Pore region

IP3 Receptors. Figure 2 Key structural features of IP3 receptors. The key domains are shown in the central block. The upper structures show the suppressor domain (PDB accession code, 1XZZ) and the IBC (1N4K) with its (red) and p (blue) domains. A proposed structure for the pore region is shown below, with the selectivity filter shown in red only two of the four subunits are shown. The lowest panel shows reconstructed 3D structures of IP3R1 viewed (left to right) from ER lumen, the cytosol and in cross-section across the ER membrane (reproduced with permission from [4]). 

Fig. 5. Proposed topology of K channel subunits inserted into the membrane. COO carboxy-terminal. The proposed membrane-spanning segments SI-S6 in the core region of channel proteins are displayed linearly. H5 may be part of the K channel pore. The amino-terminal inactivation gate is symbolized by a positively charged ball which could occlude the pore region. The extracellular side is thought to be at top and the intracellular side at bottom.

In Figure 5 of reference 16, the pore region is based on the KcsA K channel from PDB 1BL8. Co-crystallized with Fab monoclonal antibodies from mouse. 

Possible hydrogen bonds in the pore region of HRV14 bound to WIN 61605 (ball and stick). The waters (spheres W1 and W2) could potentially form hydrogen bonds to WIN 61605 as well as the side chains of Asnl219 and Seri 107 as well as the backbone of Leul 106 (residues highlighted as tubes). The viewer is looking from the virion exterior. 

Each subunit has two transmembrane a helices as well as a third, shorter helix that contributes to the pore region. The outer cone is formed by one of the transmembrane helices of each subunit. The inner cone, formed by the other four transmembrane helices, surrounds the ion channel and cradles the ion selectivity filter. 

Fig. 10. Probabilities of finding an n-alkane in each of the three pore regions of silicalite as a function of carbon number, Nc. Reprinted with permission from Ref. 111. Copyright 1994 American Chemical Society.

Dynamic adsorption of 2,2-dimethylbutane into MCM-22 expressed as amount sorbed vs. time showed a peculiar three step uptake profile [6]. This was interpreted as reflecting adsorption into different pore regions. MCM-36 showed similar three step plot but with enhanced capacity for the first, fast uptake stage. This is again a reflection of pillaring, which modified some pore features while not affecting others. MCM-41 exhibited much lower dynamic sorption capacity for 2,2-dimethylbutane than both MCM-22 and MCM-36 and would therefore produce a reduction in the overall sorption value if present. 

Avila, G., and Dirksen, R. T. (2001a). Functional Effects of Central Core Disease Mutations in the Cytoplasmic Region of the Skeletal Muscle Ryanodine Receptor. J Gen Physiol 118(3) 277—90. Avila, G., O Brien, J. J., and Dirksen, R. T. (2001b). Excitation-Contraction Uncoupling by a Human Central Core Disease Mutation in the Ryanodine Receptor. Proc Natl AcadSci USA 98(7) 4215—20. Avila, G., O Connell, K. M., Dirksen, R. T. (2003). The Pore Region of the Skeletal Muscle Ryanodine Receptor is a Primary Locus for Excitation-Contraction Uncoupling in Central Core Disease. J Gen Physiol 121(4) 277-86. 

Here, E n = 0 on Sp (Neumann type boundary condition), where n is the unit outward normal from the pore region, and T> is compact. E can be interpreted as the microscopic electric field induced in the pore space when a unit macroscopic field e is applied, assuming insulating solid phase and uniform conductivity in the pore fluid. Its pore volume average is directly related to the tortuosity ax ... 

The field e-2 v is the current induced when a unit electric field is applied for a medium having insulating solid phase and conductivity er(r) = 1 —expi —fi/e) in the pore region. Current conservation yields ... 

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