Hi Nat, there are a number of viruses in which a domain swap occurs inside the capsid, with the hinge sequence being highly conserved among their respective families. Perhaps I'm missing your point, but I won't attribute that kind of domain swap to any sort of crystal packing artifact.
Jon 2012/2/10 Nat Echols <nathaniel.ech...@gmail.com> > Just to clarify - I actually think the original assumption that Jacob > posted is generally reasonable. But it needn't necessarily follow > that the conformation we see in crystal structures is always > representative of the solution state; given the extreme range of > conditions in which crystals grow, I would be surprised if there > weren't counter-examples. I'm not familiar enough with the literature > on domain swapping (e.g. diptheria toxin) to know if any of those > structures are crystal packing artifacts. > > On Fri, Feb 10, 2012 at 1:04 PM, George <gkontopi...@vet.uth.gr> wrote: > >>Packing billions of copies into a compact lattice > > Not so compact there is 40-80% water > >>freezing it to 100K > > We have frozen many times protein solutions in liquid nitrogen and then > thaw > > and were working OK > >> non-physiological amounts of salt and various organics > > What is the amount of salt and osmotic pressure in the cell?? > >>non-physiological pH too > > What is the non-physiological pH too? I am sure that some enzymes they > are > > not working in pH 7. Also most of the proteins they have crystallized in > pH > > close to 7 so I would not say non-physiological. > > > > George > > > > PS There are lots of solution NMR structures as well supporting the > > physiological crystal structures > > > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Nat > > Echols > > Sent: Friday, February 10, 2012 10:35 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Crystal Structures as Snapshots > > > > On Fri, Feb 10, 2012 at 12:29 PM, James Stroud <xtald...@gmail.com> > wrote: > >> How could they not be snapshots of conformations adopted in solution? > > > > Packing billions of copies of an irregularly-shaped protein into a > > compact lattice and freezing it to 100K isn't necessarily > > representative of "solution", especially when your solution contains > > non-physiological amounts of salt and various organics (and possibly > > non-physiological pH too). > > > > -Nat > > > -- Dr. Jon Agirre Postdoctoral Scientist - Protein and Virus X-ray Crystallography Group Biophysics Unit (CSIC-UPV/EHU) +0034946013357
