Lipid composition and salt concentration as regulatory factors of the anion selectivity of VDAC studied by coarse-grained molecular dynamics simulations

Abstract

The voltage-dependent anion channel (VDAC) is a mitochondrial outer membrane protein whose fundamental function is to facilitate and regulate the flow of metabolites between the cytosol and the mitochondrial intermembrane space. Using coarse-grained molecular dynamics simulations, we investigated the dependence of VDAC selectivity towards small inorganic anions on two factors: the ionic strength and the lipid composition. In agreement with experimental data we found that VDAC becomes less anion selective with increasing salt concentration due to the screening of a few basic residues that point into the pore lumen. The molecular dynamics simulations provide insight into the regulation mechanism of VDAC selectivity by the composition in the lipid membrane and suggest that the ion distribution is differently modulated by POPE compared to the POPC bilayer. This occurs through the more persistent interactions of acidic residues located at both rims of the β-barrel with head groups of POPE which in turn impact the electrostatic potential and thereby the selectivity of the pore. This mechanism occurs not only in POPE single component membranes but also in a mixed POPE/POPC bilayer by an enrichment of POPE over POPC lipids on the surface of VDAC. Thus we show here that computationally-inexpensive coarse-grained simulations are able to capture, in a semi-quantitative way, essential features of VDAC anion selectivity and could pave the way toward a molecular level understanding of metabolite transport in natural membranes.

Computational Modeling of Realistic Cell Membranes

“…A recent extension of this work points at a dependence of these interactions on the conformational state of the protein. 434 Other examples of nonspecific lipid binding include the recruitment of short-tail lipids around OmpA, 435 of anionic (POPA) lipids at the gap junction hemichannel connexion-26, 436 the nonspecific binding of POPS to TM and juxtamembrane domains of cytokines 437 and to integrin, 438 weak binding of annular PC/PE lipids to MsbA flippase, 439 accumulation of cholesterol at the C-terminal helix of a phospholipase scramblase, 440 accumulation of GM1 around WALP peptides 362 and aquaporin, 185 preferential binding of PE over PC lipids in secondary transporters 441 and VDAC, 442 and redistribution of PC lipids around the gramicidin A channel dependent on tail length and unsaturation. 443 A related topic is the membrane binding of peripheral proteins, which often requires the presence of specific lipids that provide the necessary driving force for stable protein− membrane interactions.…”

Computational Modeling of Realistic Cell Membranes

“…A recent extension of this work points at a dependence of these interactions on the conformational state of the protein. 434 Other examples of nonspecific lipid binding include the recruitment of short-tail lipids around OmpA, 435 of anionic (POPA) lipids at the gap junction hemichannel connexion-26, 436 the nonspecific binding of POPS to TM and juxtamembrane domains of cytokines 437 and to integrin, 438 weak binding of annular PC/PE lipids to MsbA flippase, 439 accumulation of cholesterol at the C-terminal helix of a phospholipase scramblase, 440 accumulation of GM1 around WALP peptides 362 and aquaporin, 185 preferential binding of PE over PC lipids in secondary transporters 441 and VDAC, 442 and redistribution of PC lipids around the gramicidin A channel dependent on tail length and unsaturation. 443 A related topic is the membrane binding of peripheral proteins, which often requires the presence of specific lipids that provide the necessary driving force for stable protein− membrane interactions.…”

Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies

“…Multiscale simulations have also been used to show how other lipids affect β-barrel protein function. For instance, phosphatidylethanolamine of the mitochondrial OM influences the anion selectivity of VDAC, and thereby regulates its function [95], while CG-MD simulations highlighted how ceramide lipids can bind to VDAC2 to trigger mitochondrial apoptosis, thus acting as a tumor suppressing lipid [96]. Integrating MD and Brownian dynamics and electric field simulations with biochemical data has resulted in the ability to model protein complexes, such as the complex formed by the mitochondrial VDAC1 and hexokinase-II, which would have been extremely challenging to achieve solely by experimental means, due to the interaction of hexokinase-II with the membrane https://doi.org/10.26434/chemrxiv-2023-mfc5k ORCID: https://orcid.org/0000-0003-4524-4773 Content not peer-reviewed by ChemRxiv.…”

A Calcium Guard in the Outer Membrane: Is VDAC a Regulated Gatekeeper of Mitochondrial Calcium Uptake?

“…However, gating of the channel was experimentally induced by voltage, and although several mechanisms to create and regulate a membrane potential over the OMM were postulated [24][25][26], it remains controversial whether this is a physiologically relevant trigger of gating. Several other factors including Ca 2+ [27], metabolites [28], the lipidic environment [29][30][31][32], temperature [33], small molecules [10,34,35], interacting proteins [6,36,37], and biochemical modifications of the channel itself [38,39] were reported to either modify voltage-induced gating or to induce channel closure on their own. Among those is also the intriguing hypothesis of an entirely different mode of channel gating, namely a closure by occlusion of the large VDAC pore by a "molecular plug" mechanism (Figure 1).…”

“…The neuroprotective cholesterol-like lipid olesoxime prevented the interaction of VDAC with α-synuclein and, thereby, affected not only VDAC voltage gating but also binding of α-synuclein to the channel [67]. As a third way to regulate VDAC through the lipidic environment, molecular dynamics simulations suggested that interactions of lipids with acidic residues of VDAC might modulate the anion selectivity of the channel [30].…”

