PUFA contacts to <i>Shaker</i> tetramer residues in the open and closed states.

<p>The contact frequencies of amino acid residues within 3.5 Å of PUFA carboxyl head groups and carbon tails are displayed for the open <b>(AB)</b> and closed <b>(CD)</b> states. The red dotted line differentiates contacts on helices S1 and S2 or helices S3 and S4 of the VSD. Side-view of a VSD and interacting residues are displayed separately for the PUFA carboxyl head groups and tails for each state of the channel (insets).</p

The average minimum distances between the channel in its open and closed states and the PUFAs and SFAs.

<p>The fatty acids were sectioned into five parts consisting of carbons C_2-6 (TAIL-A), C_7-11 (TAIL-B), C_12-16 (TAIL-C), C_17-22 (TAIL-D), and the head group (HEAD). The error bars indicate the standard error of the minimum distances across the four subunits of the channel.</p

Molecular PUFA-VSD interactions in the <i>Shaker</i> channel.

<p><b>(A)</b> Close-up of a PUFA (DHA) in its initial conformation. The numbers marked in grey depict the carbons forming the <i>cis</i> double-bonds. <b>(B)</b> Side-view of one VSD equilibrated in a POPC lipid bilayer represented by a yellow iso-density surface corresponding to the positions of lipid nitrogens in the simulation at 5% occupancy. The residues shown in experimental studies to be close to the interaction site of DHA, namely residues I325, T329 located on S3, and A359, and I360 located on S4, are colored in cyan [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004704#pcbi.1004704.ref029" target="_blank">29</a>]. <b>(C)</b> Top-view of the <i>Shaker</i> tetramer with PUFAs in their starting positions. The PUFA carboxyl head group and carbon tail are colored in blue and green, respectively. The simulated dynamics of the PUFAs surrounding the <i>Shaker</i> tetramer is represented by a brown mesh iso-density surface at 27% occupancy. The cut-off was chosen to visualize the differences between the PD and VSD interactions with the PUFAs.</p

SFA contacts to the <i>Shaker</i> tetramer in the open and closed states.

<p>The contact frequencies of amino acid residues within 3.5 Å of SFA carboxyl head groups and carbon tails are displayed for the open <b>(AB)</b> and closed <b>(CD)</b> states of the channel. The red dotted line differentiates between helices S1 and S2 or helices S3 and S4 of the VSD. Side-view of a VSD and interacting residues are displayed separately for the PUFA carboxyl head groups and tails for each state of the channel (insets).</p

Additional file 1: of Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome

Contains the UniProt identifications, gene symbols, and Ensembl protein identifications for the classification of the 494 valid 4TM dataset. Also included within the table is the following information: signal peptides, topology, Pfam domains, functional classifications, review status, CCDS identifier, and gene-disease associations. (XLSX 176 kb