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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

Distribution of the crossed distances.Distributions of crossed distances between pairs of non-adjacent subunits for Leu at 16′, Val at 13′, Leu at 9′, Glu at 20′ and Gly at -2′; data collected from the five subunits. The vertical dashed blue line represents the value in the starting homology modeled configuration. Black bars: unrestrained; red bars: restrained; green bars: free simulations (data collected from the four free trajectories).
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pone.0133011.g005: Distribution of the crossed distances.Distributions of crossed distances between pairs of non-adjacent subunits for Leu at 16′, Val at 13′, Leu at 9′, Glu at 20′ and Gly at -2′; data collected from the five subunits. The vertical dashed blue line represents the value in the starting homology modeled configuration. Black bars: unrestrained; red bars: restrained; green bars: free simulations (data collected from the four free trajectories).

Mentions: In this simulation, a spontaneous conformational change is observed at the equilibration stage in few ps, as soon as the protein positional restraints are removed, and it is irreversible over the following 200 ns time scale of the MD trajectory. This change is characterized by a sudden decrease of the inter-residues crossed distances between M2 helices (S5 Fig, dotted lines). The drop in crossed distances is a consequence of an overall anticlockwise rigid movement of the M2 helices, which causes rotation of sidechains of hydrophobic residues Leu9′, Val13′, Leu16′ towards the inner part of the channel (Fig 4A). Distributions of the distances between couples of residues pertaining to the same hydrophobic ring are shown in Fig 5.


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)

Distribution of the crossed distances.Distributions of crossed distances between pairs of non-adjacent subunits for Leu at 16′, Val at 13′, Leu at 9′, Glu at 20′ and Gly at -2′; data collected from the five subunits. The vertical dashed blue line represents the value in the starting homology modeled configuration. Black bars: unrestrained; red bars: restrained; green bars: free simulations (data collected from the four free trajectories).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133011.g005: Distribution of the crossed distances.Distributions of crossed distances between pairs of non-adjacent subunits for Leu at 16′, Val at 13′, Leu at 9′, Glu at 20′ and Gly at -2′; data collected from the five subunits. The vertical dashed blue line represents the value in the starting homology modeled configuration. Black bars: unrestrained; red bars: restrained; green bars: free simulations (data collected from the four free trajectories).
Mentions: In this simulation, a spontaneous conformational change is observed at the equilibration stage in few ps, as soon as the protein positional restraints are removed, and it is irreversible over the following 200 ns time scale of the MD trajectory. This change is characterized by a sudden decrease of the inter-residues crossed distances between M2 helices (S5 Fig, dotted lines). The drop in crossed distances is a consequence of an overall anticlockwise rigid movement of the M2 helices, which causes rotation of sidechains of hydrophobic residues Leu9′, Val13′, Leu16′ towards the inner part of the channel (Fig 4A). Distributions of the distances between couples of residues pertaining to the same hydrophobic ring are shown in Fig 5.

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