Computational Modeling of Realistic Cell Membranes

“…A recent extension of this work points at a dependence of these interactions on the conformational state of the protein. 434 Other examples of nonspecific lipid binding include the recruitment of short-tail lipids around OmpA, 435 of anionic (POPA) lipids at the gap junction hemichannel connexion-26, 436 the nonspecific binding of POPS to TM and juxtamembrane domains of cytokines 437 and to integrin, 438 weak binding of annular PC/PE lipids to MsbA flippase, 439 accumulation of cholesterol at the C-terminal helix of a phospholipase scramblase, 440 accumulation of GM1 around WALP peptides 362 and aquaporin, 185 preferential binding of PE over PC lipids in secondary transporters 441 and VDAC, 442 and redistribution of PC lipids around the gramicidin A channel dependent on tail length and unsaturation. 443 A related topic is the membrane binding of peripheral proteins, which often requires the presence of specific lipids that provide the necessary driving force for stable protein− membrane interactions.…”

Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies

“…Multiscale simulations have also been used to show how other lipids affect β-barrel protein function. For instance, phosphatidylethanolamine of the mitochondrial OM influences the anion selectivity of VDAC, and thereby regulates its function [95], while CG-MD simulations highlighted how ceramide lipids can bind to VDAC2 to trigger mitochondrial apoptosis, thus acting as a tumor suppressing lipid [96]. Integrating MD and Brownian dynamics and electric field simulations with biochemical data has resulted in the ability to model protein complexes, such as the complex formed by the mitochondrial VDAC1 and hexokinase-II, which would have been extremely challenging to achieve solely by experimental means, due to the interaction of hexokinase-II with the membrane https://doi.org/10.26434/chemrxiv-2023-mfc5k ORCID: https://orcid.org/0000-0003-4524-4773 Content not peer-reviewed by ChemRxiv.…”

A Calcium Guard in the Outer Membrane: Is VDAC a Regulated Gatekeeper of Mitochondrial Calcium Uptake?

“…However, gating of the channel was experimentally induced by voltage, and although several mechanisms to create and regulate a membrane potential over the OMM were postulated [24][25][26], it remains controversial whether this is a physiologically relevant trigger of gating. Several other factors including Ca 2+ [27], metabolites [28], the lipidic environment [29][30][31][32], temperature [33], small molecules [10,34,35], interacting proteins [6,36,37], and biochemical modifications of the channel itself [38,39] were reported to either modify voltage-induced gating or to induce channel closure on their own. Among those is also the intriguing hypothesis of an entirely different mode of channel gating, namely a closure by occlusion of the large VDAC pore by a "molecular plug" mechanism (Figure 1).…”

“…The neuroprotective cholesterol-like lipid olesoxime prevented the interaction of VDAC with α-synuclein and, thereby, affected not only VDAC voltage gating but also binding of α-synuclein to the channel [67]. As a third way to regulate VDAC through the lipidic environment, molecular dynamics simulations suggested that interactions of lipids with acidic residues of VDAC might modulate the anion selectivity of the channel [30].…”

Computational Modeling of Realistic Cell Membranes

“…A recent extension of this work points at a dependence of these interactions on the conformational state of the protein. 434 Other examples of nonspecific lipid binding include the recruitment of short-tail lipids around OmpA, 435 of anionic (POPA) lipids at the gap junction hemichannel connexion-26, 436 the nonspecific binding of POPS to TM and juxtamembrane domains of cytokines 437 and to integrin, 438 weak binding of annular PC/PE lipids to MsbA flippase, 439 accumulation of cholesterol at the C-terminal helix of a phospholipase scramblase, 440 accumulation of GM1 around WALP peptides 362 and aquaporin, 185 preferential binding of PE over PC lipids in secondary transporters 441 and VDAC, 442 and redistribution of PC lipids around the gramicidin A channel dependent on tail length and unsaturation. 443 A related topic is the membrane binding of peripheral proteins, which often requires the presence of specific lipids that provide the necessary driving force for stable protein− membrane interactions.…”

Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies

“…Multiscale simulations have also been used to show how other lipids affect β-barrel protein function. For instance, phosphatidylethanolamine of the mitochondrial OM influences the anion selectivity of VDAC, and thereby regulates its function [95], while CG-MD simulations highlighted how ceramide lipids can bind to VDAC2 to trigger mitochondrial apoptosis, thus acting as a tumor suppressing lipid [96]. Integrating MD and Brownian dynamics and electric field simulations with biochemical data has resulted in the ability to model protein complexes, such as the complex formed by the mitochondrial VDAC1 and hexokinase-II, which would have been extremely challenging to achieve solely by experimental means, due to the interaction of hexokinase-II with the membrane https://doi.org/10.26434/chemrxiv-2023-mfc5k ORCID: https://orcid.org/0000-0003-4524-4773 Content not peer-reviewed by ChemRxiv.…”

A Calcium Guard in the Outer Membrane: Is VDAC a Regulated Gatekeeper of Mitochondrial Calcium Uptake?

“…However, gating of the channel was experimentally induced by voltage, and although several mechanisms to create and regulate a membrane potential over the OMM were postulated [24][25][26], it remains controversial whether this is a physiologically relevant trigger of gating. Several other factors including Ca 2+ [27], metabolites [28], the lipidic environment [29][30][31][32], temperature [33], small molecules [10,34,35], interacting proteins [6,36,37], and biochemical modifications of the channel itself [38,39] were reported to either modify voltage-induced gating or to induce channel closure on their own. Among those is also the intriguing hypothesis of an entirely different mode of channel gating, namely a closure by occlusion of the large VDAC pore by a "molecular plug" mechanism (Figure 1).…”

“…The neuroprotective cholesterol-like lipid olesoxime prevented the interaction of VDAC with α-synuclein and, thereby, affected not only VDAC voltage gating but also binding of α-synuclein to the channel [67]. As a third way to regulate VDAC through the lipidic environment, molecular dynamics simulations suggested that interactions of lipids with acidic residues of VDAC might modulate the anion selectivity of the channel [30].…”