I have a protein that contains an active site residue at the end of an alpha-helix. It has long been postulated that the dipole moment of this helix contributes to its activity. I want to compare this protein with a closely related homolog which has subtle changes in the environment of this active site residue. I have pretty good x-ray crystal structures of both proteins.
From computational point of view, since you have the 3D structures, you will need a force field, and create the topology files, which have the coordinates and charges. Then, the dipole is simply calculated by the formula d=sum_i r_i q_i, where sum run over all atoms of the alpha helix and r_i and q_i are respectively the coordinates and the partial charges. Only you have to make sure that your system (alpha-helix) is neutral, otherwise the dipole will depends on the origin of the coordinate system, in this case you may chose the center of mass for example. Standard force fields for proteins are CHARMM, AMBER, GROMACS, OPLS.
A word of caution: this approach might overestimate the effect of the helix dipole, see thoughts of a recent Nobel prize winner Arieh Warshel on that point http://pubs.acs.org/doi/abs/10.1021/ct700127w (Section 3.8)
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