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Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics.

Tewari SG, Zhou Y, Otto BJ, Dash RK, Kwok WM, Beard DA - Front Physiol (2015)

Bottom Line: Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model.Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state.Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI, USA.

ABSTRACT
The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance.

No MeSH data available.


Different Markov models that were attempted to fit WT and PTMed VDAC data. (A) The open loop Markov model that could describe the WT and PTM VDAC activity. S1–S5 represent distinct VDAC conformations. S3: Maximally open VDAC conformation; (S5, S1, S4): Sub-conductance state of VDAC (all three have the same conductance level); S2: Minimally open or closed state of VDAC. (B–F) Failed/inappropriate models. In all the Markov models S3 and S2 refer to maximally open and minimally open VDAC state, respectively.
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Figure 1: Different Markov models that were attempted to fit WT and PTMed VDAC data. (A) The open loop Markov model that could describe the WT and PTM VDAC activity. S1–S5 represent distinct VDAC conformations. S3: Maximally open VDAC conformation; (S5, S1, S4): Sub-conductance state of VDAC (all three have the same conductance level); S2: Minimally open or closed state of VDAC. (B–F) Failed/inappropriate models. In all the Markov models S3 and S2 refer to maximally open and minimally open VDAC state, respectively.

Mentions: The reconstituted VDAC activity recorded from the planar lipid bilayer experiments is sampled with a time-interval of fixed length (τ) and represented as a sequence of discrete-time channel events I = (Ik)Nk = 1, where N is the number of data-points in the recording and Ik is the single channel current at time tk. A typical VDAC current recording has multiple open and closed (or minimally open) states with a dominant sub-state that can be regarded as half-open or a half-closed state. Thresholding of VDAC current is employed to identify channel openings and closures which are classified into three distinct conductance states: open (O), sub-state (OS), or closed (C) event:(1)Ek=E(tk)={O, if /Ik/>/IO/,C, if /Ik/</IC/,OS, otherwise,where /IO/ > /IC/. The thresholds IO and IC are set at fixed values to identify distinct VDAC conductance states. These threshold values are different for WT and PTMed VDAC activity, however were chosen to be same within a given data type (i.e., WT, S137E, etc.). The threshold values used are tabulated in Table 1. The event sequence (Ek)Nk = 1 obtained in Equation 1 can be represented by a Markov model. A Markov model is a symmetric directed graph. The set of vertices contain distinct Markov states {S1, S2, … Sn} and the set of edges contain the non-negative constants qij (i,j: 1, 2, …, n) that govern the transition rate from state Si to state Sj. Figure 1 shows different Markov models.


Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics.

Tewari SG, Zhou Y, Otto BJ, Dash RK, Kwok WM, Beard DA - Front Physiol (2015)

Different Markov models that were attempted to fit WT and PTMed VDAC data. (A) The open loop Markov model that could describe the WT and PTM VDAC activity. S1–S5 represent distinct VDAC conformations. S3: Maximally open VDAC conformation; (S5, S1, S4): Sub-conductance state of VDAC (all three have the same conductance level); S2: Minimally open or closed state of VDAC. (B–F) Failed/inappropriate models. In all the Markov models S3 and S2 refer to maximally open and minimally open VDAC state, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4292549&req=5

Figure 1: Different Markov models that were attempted to fit WT and PTMed VDAC data. (A) The open loop Markov model that could describe the WT and PTM VDAC activity. S1–S5 represent distinct VDAC conformations. S3: Maximally open VDAC conformation; (S5, S1, S4): Sub-conductance state of VDAC (all three have the same conductance level); S2: Minimally open or closed state of VDAC. (B–F) Failed/inappropriate models. In all the Markov models S3 and S2 refer to maximally open and minimally open VDAC state, respectively.
Mentions: The reconstituted VDAC activity recorded from the planar lipid bilayer experiments is sampled with a time-interval of fixed length (τ) and represented as a sequence of discrete-time channel events I = (Ik)Nk = 1, where N is the number of data-points in the recording and Ik is the single channel current at time tk. A typical VDAC current recording has multiple open and closed (or minimally open) states with a dominant sub-state that can be regarded as half-open or a half-closed state. Thresholding of VDAC current is employed to identify channel openings and closures which are classified into three distinct conductance states: open (O), sub-state (OS), or closed (C) event:(1)Ek=E(tk)={O, if /Ik/>/IO/,C, if /Ik/</IC/,OS, otherwise,where /IO/ > /IC/. The thresholds IO and IC are set at fixed values to identify distinct VDAC conductance states. These threshold values are different for WT and PTMed VDAC activity, however were chosen to be same within a given data type (i.e., WT, S137E, etc.). The threshold values used are tabulated in Table 1. The event sequence (Ek)Nk = 1 obtained in Equation 1 can be represented by a Markov model. A Markov model is a symmetric directed graph. The set of vertices contain distinct Markov states {S1, S2, … Sn} and the set of edges contain the non-negative constants qij (i,j: 1, 2, …, n) that govern the transition rate from state Si to state Sj. Figure 1 shows different Markov models.

Bottom Line: Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model.Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state.Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Integrative Physiology, University of Michigan Ann Arbor, MI, USA.

ABSTRACT
The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance.

No MeSH data available.