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