I vaguely recalled reading a paper from Janet Thornton's group showing that there was a non-random distribution of N-terminus to C-terminus distances in proteins, with the distance being less on average than you would expect if the C-terminus were at a random position on the surface relative to the N-terminus. Google led me to a more recent paper on this topic:
MMG Krishna and SW Englander, PNAS 102: 1053-1058 (2005) They relate this preference to folding mechanisms, although I also recall hearing the argument once that it was a sort of meta-evolutionary result: proteins with their N- and C-termini close are better suited to productive gene fusion events. I don't know how significant that would be as a source of evolutionary pressure, but it's an interesting concept. In any case, this paper may lead you to some other relevant literature. Best wishes, Randy Read On 19 Apr 2012, at 02:14, Sam Jimmeson wrote: > Hello, > I'm trying to figure out a way to search the entire PDB and find proteins > that have N-terminal(Calpha) to C-terminal(Calpha) through space distances of > between 10-20A. I was trying to decide if CONTACT or DISTANG would be better > to use for this, or if there is an easier way using some other tool. Has > anyone else ever done this? Thanks for any advice. > -Sam ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
