Hi Jacob, For Ca2+-CaM, and flexible proteins in general, the average conformation in solution may differ from the most crystallizable conformation. However, any crystallized conformation had to be sampled in solution at some point in order to form a crystal, and thus the crystal structure tells us something about the range of conformations accessible to the protein under the crystallization conditions. In Ca2+-CaM, the presence of MPD is probably more responsible for the continuous central helix than the pH, but early analysis of the thermal factors in that region of the crystal structure predicted flexibility in the center of this helix that was subsequently observed by NMR to be a flexible linker region. More generally, I'd argue that crystal disorder is a subset of solution motion: i.e. disorder observed in crystalline protein almost certainly corresponds to motions that occur in solution (perhaps with altered amplitude), but not all solution motions are observed as disorder in the crystal. Best regards, Mark
Mark A. Wilson Associate Professor Department of Biochemistry/Redox Biology Center University of Nebraska N118 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu Jacob Keller <j-kell...@fsm.northwestern.edu> Sent by: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> 02/10/2012 03:37 PM Please respond to Jacob Keller <j-kell...@fsm.northwestern.edu> To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] Crystal Structures as Snapshots Isn't calcium-calmodulin one of the archetypical examples of the crystal structure probably not representing the solution structure (perhaps because the crystallization pH = 4.5)? Look at that linker helix--how stable can that be in solution? I don't think a single one of the NMR ca-calmodulin structures/conformers has the central helix like that. Jacob On Fri, Feb 10, 2012 at 3:31 PM, Nat Echols <nathaniel.ech...@gmail.com> wrote: > 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 >> -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
