Figure 1.
The Src SH2 domain complexed with pYEEI.
(A) Cartoon representation of the complex. Residues ArgαA2 and ArgβB5 of the SH2 domain are in blue, residue Ile(pY+3) of the phosphopeptide is in magenta. (B) Electrostatic surface potential representation of the same complex. The phosphotyrosine sits in a highly electropositive hole, while residue Ile(pY+3) is inserted into the hydrophobic hole on the surface of the SH2 domain.
Table 1.
Relative binding affinity of various phosphopeptides with the Src SH2 domain.
Figure 2.
Spatial and energy distribution of the SA replicas of pYEEI and pYVPM complexed with Src SH2.
(A and D) after energy minimization at 3000K; (B and E) after cooling with 50ps per temperature step; (C and F) after cooling with 500ps per temperature step.
Figure 3.
Conformational trends of pYEEI and pYVPM complexed with the Src SH2 domain.
Backbone representation of the 50 computational replicas of pYEEI (A–C) and of pYVPM (D–F) superimposed on the crystal structures of these phosphopeptides in complex with the Src SH2 domain. (A and D) after energy minimization at 3000K; (B and E) after cooling with 500ps per temperature step. The backbone of the SH2 domain is in black, the SA replicas are in red. (C and F) Phosphopeptide backbone of the representative structure of the largest cluster after cooling with 500ps per temperature step, with side-chains of pTyr and of residue in position pTyr+3 (in red). The backbone of the crystal structure of the phosphopeptides and the side chains of the pTyr and residue pTyr+3 is in green. The SH2 domain is represented as an electrostatic potential surface. The representative structure of a cluster is the structure closest to the average structure of the cluster.
Figure 4.
Spatial distribution of Simulated Annealing replicas of the pYEEX series between the extended and helical conformation after cooling at 500ps per step.
From top to bottom: pYEEI, pYEEL, pYEEV, pYEEA, pYEEG.
Figure 5.
Conformational trends of the pYEEX series of peptides complexed with the Src SH2 domain.
(A) Cartoons of representative structures of the “extended” conformation cluster of the pYEEX series superimposed on the structure of pYEEI complexed with the Src SH2 domain; (B) Representative structures of the “helical” conformation cluster of pYEEX series, superimposed on an ideal helix. The reference conformations for extended and helical clusters are in magenta, pYEEI, red, pYEEL, yellow, pYEEV, green, pYEEA blue, pYEEG, light blue.
Figure 6.
Spatial distribution of the replicas between extended and β-turn conformation for pYVNV (black) and pYENI (red), after cooling with 500ps per temperature step.
Figure 7.
Conformational trends of the pYVNV and pYENI complexed with the Src SH2 domain.
(left) Backbone representations of the 50 replicas (red) superimposed on the crystal structure of the pYVNV-ThrEF1Trp Src SH2 domain complex and the modeled extended conformation of pYVNV for (A) pYVNV and (C) pYENI. (right) Backbone of the representative structure of the main cluster (red) and minor cluster (pink) with the side-chain of residue Asn(pTyr+2) for (B) pYVNV and (D) pYENI. Backbone of SH2 domain in black, modeled extended conformation of pYVNV in yellow, β-turn conformation of pYVNV in blue.
Figure 8.
Hydrogen bonds formed by Asn(pY+2) in pYVNV and pYENI complexed with SH2 domains.
(A) pYVNV complexed with the ThrEF1Trp mutant of Src SH2; (B) pYVNV complexed with wt Src SH2 (representative of the major cluster); (C) pYENI complexed with wt Src SH2 (representative of the major cluster). The phosphopeptide backbone is represented as a cartoon.