Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

• Published in: Molecular and cellular biochemistry 2022-01, Vol.477 (1), p.153-165
• Main Authors: Dibrov, Alexander, Mourin, Muntahi, Dibrov, Pavel, Pierce, Grant N.
• Format: Article
• Language: English
• Subjects: Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Binding sites; Biochemistry; Biomedical and Life Sciences; Boundary conditions; Cardiology; Cholera; Crystal structure; Dynamic stability; Life Sciences; Lipid bilayers; Lipids; Medical Biochemistry; Molecular dynamics; Molecular Dynamics Simulation; Multienzyme Complexes - chemistry; Multienzyme Complexes - genetics; NAD(P)H Dehydrogenase (Quinone) - chemistry; NAD(P)H Dehydrogenase (Quinone) - genetics; NADH; Nicotinamide adenine dinucleotide; Oncology; Pathogens; Quinone oxidoreductase; Quinones; Simulation; Vibrio cholerae - enzymology; Vibrio cholerae - genetics; Waterborne diseases
• ISSN: 0300-8177; 1573-4919
• DOI: 10.1007/s11010-021-04266-3

The Na + -translocating NADH:quinone oxidoreductase (Na + -NQR) is the major Na + pump in aerobic pathogens such as Vibrio cholerae . The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na + -NQR. While the mechanisms underlying Na + -NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na + -NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na + -NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.