Prototype acetylcholine channel geometry

The Journal of General Physiology, 1998

Ion channel function depends on the chemical and physical properties and spatial arrangement of the residues that line the channel lumen and on the electrostatic potential within the lumen. We have used small, sulfhydryl-specific thiosulfonate reagents, both positively charged and neutral, to probe the environment within the acetylcholine (ACh) receptor channel. Rate constants were determined for their reactions with cysteines substituted for nine exposed residues in the second membrane-spanning segment (M2) of the α subunit. The largest rate constants, both in the presence and absence of ACh, were for the reactions with the cysteine substituted for αThr244, near the intracellular end of the channel. In the open state of the channel, but not in the closed state, the rate constants for the reactions of the charged reagents with several substituted cysteines depended on the transmembrane electrostatic potential, and the electrical distance of these cysteines increased from the extrace...

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2004

We conduct a theoretical analysis to show the recently imaged structure of the acetylcholine receptor pore is in a non-conducting state. A hypothesised open state consistent with a lower resolution image is created and shown to have high conductance.

Proceedings of the National Academy of Sciences, 2005

The Journal of General Physiology, 2000

A ring of aligned glutamate residues named the intermediate ring of charge surrounds the intracellular end of the acetylcholine receptor channel and dominates cation conduction . Four of the five subunits in mouse-muscle acetylcholine receptor contribute a glutamate to the ring. These glutamates were mutated to glutamine or lysine, and combinations of mutant and native subunits, yielding net ring charges of Ϫ 1 to Ϫ 4, were expressed in Xenopus laevis oocytes. In all complexes, the ␣ subunit contained a Cys substituted for ␣ Thr244, three residues away from the ring glutamate ␣ Glu241. The rate constants for the reactions of ␣ Thr244Cys with the neutral 2-hydroxyethyl-methanethiosulfonate, the positively charged 2-ammonioethyl-methanethiosulfonate, and the doubly positively charged 2-ammonioethyl-2 Ј -ammonioethanethiosulfonate were determined from the rates of irreversible inhibition of the responses to acetylcholine. The reagents were added in the presence and absence of acetylcholine and at various transmembrane potentials, and the rate constants were extrapolated to zero transmembrane potential. The intrinsic electrostatic potential in the channel in the vicinity of the ring of charge was estimated from the ratios of the rate constants of differently charged reagents. In the acetylcholine-induced open state, this potential was Ϫ 230 mV with four glutamates in the ring and increased linearly towards 0 mV by ϩ 57 mV for each negative charge removed from the ring. Thus, the intrinsic electrostatic potential in the narrow, intracellular end of the open channel is almost entirely due to the intermediate ring of charge and is strongly correlated with alkali-metal-ion conductance through the channel. The intrinsic electrostatic potential in the closed state of the channel was more positive than in the open state at all values of the ring charge. These electrostatic properties were simulated by theoretical calculations based on a simplified model of the channel.

The Journal of Physiology, 2011

Non technical summary Muscle cells have receptors that are activated by the neurotransmitter acetylcholine. The probability that these channels conduct ions across cell membranes increases dramatically when transmitter molecules are present at two binding sites, which are far from the region that regulates ionic conductance. In order to understand the molecular basis of receptor 'gating' we seek to learn how neurotransmitters and other small molecules activate this protein. We used single-channel electrophysiology of receptors expressed in tissue-cultured cells to study the effects of mutations at the C-terminus of loop 9, a region near intra-protein interfaces that are known to be important with regard to gating and assembly. We found that the mutation had modest but measurable effects on channel gating (mainly those in the epsilon subunit). We also found that mutations of loop 9 in the alpha subunit increase the kinetic heterogeneity of gating, which suggests that they alter the stability of the extracellular transmembrane domain interface.

Journal of the American Chemical Society, 2005

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.

Materials Today: Proceedings, 2016

Ion channels are naturally occurring proteins that form hole in membrane. They play multiple roles in many important biological processes. Deletion or alteration of these channels often leads to serious problems in the physiological processes as it controls the flow of ions through it. The proper maintenance of the flow of ions, in turn, is required for normal health. The role of ions channels are now a proved factor behind nerve impulse. Here we have analyzed the nerve ion channel protein, with PDB entry 1BL8, which is basically an ion channel protein in Streptomyces Lividans. The equilibrium energy as well as molecular dynamics simulation is performed first. The possibility of ligand binding is investigated. The change of channel structure is found to be dependent on ligand binding. Implicit water model of the protein is subjected to molecular dynamics simulation to find their energy minimized value. Simulation of the protein in the environment of water and ions has given us important results too.

Journal of Optoelectronics and Advanced Materials

The transport of sodium ions through a model membrane channel in the presence of static magnetic fields has been investigated by non-equilibrium molecular dynamics. The effect of static magnetic fields appears to be exerted not mainly on the transiting ions, but rather on the water molecules, favouring statistically their polarization during the ion passages and leading indirectly to a slight increase of the ion current.

2004

channel properties and needs to be described compu-New York, New York 10021 tationally since no genuine structure exists. With their 2 Beckman Institute for Advanced Science ability to go beyond static structures and include the and Technology membrane environment, molecular dynamics (MD) sim-University of Illinois at Urbana-Champaign ulations based on detailed atomic models (McCammon 405 North Mathews et al., 1977) are now playing an increasingly important Urbana, Illinois 61801 role in shaping our view of how membrane channels carry out their function. MD simulations, together with a number of specific computational techniques (see Methods, below), offer a unique route for interpreting The determination of the structure of several members

PLoS Computational Biology, 2008

The nicotinic acetylcholine receptor (nAChR) is a key molecule involved in the propagation of signals in the central nervous system and peripheral synapses. Although numerous computational and experimental studies have been performed on this receptor, the structural dynamics of the receptor underlying the gating mechanism is still unclear. To address the mechanical fundamentals of nAChR gating, both conventional molecular dynamics (CMD) and steered rotation molecular dynamics (SRMD) simulations have been conducted on the cryo-electron microscopy (cryo-EM) structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation revealed a collective motion amongst C-loops, M1, and M2 helices. The inward movement of C-loops accompanying the shrinking of acetylcholine (ACh) binding pockets induced an inward and upward motion of the outer b-sheet composed of b9 and b10 strands, which in turn causes M1 and M2 to undergo anticlockwise motions around the pore axis. Rotational motion of the entire receptor around the pore axis and twisting motions among extracellular (EC), transmembrane (TM), and intracellular MA domains were also detected by the CMD simulation. Moreover, M2 helices undergo a local twisting motion synthesized by their bending vibration and rotation. The hinge of either twisting motion or bending vibration is located at the middle of M2, possibly the gate of the receptor. A complementary twisting-to-open motion throughout the receptor was detected by a normal mode analysis (NMA). To mimic the pulsive action of ACh binding, nonequilibrium MD simulations were performed by using the SRMD method developed in one of our laboratories. The result confirmed all the motions derived from the CMD simulation and NMA. In addition, the SRMD simulation indicated that the channel may undergo an open-close (O $ C) motion. The present MD simulations explore the structural dynamics of the receptor under its gating process and provide a new insight into the gating mechanism of nAChR at the atomic level.