Proteins are known to interact with other biomolecules in order to accomplish their physiological roles (1). Protein-protein interactions govern majority of the cellular processes for e.g. transcription, replication, cell signaling etc. Studying these interactions provide us insights into the mechanism and regulation of the underlying cellular process.
There are many experimental techniques, which can be employed to recognize interacting proteins, like co-immunoprecipitation, yeast-two-hybrid, western blotting etc (2, 3). Also, with the help of X-ray crystal structures of the protein-protein complexes, we can learn a great deal about the interface and hence the mechanism of action. The computational tool, Molecular docking can also be employed to study protein-protein interactions (4, 5). However, it proposes several possible solutions and identifying biologically relevant pose is a daunting task.
DockScore, is a scoring scheme which can be used to re-rank the docked poses and identify the biologically meaningful poses (Malhotra S., Kannan S. and Sowdhamini R., Structural interface parameters are discriminatory in recognizing near-native poses of protein-protein interactions. PLoS ONE, in press).
Method:
The webserver presented here employs the scoring scheme called DockScore to perform the ranking of the docked poses. It utilizes the parameters of the interface formed upon interaction of the two given protein chains. These interface parameters are surface area, conserved residues, hydrophobicity, short contacts and spatial clustering. There is an additional parameter, which is based on the presence of positively charged residues at the interface. This can be employed when the interacting protein chains are DNA-binding in nature and the presence of positively charged residues at the interface is penalized to minimize the overlap of protein-protein interaction site with that of DNA-binding region.
The interface residues are identified using the distance- based criteria, inter-chain C&Beta-C&Beta distance cut-off of 7 Å. Interface parameters used in scoring
1. Surface Area: It is computed using NACCESS ('NACCESS', computer program. (1993) by S. J. Hubbard, J. M. Thornton).
2. Conservation of residues: The interacting protein chains were used as a query to perform PSI-BLAST (6) in order to collect homologues against SWISSPROT and multiple sequence alignment is build-using MUSCLE (7). Conservation scores per residue are evaluated using Cons Score, as explained in Valdar and Thornton, 2001 (8). Following this, the number of conserved residues at the interface (Ci) is normalized by the number of interface residues. (N)
3. Inter-chain short contacts: Our in-house program CoilCheck (9) is employed to identify short contacts. Here Energyhighest is the highest energy value in the pool of docked poses, Energylowest is the lowest energy value in the pool of docked poses and Energycomplex is the energy value of the pose being scored.
4. Spatial Clustering:
The pairwise distances between the interface residues were computed between the two chains and the residues with a C&Beta-C&Beta distance cut-off of 14 Å were considered as spatially clustered residues. 'd' is the number of residues within the cut-off distance and 'N' is the number of interface residues at both chains.
5. Hydrophobic residues:
We ranked those docked poses with high numbers of hydrophobic residues with a high score, where Hi is the number of hydrophobic (A, V, L, I, M, F, W and Y) interface residues and N is the number of interface residues.
Please refer to the Methods part of DockScore article for more details on each parameter.
