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Color Plates

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Figures

Image of Color Plate 1 (chapter 2).

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Color Plate 1 (chapter 2).

Molecular cartoons of Ktn domains. (a) The Ktn domain of the KtrAB system (Roosild et al., 2002) showing the bound NADH in the Rossman fold. (b) The Ktn-SAM domains of the MthK channel (Jiang et al., 2002a) showing the bound Ca(gray spheres) and the positions of the three critical Arg residues in the KefC protein (red). The two Ktn domains are oriented in the same way so that their relatedness can be discerned. (c) A single Ktn-SAM domain from MthK showing the positions of 〈-helices and ®-sheets described in the text. The figure was drawn with CHIME (Martz, 2002).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 2 (chapter 2).

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color plate 2 (chapter 2).

The organization of Ktn and SAM domains in the MthK channel. The channel is shown in backbone (red) and is visible below (a) and through the central “pore” (b) of the Ktn-SAM domains. Ktn domains (pale gray) and SAM domains (dark gray) are each dimers constructed from one subunit attached to each channel-forming domain and one soluble domain synthesized from an intragenic translation start site. The protein is displayed viewed from the side and from the cytoplasmic face. In the original crystal structure another channel-forming domain is located above the Ktn-SAM complex, but this is omitted from this representation to indicate the probable structure of the MthK channel with an octameric assembly of Ktn-SAM domains. The figure was drawn with CHIME (Martz, 2002).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 3 (chapter 2).

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color plate 3 (chapter 2).

The V427A/F407L mutation pair indicated using the Ktn structure (Roosild et al., 2002). The positions of the ®1-〈1-®2-〈2 sequences are indicated; the Rossman fold is highlighted in yellow. The position of NADH binding is shown to indicate the potential proximity of the V427A mutation in KefC to the Rossman fold. The residues in red are L14 and A34, which are the equivalents of the V427A mutation and its F407L suppresser. The figure was drawn with CHIME (Martz, 2002).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 4 (chapter 2).

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color plate 4 (chapter 2).

Glutathione and gating of KefC. (a) The structure of glutathione is depicted and the length of the molecule determined using the CHIME program (Martz, 2002). (b) The KefC Ktn-SAM domain organization with respect to the HALESDIEP sequence in the membrane domain, to glutathione, and to the KefF protein based on the MthK structure. A pair of Ktn-SAM domains (each domain colored either blue or yellow) are depicted in contact with the membrane surface, such that one set of the Arg clusters (red) (see text) is placed in close opposition to the HALESDIEP sequence in accordance with genetic data (Roosild et al., 2002). The other set of Arg residues face the cytoplasm. The bridge between Ktn-SAM and HALESDIEP may be a direct salt bridge between R527 and E262 or may be created via GSH acting as an intermediary. The latter may account for the extreme sensitivity of the E262K and E262R mutants to the removal of GSH. The figure was drawn with CHIME (Martz, 2002).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 5 (chapter 4).

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color plate 5 (chapter 4).

Detection of gating movements. Changes in EPR parameters (coupling [A] and mobility [B]) for KcsA between open (pH4) and closed (pH7) are mapped onto the opposite inner helix of MthK. Residues have been replaced with spinlabel side chains. The lines separate the helix before and after the conserved glycine (G99). (C) Changes in side-chain surface accessibility from the KcsA crystal structure to an open KcsA model based on MthK are mapped.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 6 (chapter 6).

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color plate 6 (chapter 6).

Models of the voltage-sensing domain. (A) The crystal structure of the isolated voltage-sensing domain oriented in the bilayer (dashed lines) as predicted for the open channel. (B and C) Model in which S4 has moved inwardly by two (B) and four (C) helical screw steps. (D) Model of the resting conformation. S1-S3a segments are gray; S3b- S4-L45 segments are magenta. Positively charged residues of S4 are blue, negatively charged residues of S1-S3 are red, and L121 and L122 are green. The italicized residue numbers are generic and apply to all voltage-gated channel sequences. (Reprinted from Shrivastava et al. [2004] with permission.)

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 7 (chapter 6).

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color plate 7 (chapter 6).

Models of the voltage-sensing domain of the KvCA and KvVC channels. (A) Open KvCa, (B) resting KvCa, (C) open KvVC, and (D) resting KvVC conformations are shown. S1-S3a segments are gray; S3b-S4-S45 segments are magenta. Positively and negatively charged residues are blue and red.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 8 (chapter 7).

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color plate 8 (chapter 7).

