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Title: unusual protein-protein docking
I have an interesting protein-protein docking problem. This is different from
the typical docking of protein A to protein B. In this case, we know how
protein
A binds part of protein B (B1). We know the structure of entire protein B
(B1+B2). I need to perform the docking experiment to figure out how protein A
binds to entire protein B. Since there is the need to apply the constraint to
the structure freedom of B2 toB1 and B2 has relatively low affinity of protein
A, I am seeking for the suitable program for this task. The specific problem is
as the following:
This is to figure out how a conserved calcium sensor, calmodulin (CaM) (protein
B) binds and activates pertussis adenylyl cyclase toxin (CyaA) (protein A). CaM
binds CyaA with 0.2 nM affinity, which leads to catalytic activation of CyaA.
CaM has two structurally homologous N-and C-terminal domains (N-CaM and C-CaM,
respectively) that are joined by a flexible helix. It is known that C-CaM can
activate CyaA but it has the 100-fold reduced affinity to CyaA than CaM. I have
recently solved the x-ray structure of C-CaM bound CyaA (Qing et al EMBO J
24:3190, 2005). In order to know how N-CaM binds CyaA to facilitate the binding
of C-CaM to CyaA, I would like to apply protein-protein docking experiment. I
have already collected some mutational data, which will allow me to refine and
negate the potential solutions. I have gone to use some servers but so far all
of them only allow me to use regular protein A to protein B docking. I would
appreciate any insights that you can provide. Thanks.
Qing Guo
University of Chicago
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