Welcome to the SAPIN webserver!

SAPIN is a framework dedicated to the Structural Analysis of Protein Interaction Networks

Protein-protein interaction (PPI) networks do not always inform on direct physical interactions, or whether several proteins binding to the same protein ‘hub’ are compatible or mutually exclusive, structurally (Kim et al., 2006). Integration of structural information with PPI networks can partially solve these limitations. First, 3D structural information of homologous structures can be used to predict physical binary (domain-domain) interactions within a larger complex of proteins (e.g. experimentally identified in a co-immunoprecipitation experiment). Second, 3D structures can be used to distinguish compatible (‘AND’) from mutually exclusive (‘XOR’) binding sites.

The SAPIN Webserver

How to use the SAPIN webserver?
SAPIN needs two input files: an interaction file (see example), and the related protein sequences provided as a fasta file (see example). SAPIN then searches for suitable complex templates of domain-domain and domain-motif interactions based on 3DID information. The interactions are evaluates by InterPreTS, and finally SAPIN selects the template that has a threshold > 2.33 Z-score, or the best score one among all candidates. If a protein uses the same domain to interact with more than one partner protein, structural superimpositions are performed, and the interacting domains are analyzed for backbone van der Waals clashes using FoldX. SAPIN provides Z-score for the clashing. A high Z-score means a higher confidence to be mutually exclusive (XOR). Compatible (‘AND’) and mutually exclusive (‘XOR’) interactions are represented using Cytoscape (see example network).

The Structural Interaction Network Related to Rhodopsin Signaling in Light/Dark Vision

Can we gain new biological insights using SAPIN?
We combined a PPI network related to rhodopsin signaling in photoreceptor cells with structural information (Kiel et al., 2011). Rod photoreceptors are specialized neuronal cells, located in the retina of mammalian eyes. They contain rhodopsin as the major protein component, a 7-transmembrane receptor, which initiates the first steps in light reception and transduction. We generated a structural interaction network for a defined proteome of about 500 proteins expressed in the rod outer segment. Adding ‘AND’/ ‘XOR’ data onto the rhodopsin PPI network, gained new biological insights into the process of mammalian vision: Competitors are frequently found in highly dynamic processes or may dynamically connect a given protein to different signaling and functional modules. The structural and interaction analyses of the core vision pathway and its cytoskeleton branch show several examples of non-compatible (‘XOR’) interactions. For example, rhodopsin may interact with transducin, arrestin, or rhodopsin kinase (in the core vision pathway). It may also interact with Rac1 or RhoA (which are antagonists in cytoskeletal dynamics) or with Arf4 (involved in trafficking). Changes in rhodopsin activation, concentration, and localization, or in its activation states, may therefore switch signaling into different pathways. Further, rhodopsin localization during ciliary transport and disk formation, and dynamic changes in concentrations and activation states in response to light, can alter the array of rhodopsin binding partners, since these are determined by the phosphorylation state of rhodopsin on the one hand and the availability or concentration of binding proteins on the other hand. Interestingly, ‘AND’ gates are mainly found in the housekeeping, structure and polarity, and metabolism branches, e.g., within large functional complexes, such as the T-complex, the proteasome, tubulin, and the ATP synthase machinery. ‘XOR’ gates, which are mainly prevalent in the vesicle structure and trafficking branch, indicate switch behavior or redundant protein functions, such as for Rab GTPases. In the vision branch, both ‘AND’ and ‘XOR’ gates synergize. This may allow dynamic tuning of light and dark states. However, all connections from the vision module to other modules are ‘XOR’ connections, suggesting that competition, together with local protein concentration changes, could be important for transmitting signals from the core vision module.