Mechanism of α-synuclein translocation through a VDAC nanopore revealed by energy landscape modeling of escape time distributions

Abstract

We probe the energy landscape governing the passage of α-synuclein, a natural "diblock copolymer"-like polypeptide, through a nanoscale pore. α-Synuclein is an intrinsically disordered neuronal protein associated with Parkinson's pathology. The motion of this electrically heterogeneous polymer in the β-barrel voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane strongly depends on the properties of both the charged and uncharged regions of the α-synuclein polymer. We model this motion in two ways. First, a simple Markov model accounts for the transitions of the channel between the states of different occupancy by α-synuclein. Second, the detailed energy landscape of this motion can be accounted for using a drift-diffusion framework that incorporates the α-synuclein binding energy and the free energy cost of its confinement in the VDAC pore. The models directly predict the probability of α-synuclein translocation across the mitochondrial outer membrane, with immediate implications for the physiological role of α-synuclein in regulation of mitochondrial bioenergetics. Time-resolved measurements of the electrical properties of VDAC occupied by α-synuclein reveal distinct effects of the motion of the junction separating the differently charged regions of the polymer.

A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology

“…5 B) for all applied potentials. The on-rate constant, k on , (the inverse of < τ on > normalized over the α-syn concentration) is highly voltage dependent where it increases exponentially with the applied voltage (Rostovtseva et al, 2015; Hoogerheide et al, 2017; Jacobs et al, 2019). For hVDAC3, the k on is 10- to 100-fold lower than mVDAC1 for all voltages and at both polarities (Fig.…”

Sequence diversity of tubulin isotypes in regulation of the mitochondrial voltage-dependent anion channel

“…The exponential dependence of the blockage time on voltage suggests a Kramers-type escape problem (40,41) that is dominated by electrostatic effects; essentially, the role of the model is to calculate the height of the energy barrier to CTT retraction from the pore. Details of the model, which involves constructing the interaction potential to be used in a first-passage time calculation in a drift-diffusion framework (41)(42)(43), can be found in the Appendix. The only free parameters are the distances between the tubulin body, where the CTT is tethered, and the pore constriction.…”

“…The measured average escape time can be approximated by a first passage time in a driftdiffusion framework (41)(42)(43). We parameterize the penetration of the carboxy-terminal tail into the VDAC channel by a distance parameter , which corresponds to the distance from the tubulin body to the VDAC channel constriction along the contour of the CTT.…”

Computational membrane biophysics: From ion channel interactions with drugs to cellular function

“…In these simulations, the system is saturated with many drug molecules to increase the probability of drug binding events. This study is one of the few reports that have pushed all-atom MD simulations of drug-ion channel systems into physiological time-scales[19, 49–53]. It showed that there are up to seven binding sites for BZC, leading to the determination of a high-affinity pore-blocking site through fenestrations, and an interesting site between the pore and voltage sensor domain of NavAb[11].…”

“…It is, however, known that some states of ion channels usually display a non-Markovian behavior, i.e., a significantly long history of initial states[109, 110]. Particularly, there is direct evidence of non-Markovian behavior ranging from gating in VDACs to polymer/ligand escape[53, 111, 112]. Therefore, it might be necessary to apply a non-Markovian State Model[113] to identify how drugs influence the conformational transitions of ion channels in individual trajectories, which are simulated from different initial states.…”