Homology Modeling and Molecular Dynamics Simulations of Transmembrane Domain Structure of Human Neuronal Nicotinic Acetylcholine Receptor

From: Biophysical Journal | Date: February 1, 2005| Author: Tang, Pei; Xu, Yan; Saladino, Alexander C | Copyright information

ABSTRACT

A three-dimensional model of the transmembrane domain of a neuronal-type nicotinic acetylcholine receptor (nAChR), (α4)^sub 2^(β2)^sub 3^, was constructed from a homology structure of the muscle-type nAChR recently determined by cryoelectron microscopy. The neuronal channel model was embedded in a fully hydrated DMPC lipid bilayer, and molecular-dynamics simulations were performed for 5 ns. A comparative analysis of the neuronal- versus muscle-type nAChR models revea...

Related newspaper, magazine, and journal articles from HighBeam Research

Molecular Dynamics Simulation Suggests Possible Interaction Patterns at Early Steps of [beta]^sub 2^-Microglobulin Aggregation
Biophysical Journal ; ... Molinari, and F. Fogolari. 2003. Amino acid empirical contact energy definition for fold recognition in the space of contact maps. BMC Biainfarmatics. 4:8. 46. Esposito, G.. R. Michelutli, G. Verdone, P. Viglino, H. Hemandez, C. Robinson, A. Amoresano, F ...
Changes in a phospholipid bilayer induced by the hydrolysis of a phospholipase A(2) enzyme: A molecular dynamics simulation study
Biophysical Journal ; ABSTRACT Phospholipase A^sub 2^ (PLA^sub 2 enzymes are important in numerous physiological processes. Their function at lipid-water interfaces is also used as a biophysical model for protein-membrane interactions. These enzymes catalyze the hydrolysis of the sn-2 bonds of various phospholipids and
Molecular Dynamics Simulations of Forced Conformational Transitions in 1,6-Linked Polysaccharides
Biophysical Journal ; ABSTRACT Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(C^sub p^G) Steps
Biophysical Journal ; ... Sequence-dependent DNA structure: dinucleotide conformational maps. J. Mol Biol. 295:71-83. Packer, M. J., M. P. Dauncey, and C ... Sequence-dependent DNA Structure: tetranucleotide conformational maps. J. Mol. Biol. 295:85-103. Poncin, M., B. Hartmann, and R. Lavery ...
Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations
Biophysical Journal ; ABSTRACT Model biological membranes consisting of peptide/lipid-bilayer complexes can nowadays be studied by classical molecular dynamics (MD) simulations at atomic detail. In most cases, the simulation starts with an assumed state of a peptide in a preformed bilayer, from which equilibrium
Homology Modeling and Molecular Dynamics Simulations of Transmembrane Domain Structure of Human Neuronal Nicotinic Acetylcholine Receptor
Biophysical Journal ; ABSTRACT A three-dimensional model of the transmembrane domain of a neuronal-type nicotinic acetylcholine receptor (nAChR), 945;4)^sub 2946;2)^sub 3^, was constructed from a homology structure of the muscle-type nAChR recently determined by cryoelectron microscopy. The neuronal channel model was
Molecular Dynamics Analysis of Structural Factors Influencing Back Door P^sub i^ Release in Myosin
Biophysical Journal ; ABSTRACT The back door has been proposed to be an exit pathway from the myosin active site for phosphate (P^sub i^) generated by adenosine 5'-triphosphate hydrolysis. We used molecular dynamics simulations to investigate the interaction of P^sub i^ with the back door and the plausibility of P^sub
Detailed Mechanism for AmtB Conducting NH^sup +^^sub 4^/NH^sub 3^: Molecular Dynamics Simulations
Biophysical Journal ; ABSTRACT The mechanism by which the ammonium transporter, AmtB, conducts NH^sup sub 4^/NH^sub 3^ into the cytoplasm was investigated using conventional molecular dynamics (MD) simulations. These simulations revealed that the neutral molecule, NH^sub 3^, passes automatically through the channel upon
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps
Biophysical Journal ; ... Sequence-dependent DNA structure: dinucleotide conformational maps. J. Mol. Biol. 295:71-83. 16. Packer, M. J., M. P. Dauncey, and ... Sequence-dependent DNA structure. Tetranucleotide conformational maps. J. Mol. Biol. 295:85-103. 17. Vermulen, A., H. Zhou, and A ...
Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism
Biophysical Journal ; ABSTRACT Molecular dynamics simulations of a total duration of 30 ns in explicit solvent were carried out on the BPV-1-E2 protein complexed to a high-affinity DNA target containing the two hydrogen-bonded ACCG.CGGT half-sites separated by the noncontacted ACGT sequence. The analysis of the