Figure A2a:
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Alignments
Trees
Domain
models
Evaluation
of models
SequenceSpace:
Clustalw aligments for the three domains of
GRK2, coloured by Blosum62 matrix properties.
Figure A2b:
Image in PDF
Figure A2c:
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Clustalw bootstrapped trees for the
three domains of GRK2, using aligments from figures A1.
GRK2 3D models of the three major domains; N- and C-terminus residues are shown:
Figure A4a,b,c,d,e,f,g:
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Evaluation of the models of each
domain and of their corresponding pdb templates, provided by Eval123D.
a,b,c,d: kinase, open and close conformations
e,f: rgs
g: ph
Top ranking tree determinants from SequenceSpace results, mapped onto GRK2 model and PAK1 structure:
29 residues predicted as tree determinants at the kinase domain:
the
proposed docking model for the three domains agrees on 16 residues at 5 �
or less
to the RGS and PH chains (the other 9 solutions, only 8-12
residues).
For PAK1, 13 predicted treedet are depicted, distributed by distance to the PDB domain as follows:
- 3�: 0
- 4�: 1
- 5�: 1
- 6�: 2
- 7�: 4
- 10�: 5
- 15�: 9
- 25�: 13
SequenceSpace vectors for GRK2 kinase
sequence family (black), GRK2 sequence (red) and
GRK2 main tree-determinant
residues (blue).
So, figures A6 derive from the fact of referring all residual distances to
this main tree-determinant residues.
Image in PDF
Quantitative analysis of SequenceSpace
results:
a: PAK1
b: docking of RGS against kinase
c: docking of PH against kinase-RGS complex
