Biopolymers, 75(4), 325-337 (2004).
Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations. More...
Biophys. J. 88, 1659-1665 (2005).
TETRAMERIC MOUSE ACETYLCHOLINESTERASE: CONTINUUM DIFFUSION RATE
CALCULATIONS BY SOLVING THE STEADY-STATE SMOLUCHOWSKI EQUATION USING
FINITE ELEMENT METHODS
The tetramer is the most important form for acetylcholinesterase in
physiological conditions, i.e., in the neuromuscular junction and the
nervous system. It is important to study the diffusion of acetylcholine
to the active sites of the tetrameric enzyme to understand the overall
signal transduction process in these cellular components.
Crystallographic studies revealed two different forms of tetramers,
suggesting a flexible tetramer model for acetylcholinesterase. Using a
recently developed finite element solver for the steady-state
Smoluchowski equation, we have calculated the reaction rate for three
mouse acetylcholinesterase tetramers using these two crystal structures
and an intermediate structure as templates. Our results show that the
reaction rates differ for different individual active sites in the
compact tetramer crystal structure, and the rates are similar for
different individual active sites in the other crystal structure and
the intermediate structure. In the limit of zero salt, the reaction
rates per active site for the tetramers are the same as that for the
monomer, whereas at higher ionic strength, the rates per active site
for the tetramers are 67%–75% of the rate for the monomer. By analyzing
the effect of electrostatic forces on ACh diffusion, we find that
electrostatic forces play an even more important role for the tetramers
than for the monomer. This study also shows that the finite element
solver is well suited for solving the diffusion problemwithin
complicated geometries. More...
AN ACTIVATION MECHANISM OF NICOTINIC ACETYLCHOLINE RECEPTOR SUGGESTED BY ACETYLCHOLINE UNBINDING
Nicotinic acetylcholine (ACh) receptor (nAChR) is a prototype ligand-gated ion channel, which converts chemical messages carried by neurotransmitters to electric signals. Although extensive studies have been done to elucidate the underlying mechanism of channel opening activated by agonist binding, the detailed picture remains unclear. Recently the structure of the ACh binding protein (AChBP) from Lymnaea stagnalis and a 4 Å cryo-electron microscopy (cryo-EM) structure of the Torpedo nAChR became available, making structural simulation in atomic detail a possibility. Here we used steered molecular dynamics to investigate the structural changes after the unbinding of acetylcholine from its binding site in the ligand binding domain (LBD) of human alpha7 type homo-pentameric nAChR. We show that the C loop opening upon ACh unbinding unlocks an untwisting motion of the LBD, in which the cys-loops rotate anti-clockwise and move downward toward the transmembrane domain (TMD), applying a twisting torque to the M2-M3 loop to kink M2 to close the channel. All five subunits contribute to the gating process in alpha7 nAChR.
PLoS Comput Biol. 1(5), e62 (2005).
TETRAMERIC MOUSE ACETYLCHOLINESTERASE ASSEMBLY WITH PRAD
Acetylcholinesterase (AChE) rapidly hydrolyzes neurotransmitters in the neuromuscular junctions and other cholinergic synapses to terminate the neuronal signal. In physiological conditions, AChE exists as tetramers associated with the PRAD component of either collagen-Q or PRiMA. Crystallographic studies have revealed that different tetramer forms may be present, and it is not clear which one is the true structure in the physiological condition. Recently a model structure PRAD-(WAT)4, which mimics the interface between PRAD and AChE tetramer, became available. In this study we built a tetrameric mouse AChE structure with the complete sequence, and docked it to the PRAD-(WAT)4 structure. The structure was optimized using energy minimization and molecular dynamics. Normal mode analysis was done to correlate the structure with the two known crystal structures of AChE tetramer. Significant movements among the soluble part of the four AChE subunits were observed, while the PRAD-(WAT)4 part held the complex together. All these evidence support the idea of a flexible tetramer model for AChE. In addition, the dynamics of PRAD shed light on the possible mechanism for the assembly of the PRAD-AChE complex. More...