CS395T Multi-scale Bio-Modeling and VisualizationProject: properties of the neuro-muscular junctionTeam members: Albert Chen, Pai-Chi Li, Weiqi Zhao, and Jessica ZhangProject report, Nov. 8th, 2005This is a short project report about modeling the volumetric properties of the combined neuro-muscular junction domain. The combined neuro-muscular junction domain includes the pre-synaptic membrane, postsynaptic membrane, AchR and AchE molecules.Without lossing generality, we simplify the model by considering a subregion of the NMJdomain which contains only one AchR molecule, one AchE molecule, part of the pre-synaptic membrane, and part of the postsynaptic membrane. The subregion is bounded in a rectangular gridded box. We focus on computing the following volumeric properties over the grids within the box: (a) electric charge density (b) hydrophobicity (c) electrostatics potentialof two different states:(i) before activation of AchR-channels (ii) after depolarization of post-synaptic membrane (post ion-permeation)Step 1: Prepare the pdb files.1. Download the pdb files of AchR and AchE of state (i) and (ii) from PDB website.2. There are two ways to represent the bilayer membranes: one in atomic level (fluid.pdb,provided by Pai-Chi) and the other in quasi-atomic level which could be computationally more efficient than the first one. One way to group the atoms in quasi-atomic level is to group the head of the membrane molecule as one quasi-atom (as shown in Figure 3, the blue spheres), and the tail of the membrane molecule as another quasi-atom (colored in black in Figure 3). The diameter of the tail quasi-atom could be half of the distance between the blue sphere bilayers. Basically, our model should be based on what kind of model the membrane and molecule groups use.3. Combine pdb files. Based on the relative positions of AchR, AchE and the membranes known from membrane group and molecule group, we can generate a uniform coordinate system and save them in a single pdb file.Step 2: Calculate properties (a) (b) (c) for state (i) and (ii).Calculate (a) (b) and (c) using TexMol and APBS, respectively. We will use the combinedpdb file as the input file. The generated volumetric data at each grid point will be saved as rawv file for TexMol and dx file for APBS.Step 3: Visualize volumeric properties.Choosing some isovalue of the electri charge density, say 1.0, we generate an isosurface. Then we can use LBIE or TexMol to display the distribution of hydrophobicity and electrostatic potential on this surface. We do the same work for both two states, hense we are able to visually compare the difference before and after the activation of
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