[ccp4bb] (off-topic) Measurement of channel pore dimensions
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
Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions
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
Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions
Try the program Hollow. Or visit USF and find the cavity script. There's also Carver out there but I never got it really to work for my purposes, but it's been written for channels. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 9:02, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu 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
Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions
Dear Bert, You could try the program Hole from http://www.ncbi.nlm.nih.gov/pubmed/9195488 J Mol Graph. http://www.ncbi.nlm.nih.gov/pubmed/9195488 1996 Dec;14(6):354-60, 376. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Smart OShttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Smart%20OS%22%5BAuthor%5D , Neduvelil JGhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Neduvelil%20JG%22%5BAuthor%5D , Wang Xhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Wang%20X%22%5BAuthor%5D , Wallace BAhttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Wallace%20BA%22%5BAuthor%5D , Sansom MShttp://www.ncbi.nlm.nih.gov/pubmed?term=%22Sansom%20MS%22%5BAuthor%5D . -Partha On Wed, Mar 23, 2011 at 9:02 AM, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu 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
Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions
Bert; I have found the online gui 3V to be very useful in calculating channel dimensions. It outputs the volume and surface area of the pore, along with a surface representation that can be visualized in Chimera or PyMOL. You can either specify a specific pore or search for pores within a given size. There is other functionality available on the website for solvent volumes, etc. http://3vee.molmovdb.org/ Regina From: Van Den Berg, Bert lambertus.vandenb...@umassmed.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, March 23, 2011 9:02:19 AM Subject: [ccp4bb] (off-topic) Measurement of channel pore dimensions 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
Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions
Though I like our program HOLLOW for visualization, I think the tool for this job is MOLE (http://mole.chemi.muni.cz). You can use the online version to quickly generate two trajectories out from the center of the channel. MOLE has some mathematical advantages over HOLE or Caver. You then merge the two pdb files and delete the overlapping points. The resulting file will have a radius of the sphere at each point along the trajectory in the Bfactor field. The radius is the maximum sphere size that would fit within channel along the trajectory which should be the center of the pore. This can then be plotted as done by Smart et al. Biophys J. 1993. Dec;65(6):2455-60.
