidase; Molecular dynamics; Tuberculosis.

Abstract

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