Hi folks Just my two ha’porth; if you go back to one of the first two structures determined by protein crystallography, haemoglobin (horse?) has multiple oxygen binding sites) which are potentially different (the binding of oxygen ion one affects the binding in the other - “allostery”). I’m not sure if the two sites are distinguishable in any 3D structures, but the possiblility would be there. No doubt experts on this BB would be able to expand on this or tell me that I’m wrong…
My answer to the OP would be along the lines of “I wouldn’t be surprised by this at all”... Harry > On 6 Mar 2022, at 18:02, Dom Bellini - MRC LMB <dbell...@mrc-lmb.cam.ac.uk> > wrote: > > I dont think it is necessary to prove what others have said so far, but if > you would like some concrete evidence to support those statements: > > we cocrystallized a protein together with a small peptide, producing a > crystal with for molecules in the AU but only one promoter showed clear > density for the bound peptide (crystal contacts played a part in this); then > the construct was shorten a bit and cocrystallized in a different space group > still, by chance, with 4 molecules in the AU, but this time we could clearly > see the peptide bound to all 4 copies. So indeed each protomer in the AU can > be affected differently in the way they bind a ligand, depending on all > causes (and perhaps even more) that people have already mentioned. > > BW, > > D > > On 06/03/2022 12:38, David J. Schuller wrote: >> I think it would be a mistake to generalize. >> I have seen a situation in which 1 of 4 sites was occupied, the ligand was >> not included in the crystallization solution(which means it must have been >> bound beforehand) and the site participated in crystal contacts. I do not >> doubt that examples of the opposite causality exist. And the data I used to >> make my conclusions in my own example came from outside the structure itself. >> >> ======================================================================= >> All Things Serve the Beam >> ======================================================================= >> David J. Schuller >> modern man in a post-modern world >> MacCHESS, Cornell University >> schul...@cornell.edu >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Palm, >> Gottfried <p...@uni-greifswald.de> >> Sent: Sunday, March 6, 2022 4:10 AM >> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >> Subject: Re: [ccp4bb] ligand binds to one molecule >> >> Dear all, >> I don't think, there is much to add to the statement of Bernhard or James >> that different protomers in the asymmetric unit (must) have some difference >> in there contacts and therefore often in their conformation. What it doesn't >> answer is a chicken or the egg question: >> do the different environments in the crystal allow or force different >> conformations (e.g. open or closed loops) and/or different (active) site >> occupancies or >> do different states in an oligomer allow or force crystallization only in a >> packing and space group with multiple states? >> Latter could be due to an anti-cooperative binding to a dimer. We have seen >> this in the dimeric Tet repressor: wt binds the ligand (a tetracycline) in >> each monomer of the dimer with one chain in the asymmetric unit, but some of >> the mutants bind only one ligand per dimer (confirmed by ITC, Biochimica et >> Biophysica Acta, 2020). Despite the same packing, this forces reduction of >> space group symmetry from I422 to P422 (omitting screws). >> From the crystal structures alone, I think, one cannot prove what comes >> first. From my gut feeling, in most cases multiple states in solution force >> multiple states in the crystal - in other words - I tend to say, multiple >> states in the crystal are "real" in the sense they also occur in solution. >> Does somebody want to comment on this? >> Greetings >> Gottfried >> >> >> Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp: >> As you stated, you have multiple protomers in the asymmetric unit, where >> they are free from >> crystallographic symmetry constraints. Generally that means different local >> environment for >> each protomer. Inspecting the sites in the different protomers (frequently >> related by various >> non-crystallographic symmetry operations) often can reveal plausible reasons >> for different occupancies. One hydrogen bond more or less for example can >> mean a >> difference of 4 orders of magnitude in Kd. >> >> Best, BR >> >> -----Original Message----- >> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of <Shymaa Damfo> >> Sent: Saturday, March 5, 2022 12:01 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] ligand binds to one molecule >> >> Hello all, >> >> In homo-dimeric or homo-oligomeric protein crystal structures, what would be >> the reason for having a ligand (chemical compound or fragment) binds to one >> molecule and not all molecules in the asymmetric unit? >> >> I have soaked a fragment that has an affinity of 200 uM to a viral protein >> but I can only see it binds to one molecule (we have eight molecules in the >> AU). This is was also notable as well in some published PDB (dimeric >> protein). >> >> Any suggestions? >> >> Best wishes, >> Shymaa >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > -- > Dom Bellini, Xray Crystallography Facility (1S205) > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH > Phone 01223 267839 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
