In SilicoModels for the Human α4β2 Nicotinic Acetylcholine Receptor

Abstract

The neuronal α4β2 nicotinic acetylcholine receptor (nAChR) is one of the most widely expressed nAChR subtypes in the brain. Its subunits have high sequence identity (54% and 46% for α4 and β2, respectively) with α and β subunits in Torpedo nAChR. Using known structure of the Torpedo nAChR as a template, the closed-channel structure of the α4β2 nAChR was constructed through homology modeling. Normal mode analysis was performed on this closed structure and the resulting lowest frequency mode was applied to it for a 'twist-to-open' motion, which increased the minimum pore radius from 2.7Å to 3.4Å and generated an open-channel model. Nicotine could bind to the predicted agonist binding sites in the open-channel model, but not in the closed one. Both models were subsequently equilibrated in a ternary lipid mixture via extensive molecular dynamics (MD) simulations. Over the course of 11-ns MD simulations, the open channel remained open with filled water, but the closed channel showed a much lower water density at its hydrophobic gate comprising of residues α4-V259, α4-L263 and their homologous residues in β2 subunits. Brownian Dynamics simulations of Na + permeation through the open channel demonstrated a current-voltage relationship that was in good agreement with experimental data on the conducting state of α4β2 nAChR. Besides establishment of the well-equilibrated closed-and open-channel α4β2 structural models, the MD simulations on these models provided valuable insights into critical factors that potentially modulate channel gating. Rotation and titling of TM2 helices led to changes in orientations of pore-lining residue side-chains. Without concerted movement, the reorientation of one or two hydrophobic sidechains could be enough for channel opening. The closed-and open-channel structures exhibited distinct patterns of electrostatic interactions at the interface of extracellular and transmembrane domains that might regulate the signal propagation of agonist binding to channel opening. A potential prominent role of the β2 subunit in channel gating was also elucidated in the study.

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

“…S6b). Whether our results are transferable to other CLRs remains to be established, but previous work already pointed to such a hydrophobic girdle as contributing to the gate in nAChRs (19,28,32,33). The fast ∼0.1 μs gating time scale observed herein is consistent with studies based on shorter calculations (19) but still out of reach of current electrophysiological approaches limited to a ∼10 μs resolution.…”

“…Electron density has been measured in this region of GLIC and was attributed to Cs þ , Rb þ , and Zn 2þ cations (14). These results on hydration and ion propensity are also in good qualitative agreement with an 11-ns MD simulation on nAChR (33).…”

Molecular mechanism of interactions of the physiological anti-hypertensive peptide catestatin with the neuronal nicotinic acetylcholine receptor

“…This observation is similar to the conformations (in the corresponding subunits) in the X-ray structure of the Torpedo nAChR (Unwin, 2005), the modeled structure of the human a4b2 nAChR (Haddadian et al, 2008) and the modeled structure of the human a7 nAChR (Brannigan et al, 2008;Law et al, 2005).…”

“…We used the similar strategy that was recently used to model the human (a4) 2 (b2) 3 nAChR (Haddadian et al, 2008). In brief, sequences of the human a3 (P32297) and b4 (P30926) subunits were obtained from the SwissProt protein knowledgebase at the Expasy Server (http://www.expasy.ch/ sprot).…”

“…To study interactions of the human CST peptide with the human nAChR, an in silico model structure for the human a3b4 receptor subtype was developed by following a recently reported protocol for modeling the human a4b2 subtype (Haddadian et al, 2008). Accordingly, the available refined structure of the electric ray Torpedo marmorata (a) 2 bcd nAChR (PDB ID: 2BG9) was used as a template to build the pentameric human (a3) 2 (b4) 3 nAChR structure (Fig.…”