Crystal Structures as Snapshots--Summary

From: Jacob Keller
Date: 15 February 2012 20:48

Dear Crystallographers,

thanks for all of the responses and conversation. I have culled
together the various references which have been sent on the BB and
which I have come up with, and posted them below. Worthy of special
mention, I think, is the first one (Lange et al), in which 46 (!)
different crystal structures are pitted against a lot of RDC NMR data,
and the match seems to be excellent (although it seems you probably
have to know both methods fairly well to evaluate this properly.)
Anyway, for asserting that variances between crystal structures at
least in some cases represent differences between
physiologically-relevant states in solution, the Lange paper is really
on the mark.

Thanks again,

Jacob

Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KF, Becker S,
Meiler J, Grubmüller H, Griesinger C, de Groot BL.
Recognition dynamics up to microseconds revealed from an RDC-derived
ubiquitin ensemble in solution.
Science. 2008 Jun 13;320(5882):1471-5. PubMed PMID: 18556554.


Kondrashov, D.A., Zhang, W., Aranda, R.t., Stec, B., and Phillips,
G.N., Jr. (2008). Sampling of the native conformational ensemble of
myoglobin via structures in different crystalline environments.
Proteins 70, 353-362.

Zhang, X. J., Wozniak, J. A., and Matthews, B. W. (1995) Protein
flexibility and adaptability seen in 25 crystal forms of T4 lysozyme,
Journal of molecular biology 250, 527-552.

Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein
farnesyltransferase at atomic resolution. Nature Oct 10;
419(6907):645-50.
http://www.ncbi.nlm.nih.gov/pubmed?term=The%20reaction%20path%20of%20protein%20farnesyltransferase%20at%20atomic%20resolution

J. R. Kiefer, C. Mao, J. C. Braman and L. S. Beese (1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA polymerase
crystal" Nature 6664:304-7.
http://www.ncbi.nlm.nih.gov/pubmed?term=Visualizing%20DNA%20replication%20in%20a%20catalytically%20active%20Bacillus%20DNA%20polymerase%20crystal

Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH, Stuart DI (2004)
"Atomic snapshots of an RNA packaging motor reveal conformational
changes linking ATP hydrolysis to RNA translocation."
Cell 118(6):743-55
http://www.cell.com/abstract/S0092-8674(04)00837-2

Nature. 2009 Dec 3;462(7273):669-73.
Hidden alternative structures of proline isomerase essential for catalysis.
Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T.




*******************************************
Jacob Pearson Keller

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From: James Stroud


I feel compelled to throw a few references into the ring.


NFAT is a protein where you get a good sampling of snapshots:

1. Folded up as a monomer when interacting with partner proteins:

 http://www.ncbi.nlm.nih.gov/pubmed/9510247
 http://www.ncbi.nlm.nih.gov/pubmed/16873067

2. Extended as a dimer:

 http://www.ncbi.nlm.nih.gov/pubmed/12949493

3. Folded up as a monomer when interacting with a partner protein which happens to be itself as an extended dimer:

 http://www.ncbi.nlm.nih.gov/pubmed/18462673

4. Wrapped around DNA as a monomer without partners:.

 http://www.ncbi.nlm.nih.gov/pubmed/14643663


In this last reference you get a sample of extended, wrapped around, and folded up all in the same unit cell!


James