Alignment of KirBac sequence with Kir7.1 and Kir2.1. Locations of the M1-P-M2 segments are indicated above the sequences. The numbers under the Kir2.1 sequence indicate features that are well conserved among most eukaryotic Kirs but do not occur in KirBacs or other K channels. Only residues that differ from KirBac1.1 are shown for other KirBac sequences. The KirBac sequences are from (KirBac1.1), (KirBac1.2), strain LB400 (KirBac1.3), (KirBac2.1), and (KirBac3.1).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 9 (chapter 7).

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color plate 9 (chapter 7).

Alignment of the M1-P-M2 region of the KirBac family with three non-Kir (Shaker Kv, a sequence from that belongs to the Kbac 6TM1 family, and KcsA) and with three eukaryotic Kirs (Kir7.1, Kir4.1, and Kir2.1). Only those residues that differ from KirBac1.1 are shown for the other KirBacs. The relatively large number of residues in the first and last three sequences are identical to at least one residue in the KirBac sequences. Features unique to Kirs are indicated by numbers under the sequences.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 10 (chapter 8).

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Color Plate 10 (chapter 8).

Structure of glutamate receptors. (A) Schematic of a single subunit from the (tetrameric) GluR. (B) Homology model of TM domain of GluR0 (for clarity only two of the four subunits are shown). (C) Ligand-binding domain structure of GluR0.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 11 (chapter 8).

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Color Plate 11 (chapter 8).

Intersubdomain motions in a 20-ns simulation of GluR0 (in the presence of bound glutamate). (A) The D1-D2 intersubdomain distance is shown as a function of time. The arrows indicate the times at which snapshots of structures, illustrated in panels B and C, were taken. (B and C) Snapshots along the simulation at ˜ 0 and ˜ 9 ns, revealing the closed and open conformations of the D1/D2 cleft.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 12 (chapter 8).

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Color Plate 12 (chapter 8).

Comparison of the hinge-bending motion of LAOBP, GluR0, and GluR2 as revealed by principal omponents analysis of simulations. The green bars indicate the direction of motion of the C〈?atoms corresponding to the hingebending motion as revealed by principal components analysis of 10-ns MD simulations of the corresponding proteins. The schematic diagrams below the structures indicate the nature of the hinge-bending motion revealed.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 13 (chapter 9).

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Color Plate 13 (chapter 9).

Top (left) and side (right) views of an AQP tetramer in a fully hydrated lipid bilayer (Zhu et al., 2001; Jensen et al., 2001; Tajkhorshid et al., 2002). The model includes 106,000 atoms. The monomers are shown using cartoon representations. The phosphate groups of lipids are shown using vdW representation to illustrate the variation of membrane thickness at its interface to the protein. Four water pores each formed by a monomer are discernible from the top view. A fifth pore is formed in the middle of the tetramer.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 14 (chapter 9).

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Color Plate 14 (chapter 9).

The pathway for glycerol transport in GlpF is formed by the nonhelical halves (shown in red tube) of the two reentrant loops and the two conserved asparagine side chains (shown in licorice representation) of the NPA motifs in the middle of the channel.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 15 (chapter 9).

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Color Plate 15 (chapter 9).

Substrate conduction pathway in AQPs formed by backbone oxygen atoms of the reentrant loops. Carbonyl oxygens are shown in red. The peculiar secondary structure of the nonhelical halves of the loops is stabilized by specific hydrogen bonds with two highly conserved glutamates shown in CPK representation. Asparagine side chains of the NPA motifs are also shown.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of color plate 16 (chapter 9).

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color plate 16 (chapter 9).

PMF along the pathway of glycerol conduction in GlpF, constructed from SMD simulations (Jensen et al., 2002). The PMF is superimposed on a GlpF channel, in which several positions adopted by glycerol along its transport are highlighted.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 17 (chapter 9).

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Color Plate 17 (chapter 9).

A snapshot from an MD simulation of GlpF. Only one monomer is shown. A single file of water forms in the channel during the simulation. The orientation of water molecules in the single file is reversed in the two halves of the channel due to the electric field of the protein. This bipolar configuration of water prevents proton conduction (Tajkhorshid et al., 2002; Jensen et al., 2003).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 18 (chapter 9).

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Color Plate 18 (chapter 9).

Homoheptameric architecture of MscS. (A) Cartoon representation of the MscS crystal structure. Each subunit is presented in a different color. The suggested membrane position (Bass et al., 2002) is shown as a gray bar. (B) Top view of the transmembrane domain (residues 27 to 128). Pore residues (96 to 113) are shown in surface representation. Each subunit is labeled by a color and a letter. (C) “Solvent-excluded” surface representation of MscS. Seven cytoplasmic openings are located on the side (one visible in front) and one at the bottom.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 19 (chapter 9).

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Color Plate 19 (chapter 9).

