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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

Pore profile.Pore radius profiles along the pore region in the homology model configuration (blue curve), in the collapsed (black) and open (red) structures averaged over the last 100ns of the unrestrained and restrained trajectories, respectively. Also reported the profiles for open channels (GluCl and GLIC from X-rays) and closed channels (Torpedo nAChR from EM and ELIC from X-rays). Pore radius computed with MolAxis [80]. MolAxis is a channel finding algorithm, in which molecular channels are represented using “corridors”, i.e. probable routes taken by a small molecule passing through a channel. MolAxis uses an algorithm that allows fast identification of corridors in the complementary space of the molecule. The black arrows, from left to right, indicate Glu20′, Leu9′, Thr6′ and Gly2′.
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pone.0133011.g008: Pore profile.Pore radius profiles along the pore region in the homology model configuration (blue curve), in the collapsed (black) and open (red) structures averaged over the last 100ns of the unrestrained and restrained trajectories, respectively. Also reported the profiles for open channels (GluCl and GLIC from X-rays) and closed channels (Torpedo nAChR from EM and ELIC from X-rays). Pore radius computed with MolAxis [80]. MolAxis is a channel finding algorithm, in which molecular channels are represented using “corridors”, i.e. probable routes taken by a small molecule passing through a channel. MolAxis uses an algorithm that allows fast identification of corridors in the complementary space of the molecule. The black arrows, from left to right, indicate Glu20′, Leu9′, Thr6′ and Gly2′.

Mentions: Results so far reported depict two different situations in the collapsed and putative open forms (both from the restrained and the free trajectories), in what concerns the pore geometry and the consequent hydration behavior. Fig 8 shows the pore radius along the channel axis (region corresponding to the M2 helices). We compare our homology model, the collapsed channel and the putative open channel obtained from the restrained simulation, together with the profiles from the structures of GluCl [41] (X-rays, open in the presence of ivermectin), GLIC [15] (X-rays, open), ELIC [17] (X-rays, closed), and Torpedo nAChR [9] (EM, closed). The pore profiles calculated in the free trajectories are shown in S8 Fig. The collapsed structure has one constriction point, corresponding to the Leu9′ rings, with a minimum radius of ∼ 2 Å. This constriction point at Leu9′ is in common with the ELIC profile. It has been also observed in the relaxed native GluCL both in the presence and in the absence of ivermectin [54], and in a model of a Glycine receptor built on GLIC [84] (radius equal to 1.4 Å at 9′), both in the presence or absence of ethanol, included in the simulation with the aim to stabilize the Glycine receptor in an open form.


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)

Pore profile.Pore radius profiles along the pore region in the homology model configuration (blue curve), in the collapsed (black) and open (red) structures averaged over the last 100ns of the unrestrained and restrained trajectories, respectively. Also reported the profiles for open channels (GluCl and GLIC from X-rays) and closed channels (Torpedo nAChR from EM and ELIC from X-rays). Pore radius computed with MolAxis [80]. MolAxis is a channel finding algorithm, in which molecular channels are represented using “corridors”, i.e. probable routes taken by a small molecule passing through a channel. MolAxis uses an algorithm that allows fast identification of corridors in the complementary space of the molecule. The black arrows, from left to right, indicate Glu20′, Leu9′, Thr6′ and Gly2′.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133011.g008: Pore profile.Pore radius profiles along the pore region in the homology model configuration (blue curve), in the collapsed (black) and open (red) structures averaged over the last 100ns of the unrestrained and restrained trajectories, respectively. Also reported the profiles for open channels (GluCl and GLIC from X-rays) and closed channels (Torpedo nAChR from EM and ELIC from X-rays). Pore radius computed with MolAxis [80]. MolAxis is a channel finding algorithm, in which molecular channels are represented using “corridors”, i.e. probable routes taken by a small molecule passing through a channel. MolAxis uses an algorithm that allows fast identification of corridors in the complementary space of the molecule. The black arrows, from left to right, indicate Glu20′, Leu9′, Thr6′ and Gly2′.
Mentions: Results so far reported depict two different situations in the collapsed and putative open forms (both from the restrained and the free trajectories), in what concerns the pore geometry and the consequent hydration behavior. Fig 8 shows the pore radius along the channel axis (region corresponding to the M2 helices). We compare our homology model, the collapsed channel and the putative open channel obtained from the restrained simulation, together with the profiles from the structures of GluCl [41] (X-rays, open in the presence of ivermectin), GLIC [15] (X-rays, open), ELIC [17] (X-rays, closed), and Torpedo nAChR [9] (EM, closed). The pore profiles calculated in the free trajectories are shown in S8 Fig. The collapsed structure has one constriction point, corresponding to the Leu9′ rings, with a minimum radius of ∼ 2 Å. This constriction point at Leu9′ is in common with the ELIC profile. It has been also observed in the relaxed native GluCL both in the presence and in the absence of ivermectin [54], and in a model of a Glycine receptor built on GLIC [84] (radius equal to 1.4 Å at 9′), both in the presence or absence of ethanol, included in the simulation with the aim to stabilize the Glycine receptor in an open form.

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