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There is one additional point perhaps worth making: As already noted in the thread, if you have a NCS homo-oligomer, the different copies in general have different environment, and proper inspection of the contacts reveals the details. On multiple occasions during inspections and review I have noticed that such is not always interpreted or welcome as a functionally necessary manifestation of the plasticity of the protein in question. In case of binding sites, in contrast it occurs that the 'best' one where a ligand actually exists or assumes a pose/environment perceived as useful for the proposed hypothesis is picked as the representative (figure), and from there the story evolves. This misses the point, and somewhat reeks of confirmation bias (the neglect of negative or 'unsuitable' results) leading straight down the road to scientific serfdom in terms of becoming a slave of one's own (pre)conceptions.... Best regards, BR On Wed, Jan 29, 2014 at 10:24 AM, Kay Diederichs < [log in to unmask]> wrote: > Hi Shane, > > some crystal forms of trimeric AcrB (a multi-drug resistance secondary > transporter) have 3 (or 6) monomers in the ASU and these are substantially > different, which suggests how the protein functions. > One reference is e.g. Seeger et al. (2006) "Structural Asymmetry of AcrB > Trimer Suggests a Peristaltic Pump Mechanism " Science 313, 1295-1298 > DOI: 10.1126/science.1131542 (sorry for the self-plug!) > > best, > > Kay > > > > On Mon, 27 Jan 2014 13:08:33 -0500, Shane Caldwell < > [log in to unmask]> wrote: > > >Hi ccp4bb, > > > >I'm putting together a talk for some peers that highlights strengths and > >weaknesses of structural models for the outsider. For one point, I'd like > >to find some examples of proteins that show very different conformations > >between different copies in the ASU. One example I know of is c-Abl > (1OPL), > >which crystallizes with both autoinhibited and active forms in the ASU, > >with dramatically different domain organization. I'd like to find some > >additional examples - can anyone suggest some other structures that have > >multiple copies with large structural variations? > > > >Thanks in advance! > > > >Shane Caldwell > >McGill University > > > -- ----------------------------------------------------------------- Bernhard Rupp (Hofkristallrat a. D) 001 (925) 209-7429 +43 (676) 571-0536 [log in to unmask] [log in to unmask] http://www.ruppweb.org/ ----------------------------------------------------------------- The hard part about playing chicken is to know when to flinch -----------------------------------------------------------------