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Abstract
<p class="first" id="d498556e242">Phosphatidylinositol 4,5-bisphosphate (PIP
<sub>2</sub>) in the plasma membrane regulates the function of many ion channels,
including M-type
(potassium voltage-gated channel subfamily Q member (KCNQ), K
<sub>v</sub>7) K
<sup>+</sup> channels; however, the molecular mechanisms involved remain unclear.
To this end,
we here focused on the KCNQ3 subtype that has the highest apparent affinity for PIP
<sub>2</sub> and performed extensive mutagenesis in regions suggested to be involved
in PIP
<sub>2</sub> interactions among the KCNQ family. Using perforated patch-clamp recordings
of heterologously
transfected tissue culture cells, total internal reflection fluorescence microscopy,
and the zebrafish (
<i>Danio rerio</i>) voltage-sensitive phosphatase to deplete PIP
<sub>2</sub> as a probe, we found that PIP
<sub>2</sub> regulates KCNQ3 channels through four different domains: 1) the A–B helix
linker
that we previously identified as important for both KCNQ2 and KCNQ3, 2) the junction
between S6 and the A helix, 3) the S2–S3 linker, and 4) the S4–S5 linker. We also
found that the apparent strength of PIP
<sub>2</sub> interactions within any of these domains was not coupled to the voltage
dependence
of channel activation. Extensive homology modeling and docking simulations with the
WT or mutant KCNQ3 channels and PIP
<sub>2</sub> were consistent with the experimental data. Our results indicate that
PIP
<sub>2</sub> modulates KCNQ3 channel function by interacting synergistically with
a minimum of
four cytoplasmic domains.
</p>
The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein–protein and protein–small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at . The methods behind the servers are very efficient, allowing large-scale docking experiments.
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