On 3/23/11 9:02 AM, Van Den Berg, Bert wrote:
Hello all,
Does anyone know how to get values for pore sizes of membrane
channels? I'm not interested in A x B angstrom values measured between
atom centers and assuming a regular pore shape, but a "real-life"
value of either surface area at the narrowest point or the volume of a
block centered on the narrowest point of the pore.
Thanks, Bert
Hi Bert -
This is quick and dirty (perhaps too dirty for your purposes), but you
could do the following in PyMOL or something similar:
- draw the molecular surface of the channel of interest
- identify by eye (or from the manuscript) the narrowest point in the pore
- place a dummy atom in the middle of the pore at this point
- draw a sphere of varying radius using this atom as the center
- figure out the largest sphere which still fits inside the channel
I would guess that this would give you a number for the radius accurate
to 0.5 A, maybe better. It's not a true cross-sectional area, but that
doesn't seem as biologically relevant to me as whether a certain sphere
(e.g. calcium or magnesium ions) can fit through the pore.
Hope that helps,
Matt
--
Matthew Franklin, Ph. D.
Senior Research Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(646) 275-7165
