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theses

The Voltage Dependent Anion Channel (VDAC) is a mitochondrial outer mem- brane protein that serves as a diffusion pore for ions like Ca2+,Cl-, small metabolites and nucleotides like ATP, ADP and NADH, thereby regulating metabolic and energetic flux across the outer mitochondrial membrane. Previous studies have indicated that Nicotinamide adenine dinucleotide in its reduced form (NADH) but not oxidized form (NAD+) minimizes conduction through VDAC. However, there is no available non-conducting structure of VDAC, and the mechanism by which NADH modulates the channel is poorly understood. Here with the help of fully-atomistic molecular dynamics simulations, we studied NADH binding to VDAC and its effect on channel dynamics and ion translocation. Simulations of VDAC were conducted using NMR structure of VDAC-NADH complex a) in the presence of NADH, and with NADH bound as in that structure, b) de-protonated in silico to NAD+ and c) removed entirely (apo) in the presence and absence of an applied transmembrane voltage. We observed a constant dissociation and re-association of NAD+ throughout the sim ulation trajectory, while NADH remained bound, reflecting a significantly lowered affinity of NAD+ for the VDAC pore. In the apo-VDAC system, the N-terminal loop dramatically changed its conformation over the course of the simulation, eventually approaching its conformation in structures experimentally determined in an apo-state. Under an applied transmembrane potential, we observed NADH chang- ing its position, but remaining stable in the pore. Our results are consistent with a mechanism in which NADH reduces conduction by partial pore block.

ETD_7531

M.S.

Includes bibliographical references

by Sai Shashank Chavali

doi:10.7282/T3902621

ETD graduate

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