I have a protein complex for which multiple sites specific mutations were carried out. A stretch on the surface of the protein shows phenotypic and biochemical changes. It has a known phosphorylating serine. Since the region of interest is away from the interface of known complexes it looks like a new PP interface. Proteomics and other approaches have suggested a few potential partners. First, I would like to study the surface and thereby deduce the possible partner protein. Secondly, using the sequence of the protein, I would like to do some bioinformatic search on potential binding residues. please suggest some useful tools, web server for carrying out these sequence and structure based PPI and approach.
If it is an allosteric site, you may try this tool: https://www.ncbi.nlm.nih.gov/pubmed/25185787
Hi,
in order to study the surface of a macromolecular complex, if a crystal structure is available (you need a PDB entry or coordinate file), you can use PISA (Proteins, Interfaces, Structures and Assemblies) at the EMBL-EBI (Krissinel, 2007). This tool predicts the amino acid residues involved in the assembly of the complex and indicates the residues involved in the protein protein interaction.
If you do not have a protein model, you can build it using Phyre2 that predicts and analyses the protein structure (Kelley et al., 2015). This tool predicts from the protein sequence the ligand binding sites and analyses the effect of amino acid variants.
PISA: http://www.ebi.ac.uk/pdbe/pisa/
Phyre2: http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
Hope this helps.
Dear S. Kailasam
If you have identified both interacting protein, then you can perform PPI studies as described below:
Since, as you must have read that Protein-protein interactions mostly involve shallow binding grooves. These can be identified by various tools namely MetaPocket, Site-ID, Pocketfinder, etc..
After you identify these shallow grooves on both the proteins, go for protein-protein docking studies using packages like ZDOCK, HADDOCK, etc.
After analysing the lowest energy poses try to simulate protein poses in solvent condition for a 50 to 100ns. The best pose can then be analyzed subsequently based on interaction energy in solvent system.
If the interacting proteins have not been identified, then you can perform string database search to identify possible interacting proteins. These protein can be further analyzed by above protocol.
Dear S. Kailasam
You can find by using the Search Tool for the Retrieval of Interacting Genes (STRING) database (http://www. string-db.org/). It is possible that it provide to PPI network of the overlapping any differentially expressed genes. Also, this is helpful for procuring known interactions and predicted interactions for you.
Hi Sneha, nice hear from you after a long time.
Can u elaborate on the following statement "....suggested to ensure that the region did not turn up in the biochemical assay because of its allosteric influence on the binding interface."
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