Choudhary, Om
(2014)
Probing the biophysical properties of the murine voltage dependent anion channel (mVDAC1) structure: Insight from continuum electrostatics and Markov state models.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
Abstract
The voltage-dependent anion channel (VDAC) is the major pathway mediating the transfer of metabolites and ions across the mitochondrial outer membrane. The open state of the channel passes millions of ATP molecules per second and is anion selective, while the closed state exhibits no detectable ATP flux and is cation selective. The high-resolution structure of VDAC1 revealed a 19 stranded β-barrel with an α-helix occupying the pore. To probe VDAC1’s biophysical properties, we first carried out continuum electrostatics calculations on the murine VDAC1 (mVDAC1) structure. Poisson-Boltzmann (PB) calculations show that the ion transfer free energy through the channel is favorable for anions, suggesting that mVDAC1 represents the open state. This claim is buttressed by Poisson–Nernst–Planck calculations that predict a high single-channel conductance indicative of the open state and an anion selectivity of 1.75, nearly a two-fold selectivity for anions over cations. These calculations were then repeated on mutant channels and gave selectivity changes in accord with experimental observations.
We next investigated two proposals for how the channel gates between the open and the closed state. Both models involve the movement of the N-terminal helix, but neither motion produced the observed voltage sensitivity, nor did either motion result in a cation-selective channel, which is observed experimentally. Thus, we were able to rule out certain models for channel gating, but the true motion is yet to be determined.
Finally, to understand ATP permeation through VDAC, our collaborators solved the structure of mVDAC1 in the presence of ATP revealing a low-occupancy binding site. We
first carried out long, unbiased, multi-microsecond simulations of mVDAC1 in the presence of ATP on the Anton Supercomputer. Guided by the mVDAC1-ATP co-crystal coordinates, we then initiated hundreds of molecular dynamics (MD) simulations to construct a Markov state model (MSM) of ATP permeation. These MSM results show a high ATP flux generated from multiple pathways through the channel, consistent with our structural data and previously reported physiological rates. Continuum calculations and fully atomistic MSM both demonstrate that the solved structures are indicative of an open state of the channel.
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| Item Type: |
University of Pittsburgh ETD
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| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
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| Date: |
4 February 2014 |
| Date Type: |
Publication |
| Defense Date: |
15 November 2013 |
| Approval Date: |
4 February 2014 |
| Submission Date: |
4 December 2013 |
| Access Restriction: |
1 year -- Restrict access to University of Pittsburgh for a period of 1 year. |
| Number of Pages: |
91 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Computational Biology |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
VDAC continuum molecular dynamics simulations Markov state models |
| Date Deposited: |
04 Feb 2014 16:30 |
| Last Modified: |
15 Nov 2016 14:16 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/20190 |
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