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A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G - PLoS ONE (2015)

Bottom Line: Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far.The channel remains stable and hydrated over the whole runs.Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

View Article: PubMed Central - PubMed

Affiliation: Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.

ABSTRACT
Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 μs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

No MeSH data available.


Related in: MedlinePlus

Hydration behavior.Left and central panels: time evolution of water count within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ in the pore channel. Black curves: unrestrained; red curves: restrained; green curve: trajectory Free4. Right panel: percentages of of hydrogen bond formation between water molecules and protein residues along the trajectories. Black bars: unrestrained; red bars: restrained; green bars: trajectory Free4. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between the two partners, is less than 2Å.
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pone.0133011.g007: Hydration behavior.Left and central panels: time evolution of water count within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ in the pore channel. Black curves: unrestrained; red curves: restrained; green curve: trajectory Free4. Right panel: percentages of of hydrogen bond formation between water molecules and protein residues along the trajectories. Black bars: unrestrained; red bars: restrained; green bars: trajectory Free4. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between the two partners, is less than 2Å.

Mentions: To investigate a possible role of water in stabilizing the pore from collapse successive to the effect of the restraint, we analyzed the water dynamics at the level of the hydrophilic rings in the pore, where a significant and persistent water population is expected. First, the number of water molecules found within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ rings has been counted along the unrestrained, restrained and the Free4 trajectory, selected as representative of the four free trajectories in which the restraints were not applied. The time behavior of the selected water count is shown in Fig 7, left and central panels. In addition, residue-water hydrogen bond analysis has been performed. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between water and protein residue, is less than 2.0Å. The persistence of the selected hydrogen bond along the simulations, defined as the percentage of time along a full trajectory that the bond is formed, is also shown in Fig 7, right panel (data averaged over the five subunits).


A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G - PLoS ONE (2015)

Hydration behavior.Left and central panels: time evolution of water count within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ in the pore channel. Black curves: unrestrained; red curves: restrained; green curve: trajectory Free4. Right panel: percentages of of hydrogen bond formation between water molecules and protein residues along the trajectories. Black bars: unrestrained; red bars: restrained; green bars: trajectory Free4. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between the two partners, is less than 2Å.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514475&req=5

pone.0133011.g007: Hydration behavior.Left and central panels: time evolution of water count within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ in the pore channel. Black curves: unrestrained; red curves: restrained; green curve: trajectory Free4. Right panel: percentages of of hydrogen bond formation between water molecules and protein residues along the trajectories. Black bars: unrestrained; red bars: restrained; green bars: trajectory Free4. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between the two partners, is less than 2Å.
Mentions: To investigate a possible role of water in stabilizing the pore from collapse successive to the effect of the restraint, we analyzed the water dynamics at the level of the hydrophilic rings in the pore, where a significant and persistent water population is expected. First, the number of water molecules found within 3 Å from any atom of Ser2′, Ser10′, Thr6′ and Thr12′ rings has been counted along the unrestrained, restrained and the Free4 trajectory, selected as representative of the four free trajectories in which the restraints were not applied. The time behavior of the selected water count is shown in Fig 7, left and central panels. In addition, residue-water hydrogen bond analysis has been performed. The hydrogen bond is considered to be formed when the minimum distance among all possible donor/acceptor distances, between water and protein residue, is less than 2.0Å. The persistence of the selected hydrogen bond along the simulations, defined as the percentage of time along a full trajectory that the bond is formed, is also shown in Fig 7, right panel (data averaged over the five subunits).

Bottom Line: Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far.The channel remains stable and hydrated over the whole runs.Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

View Article: PubMed Central - PubMed

Affiliation: Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.

ABSTRACT
Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 μs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.

No MeSH data available.


Related in: MedlinePlus