Simulated conformations of MscS. Top views of final states of simulations sim1 (A), sim2a (B), and sim2b (C). The transmembrane domain is shown in surface representation and the lipid bilayer in space-filling representation. The color code for each protein subunit is the same as in Color Plate 18B . The simulations were carried out on a protein, lipid, water, and ion system with 224,340 atoms.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 20 (chapter 9).

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Color Plate 20 (chapter 9).

Water permeation of MscS in open and closed forms. Shown is the occupancy of the hydrophobic (transmembrane) pore of MscS by water molecules as a function of time for simulations (A) sim1, (B) sim2a, and (C) sim2b. The number of water molecules inside the pore was monitored every picosecond assuming the positions of Cα atoms of residues 96 and 113 as pore ends. Snapshots of the pore (shown in surface representation and colored by residue type) with water molecules are shown for representative states.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 21 (chapter 9).

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Color Plate 21 (chapter 9).

Gating of MscS. (A) Movement of transmembrane helices. Transmembrane domains are shown in ribbon representation. Red shows the state of helices in simulation sim2a (open pore) and green shows the state of helices in simulation sim2b (closed pore). (B) Contacts between TM1-TM2 loop and the TM3B helix of adjacent subunits. Segments of helices TM1, TM2, and TM3 of subunit B are shown in blue along with helix TM3 of subunit A shown in light blue, all in tube representation. Residue Asp62 of subunit B and residue Arg128 of subunit A are shown in space-filling representation. The interaction of both residues is clearly discernible. The large arrow indicates the suggested movement of transmembrane domains during channel opening.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 22 (chapter 11).

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Color Plate 22 (chapter 11).

Ribbon representation of the ClC-Set1 dimer viewed from outside the membrane. Monomers are in blue and red with the Cl ions indicated as magenta CPK spheres. The positions mutated in the study of Duffield et al. (2003) are indicated by CPK spheres colored as follows: green, A179, A188, A189, I200, I223, P405, and M425; yellow, F438; red/pink, S225 and T407; numbered according to ClC-Set1.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 23 (chapter 11).

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Color Plate 23 (chapter 11).

Cartoon of a ClC-Set1 monomer viewed from within the plane of the membrane from the direction of the opposing monomer with the extracellular face at the top. Helices are indicated by cylinders, colored from blue (N terminus) to red (C terminus), with labels according to Dutzler et al. (2002). The Cl ion is indicated as a magenta CPK sphere.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 24 (chapter 11).

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Color Plate 24 (chapter 11).

Ribbon representation of a ClC-Set1 monomer as for Color Plate 23 . Helices whose dipoles stabilize the Cl ion at the simple gate are colored from blue (N terminus) to red (C terminus) and labeled. For clarity, helices P and H and their connecting loops have been omitted.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 25 (chapter 11).

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Color Plate 25 (chapter 11).

Ribbon representation of ClC-Set1 selectivity filter. The side chain of Glu148 is shown with the epsilon oxygen atoms indicated in red.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 26 (chapter 11).

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Color Plate 26 (chapter 11).

Ribbon representation of the CBS domains of ClC-Hs1 based on the structure of the CBS domains of inosine monophosphate dehydrogenase (PDB code 1zfj). The sequence is colored from blue (N terminus) to red (C terminus). Sequences between CBS1 and CBS2 are not included in the model.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 27 (chapter 12).

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Color Plate 27 (chapter 12).

The structure and pore design of the MscS channel. The model shown is derived from X-ray crystallographic data (Bass et al., 2002). The side (top panels) and top (bottom panels) views are shown. Each of the seven subunits in the complex is shown in a different color in a space-filling model (left) or in a wire diagram with a single subunit shown as a ribbon diagram in gray with the pore domain highlighted in black (left center). The pore domain is enlarged to show the heptameric (right center) and simple trimeric (right; the obstructing subunit structures have been removed) structures. Note the tight packing of the glycines (green CPK residues) and alanines (blue CPK residues) of the three subunits in the right panel.

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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Image of Color Plate 28 (chapter 13).

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Color Plate 28 (chapter 13).

The hypothetical gating transition in MscL modeled as a two-stage process, proceeding from the closed (left) to expanded (center) and then to the open state (right). The first stage is opening of the main M1 gate associated with major expansion of the barrel. In the intermediate expanded state S1 helices hold together, thus representing the low-conducting substate. Separation of S1 domains associated with minor expansion leads to the fully open state. The domains are color coded: S1 (red), M1 (yellow), S2 loops (green line), M2 (blue-green), and S3 (purple). Pairs of cysteine positions shown to form disulfide bonds in cross-linking experiments are mapped on the closed- and open-state models (see text).

Citation: Kubalski A, Martinac B. 2005. Color Plates, In Bacterial Ion Channels and Their Eukaryotic Homologs. ASM Press, Washington, DC.
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