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Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.

Padhi S, Burri RR, Jameel S, Priyakumar UD - PLoS ONE (2014)

Bottom Line: Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies.The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments.The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

View Article: PubMed Central - PubMed

Affiliation: Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India.

ABSTRACT
The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu--modeled and validated based on available experimental data--umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

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Related in: MedlinePlus

The PMF shown as a function of the positions of the two permeating ions.The x-axis labels at the bottom show the position of the top ion along the channel axis, while the labels at the top show the pore-lining residues at their respective positions along the channel axis. The pathway with the lowest free energy barrier is highlighted in maroon color. Images of ion positions corresponding to the pathway with the lowest free energy barrier are shown below the plot, together with the distance between the two ions at these positions.
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pone-0112983-g008: The PMF shown as a function of the positions of the two permeating ions.The x-axis labels at the bottom show the position of the top ion along the channel axis, while the labels at the top show the pore-lining residues at their respective positions along the channel axis. The pathway with the lowest free energy barrier is highlighted in maroon color. Images of ion positions corresponding to the pathway with the lowest free energy barrier are shown below the plot, together with the distance between the two ions at these positions.

Mentions: To investigate if more than one ion can pass through the channel at a time, the free energy profile was calculated as a function of the positions of two permeating K+ ions. The free energy landscape with respect to the position along the z-axis of the first ion and the distance of the second ion from the first is shown in Figure 8. The probability distributions obtained from the biased simulations were checked for adequate sampling along both the reaction coordinates prior to construction of the free energy surface. The lowest energy pathway with respect to the position of the first ion is also marked in the plot. The structures presented below the plot show the conformations of the channel corresponding to this path at three different positions. The free energy surface as a whole shows that permeation of two ions at the same time is not thermodynamically favorable compared to the movement of one ion. If one follows the minimum energy path given in the figure, one can see that when the two ions are near the C-terminal side of the pore (bottom left corner of the figure), the ions are close in space. This is because this region is reasonably well solvated, and interactions between the two ions are shielded. As the two ions cross the hydrophilic region around Ser23 and enter the dehydrated middle region of the channel, interionic repulsion becomes significant. The reduced number of water molecules hydrating the ions, and the dry nature of this part of the pore leads to longer distances between the two ions. This means that two ions cannot enter the middle region of the channel simultaneously, and only one ion can pass at a time. Once the first ion reaches the N-terminal region, the second ion starts crossing the hydrophobic stretch in the pore. Thus a mechanism is hypothesized in which only one ion crosses the hydrophobic region of the channel at a given time while the next ion waits near the C-terminal region, until the first one reaches the N-terminal end of the pore. The kinetics of the process of ion transport is therefore seen to be controlled primarily by the hydrophobic stretch. Such a hypothesis is also consistent with previous experimental studies. Fischer and coworkers have proposed that the conductivity of Vpu follows Michaelis-Menten behavior upon increasing the salt concentration [28]. Such behavior is explained by the fact that a single ion can pass through the channel at a time, as suggested by the mechanism discussed here.


Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.

Padhi S, Burri RR, Jameel S, Priyakumar UD - PLoS ONE (2014)

The PMF shown as a function of the positions of the two permeating ions.The x-axis labels at the bottom show the position of the top ion along the channel axis, while the labels at the top show the pore-lining residues at their respective positions along the channel axis. The pathway with the lowest free energy barrier is highlighted in maroon color. Images of ion positions corresponding to the pathway with the lowest free energy barrier are shown below the plot, together with the distance between the two ions at these positions.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231112&req=5

pone-0112983-g008: The PMF shown as a function of the positions of the two permeating ions.The x-axis labels at the bottom show the position of the top ion along the channel axis, while the labels at the top show the pore-lining residues at their respective positions along the channel axis. The pathway with the lowest free energy barrier is highlighted in maroon color. Images of ion positions corresponding to the pathway with the lowest free energy barrier are shown below the plot, together with the distance between the two ions at these positions.
Mentions: To investigate if more than one ion can pass through the channel at a time, the free energy profile was calculated as a function of the positions of two permeating K+ ions. The free energy landscape with respect to the position along the z-axis of the first ion and the distance of the second ion from the first is shown in Figure 8. The probability distributions obtained from the biased simulations were checked for adequate sampling along both the reaction coordinates prior to construction of the free energy surface. The lowest energy pathway with respect to the position of the first ion is also marked in the plot. The structures presented below the plot show the conformations of the channel corresponding to this path at three different positions. The free energy surface as a whole shows that permeation of two ions at the same time is not thermodynamically favorable compared to the movement of one ion. If one follows the minimum energy path given in the figure, one can see that when the two ions are near the C-terminal side of the pore (bottom left corner of the figure), the ions are close in space. This is because this region is reasonably well solvated, and interactions between the two ions are shielded. As the two ions cross the hydrophilic region around Ser23 and enter the dehydrated middle region of the channel, interionic repulsion becomes significant. The reduced number of water molecules hydrating the ions, and the dry nature of this part of the pore leads to longer distances between the two ions. This means that two ions cannot enter the middle region of the channel simultaneously, and only one ion can pass at a time. Once the first ion reaches the N-terminal region, the second ion starts crossing the hydrophobic stretch in the pore. Thus a mechanism is hypothesized in which only one ion crosses the hydrophobic region of the channel at a given time while the next ion waits near the C-terminal region, until the first one reaches the N-terminal end of the pore. The kinetics of the process of ion transport is therefore seen to be controlled primarily by the hydrophobic stretch. Such a hypothesis is also consistent with previous experimental studies. Fischer and coworkers have proposed that the conductivity of Vpu follows Michaelis-Menten behavior upon increasing the salt concentration [28]. Such behavior is explained by the fact that a single ion can pass through the channel at a time, as suggested by the mechanism discussed here.

Bottom Line: Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies.The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments.The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

View Article: PubMed Central - PubMed

Affiliation: Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India.

ABSTRACT
The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu--modeled and validated based on available experimental data--umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

Show MeSH
Related in: MedlinePlus