PPI summary matrix table.

<p>If users click TRP channel subfamily on the left panel, they can see ‘General Information’ and ‘PPI Summary Matrix’. General information provides UniprotKB IDs and amino acid sequences with FASTA, EMBL, or GenBank format. The PPI summary matrix enables users to intuitively grasp overall PPI information. Mouse pop-up help messages (red box) show the current state of information on data contents. By clicking each symbol (S, V, C, or F), users can obtain detailed information on each PPI pair.</p

Mouse-over pop-up help messages.

<p>The TRIP Database 2.0 provides mouse-over pop-up messages, which are indicated as red boxes, to provide brief information of some icons. (A) Current state of information contents in the ‘PPI summary matrix’. (B) References in the ‘At a glance’. (C) Symbolic names in the ‘At a glance’. (D) Show/hide mark in the ‘In detail’. (E) External databases in the ‘In detail’. (F) PPI pairs in the ‘In detail’. (G) Node in the ‘Interaction Map’ pages.</p

Downloading sif files.

<p>After clicking the ‘Download’ tab (red box), users can download various sif files according to option settings, such as TRP channel subfamily type and PPI category. In addition, our database offers the option to include the STRING DB contents for data enrichment. The TRIP Database 2.0 also provides a Microsoft Excel and a CSV file.</p

External links and data integration.

<p>Through clicking a specific TRP channel isotype (TRPV4 here) and then the ‘In detail’ button (A), users can see a tabular presentation, including basic information (B), external database (C), PPI pairs (D), biological process (E), and disease (F).</p

A diagram of navigating the TRIP Database 2.0.

<p>Users can browse the database based on TRP channel subfamilies or isotypes. If users choose to begin their search based on a specific TRP channel subfamily, they will get a summary of the subfamily, including general information (isotypes, amino acid sequences, or UniprotKB IDs) and PPI information, through the PPI summary matrix. If users choose to browse based on a specific TRP channel isotype, they will see lists of TRP channel PPI pairs. For example, the interface might provide one TRP channel with all of its interactors whereas in another instance all TRP channels with one interactor. Users also can start with a keyword search in the database or download the database contents in three formats.</p

PPI information found in the supplementary data of referred articles.

<p>Of the total 579 PPI pairs listed in the TRIP Database 2.0, 83 PPI pairs were retrieved from only the supplementary data.</p

TRP channel PPI network.

<p>Users can represent the TRP channel PPI data as a network using the Cytoscape program. (A) The PPI network consists of the relations between TRP channels and their interacting proteins. (B) The extended PPI network includes two different relations: one between TRP channels and their interacting proteins and the other between the interacting proteins.</p

Stoichiometry of TG2 in solution.

<p>A. Gel-filtration chromatogram of TG2. A profile obtained from TG2 in buffer containing 20 mM Tris-HCl at pH 8.0 and 150 mM NaCl is shown. Protein size markers are indicated. B. Multi-angle light scattering (MALS) measurement of TG2 in complex with GTP. The x-axis and y-axis indicate the elution volume and molecular mass, respectively. C. Monomeric structure of TG2 in complex with GTP. The active site is shown by a red circle. The GTP binding site is magnified for better visualization.</p

Crystal structure of TG2 in complex with GTP.

<p>A. Domain boundary of TG2. Domains are gold and the amino acid residue numbers corresponding to each domain are indicated. B. Ribbon diagram of the structure of TG2 in complex with GTP. Three molecules in the asymmetric unit are shown (Chain A, Chain B and Chain C). C. Symmetric dimer formed by Chain B and Chain C is shown. D. Superposition of the structure of the TG2/GTP complex with known structures. Structurally different regions are indicated by red-dot circles.</p

Sequence alignment between inter-isotype TG family members.

<p>Amino acid residues conserved at the GTP binding site are shown in red. Amino acid residues perfectly and partially conserved across the isotype are highlighted with green or blue, respectively.</p