On the question of solution structure vs crystal structure, another comment worth considering is this:
The crystalline state of a protein can in some cases (eg a large enzyme with small substrates) be more similar to physiological conditions than a dilute solution. If crowding effects are important, the crystalline state, at ~50% (w/v), is well crowded, unlike typical solution studies that are done at concentrations more like 1% (w/v) and below. David Goodsell's illustrations (http://mgl.scripps.edu/people/goodsell/) may be illuminating here. I also find that non-crystallographers need to be told that protein crystal contacts are weak and tenuous, and I find it useful to show a cross-section of a crystal, whether showing modelled protein or electron density of multiple repeats of the unit cell. Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bostjan Kobe Sent: Friday, 12 December 2008 10:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer? I wanted to comment on a couple of things that came up during this discussion. 1. We use crystallography because it enables us to get structural information. But we have to be aware that most of the time a crystal will not be an exact reflection of the biological environment, which is usually what we want to relate our structure to. For this reason, to make any useful interpretations of the oligomeric state and how it relates to a biologically relevant situation, one needs to complement it with other studies (hopefully in a "solution" that better resembles the biological situation). 2. What you find in the asymmetric unit of a crystal does not necessarily have anything to do with the biologically relevant oligomeric state (biological unit). I commonly see researchers confuse the asymmetric unit with the biological unit, even in submitted and published papers. To phrase it in a different way, crystallographic symmetry often relate subunits in an oligomer, and conversely NCS often corresponds to just another biologically irrelevant "crystal contact". 3. It is often not trivial to distinguish "crystal contact" from the oligomeric interface. There is lots of literature on this, and software and databases that can help you distinguish between these (using the size of interface area, but also many other criteria to sort these interactions). It is often not going to be possible to do so with any high reliability without complementary experiments. Please refer to the references cited in this recent conference proceeding for extensive literature on this matter: http://www.ncbi.nlm.nih.gov/pubmed/19021571?ordinalpos=1&itool=EntrezSys tem2 .PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVD ocSu m. Best wishes Bostjan On 12/12/08 2:34 AM, "Ethan A Merritt" <merr...@u.washington.edu> wrote: > On Thursday 11 December 2008, Santarsiero, Bernard D. wrote: >> In parallel with the discussion around this off-CCP4-topic, are they any >> good examples of the opposite case, where the protein is a monomer in >> solution (as evident from light scattering, MW determination through >> centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer? > > I don't think such a question is entirely well-defined, for two reasons. > > 1) The monomer/dimer equilibrium in solution may well depend on the specific > conditions (pH, concentration, presence of ligands, temperature, etc). > Unless these conditions are replicated in your crystallization medium, > it is uncertain to what extent the solution measurement is relevant. > > 2) How extensive an interface is required in order for it to be considered > a dimer/multimer interaction? In the limiting case of very small > interfaces, the entire crystal might be consider a single oligomer, > with each lattice-packing contact constituting a monomer:monomer > interaction. That's not a very useful place to set the threshold, > but where do you set it - 100 A^2 ? 500 A^2 ? 1000 A^2? > Some definition other than surface area? > > That said, I have some interest in the question as a practical matter. > We have a new structure that is "obviously", but totally unexpectedly, > a tetramer in the crystal. In this case the monomer:monomer interaction > surface is >1500 A^2. But exactly what criteria would I use to > argue that this is a real tetramer? What criteria would I use to > argue that it is a crystal artifact? Yes, of course ideally one would > go back to the lab and survey for solution measurements that are > consistent with tetramerization, but that is not always practical, > and may lead right back to your original question. > --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 452 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
