SH2 Domain of Tyrosine Kinase

Protein phosphorylation plays an important role in intracellular signal transduction. The protein tyrosine kinase p56lck is a member of the src family and is involved in the immune response by its role in T-cell activation. The p56lck kinase contains a src homology 2 (SH2) domain that is important for proper substrate recognition. SH2 domains are modules of ~100 amino acid residues and bind to phosphotyrosine-containing motifs in a sequence-specific manner. The structure shown here contains a short phosphotyrosyl peptide (Ac-pTyr-Glu-Glu-Ile) in complex with the SH2 domain of p56lck. The peptide binds in an extended conformation across the surface of the SH2 domain, forming its most important contacts through the pTyr and Ile side-chains. High resolution structures of peptides such as these are a good starting point for the design and optimization of new inhibitors of therapeutic benefit.

We constructed 3 surfaces in total. Here is a description of these surfaces:

The input file used is a pdb file (1lkkH.pdb) of the protein with the attached peptide substrate. For each surface, we removed water from the pdb file and set the solvent radius to zero (i.e. no solvent). The remaining operations differ for each surface.

1. 1lkkH.nW.g: Use ProtOr (vanderwaals) radii for the atoms and generate the surface.

2. 1lkkH.nW.nS.g: Remove the peptide substrate from the pdb file and use ProtOr (vanderwaals) radii for the atoms.

3. 1lkkH.nW.subs.g: Extract the substrate by computing the difference of the above two files.

NOTE: The ProtOr radii is described by Gerstein, Tsai and others. See Gerstein, et al. 1995, JMB, 249:955-966 and Tsai et. al. 1999, JMB, 290:253:266

Skin Surfaces


1lkk with Substrate	1lkk without Substrate	Substrate
Enlargement \| STL File	Enlagement \| STL File	Enlagement \| STL File

The above pictures show one view of the protein (with and without the substrate) and the substrate by itself. Look at the corresponding alpha complexes too. For reasons of visibility in these images, we scaled the substrate differently from the protein model.

Alpha Shapes


1lkk with Substrate	1lkk without Substrate	Substrate
Enlargement	Enlargement	Enlargement

Pockets

We computed the pockets in the protein using the Alpha Shapes again. Many of them were too small to be likely active sites. However, there were two pockets large enough to be good candidates. We show pictures of these pockets here (both alpha complex and skin surface). Notice the similarity between the substrate and the pocket on the left.

Skin Surfaces:


Pocket 1	Pocket 2
Enlargement \| STL File	Enlargement \| STL File

Alpha Shapes:


Pocket 1	Pocket 2

Relationship between Skin Surfaces and Alpha Shapes

Think of the Alpha Shape as the skeleton and the Skin Surface as the outer appearance that surrounds the Alpha Shape. For a pocket, the relationship is the other way around because it is a local complement of both structures. In other words, the pocket in the Alpha Shapes model always contains the corresponding pocket in Skin Surface description.

By the way, the Skin Surface of a pocket is locally the same as the Skin Surface of the complementary protein. Only their respective volumes lie on opposite sides of that surface.