Many proteins contain a number of structural and functional modules such as SH3, SH2, kinase and DNA binding domains (14
). Most of these domains mediate protein interactions with other biomolecules. A collection of interaction information, such as BIND, enables the study of the relationships between protein domain architecture and protein–protein interactions. Specifically, it is possible to classify the interactors of a protein into distinct groups based on domain composition.
As part of our research and using BIND and SeqHound as platforms, we implemented FAST as an application that displays the domain annotation for a group of functionally related proteins. In BIND, these groups of related proteins can be proteins that interact with a common partner or are found together in molecular complexes. The domain annotation is from SeqHound which contains a complete RPS-BLAST analysis of the GenBank or dataset, using the Conserved Domain Database (15
) performed on our 216 Beowulf cluster.
FAST has a web-based graphical interface, based on Macromedia Flash vector graphics, that displays a set of proteins and their domains. Vector graphics format was chosen as it provides improved resolution and zooming ability over bitmap images. FAST is accessible from BIND via interaction and molecular complex records. When accessed from an interaction record, the protein and its protein interactors in BIND are displayed. When accessed from a complex record, the protein subunits are displayed. Domain composition is shown as unique coloured horizontal bars above a line representing the sequence (Fig. ). Clicking on the arrow beside each protein links a user to an expanded display where domains are shown with respect to the amino acid sequence of the protein. Users can zoom in and out to examine the boundaries of a domain of interest in more detail using the Flash control tool. A domain summary table for the protein set, containing links to information on each protein and domain, can be accessed from the FAST image page.
Figure 1 Functional Alignment Search Tool (FAST). Domain composition for a set of proteins that interact with mouse Fyn is shown as uniquely coloured horizontal bars above a line representing the sequence. Expanded view of Vav, linked to via right-pointing red (more ...)
Visualization of a list of related proteins and their domains is a powerful approach to help direct future interaction studies. For example, the human and mouse variants of the protein tyrosine kinase Fyn
each have nine recorded interactions in BIND (Fig. ). The human and mouse forms of Fyn
share six similar interactions, however, the mouse variant is known to interact with a second protein tyrosine kinase Vav
, whereas the human Fyn
currently has no recorded interaction with the human Vav
homologue. Using FAST, it is easy to see that many Fyn
-interacting proteins, including Vav
, contain common cell-signaling modules such SH2 and SH3 domains. In combination with other tools and databases such as NCBI's CDART (17
), human homologues with similar domain architectures to mouse Fyn
interactors can be identified (e.g. VAV-3
). These proteins potentially interact with human Fyn
FAST can also be used to study the topology and function of molecular complexes. A number of protein complexes were recently identified in large-scale mass-spectrometry studies (7
). FAST can help decipher the interaction topology of these complexes by grouping proteins according to their domain composition. For example, part of the proteasome complex was identified using the protein Ygl004c as bait (BIND complex ID 11939). The domain architecture of the identified proteins reveals three distinct subgroups corresponding to three functional elements that control proteasome activity: ATPase (Rpt5, Rpt4, Rpt3, Rpt2, Rpt1), proteasome (Rpn9, Rpn7, Rpn6, Rpn5, Rpn3) and proteasome regulatory subunits (Rpn8, Rpn11).