Newsletter 141
February 12, 2007


The NIH X-Ray Diffraction Interest Group

Newsletter web site: http://mcl1.ncifcrf.gov/nihxray


Happy Birthday, Dr. Davies


Alexander Wlodawer (NCI): It may be hard to believe, but David Davies will be celebrating his 80th birthday on Feb. 22nd, 2007. There is no need to tell this audience who David is and what he has accomplished - those that do not know must have been asleep for a very long time. Ten years ago, NIH honored his previous round birthday with a one-day symposium. Such symposia, however, might be taken like an invitation to retire, and David did not express any desire for such a step, either then or now. Thus, there is no symposium this time, to make sure that David will not decide to abandon his work any time soon. David, we appreciate the example that you gave us, the superb science that you produced, and your leadership role in the NIH community, as well as in the larger community of structural biologists in the US and abroad. We would like to wish you many more healthy and productive years.
     

The 4th annual SER-CAT Symposium 16 March 2007, National Cancer Institute at Frederick, Frederick, MD, USA

The 2007 Meeting of the American Crystallographic Associstion 21-26 July 2007, Salt Lake City, UT, USA

The 9th International Conference on Biology and Synchrotron Radiation 13-17 August 2007, Manchester, England


Item 1: January 2007 Publications by Members:

1:  Guan R, Mariuzza RA. 
Peptidoglycan recognition proteins of the innate immune system.
Trends Microbiol. 2007 Jan 31; PMID: 17275309

2: Chaudhuri R, Lindwasser OW, Smith WJ, Hurley JH, Bonifacino JS.
CD4 downregulation by HIV-1 Nef is dependent on clathrin and
involves
a direct interaction of Nef with the AP2 clathrin adaptor.
J Virol. 2007 Jan 31; PMID: 17267500

3: Nakamura K, Moore R, Negishi M, Sueyoshi T.
Nuclear pregnane X receptor cross-talk with FOXA2 to mediate the
drug-induced regulation of lipid metabolism in fasting mouse liver.

J Biol Chem. 2007 Jan 30; PMID: 17267396

4: Wally J, Buchanan SK.
A structural comparison of human serum transferrin and human
lactoferrin.

Biometals. 2007 Jan 11; PMID: 17216400

5: Wlodawer A.
Natalia Sergeevna Andreeva 1922-2006.
Nat Struct Mol Biol. 2007 Jan;14(1):2. PMID: 17203064

Item 2: Tips and Tricks

Wei Yang (NIDDK): Crystallization of Protein-DNA Complexes (updated)
    Macromolecular interaction is essential, necessary and unavoidable in a living organism. Specific interactions among macromolecules are required for molecular machinery assembly and for progression and regulation of metabolic reactions.  To fully understand a biological process, it is essential to determine the atomic structures of and interactions among components of a macromolecular complex and to decipher how these structures and interactions change during a reaction or signaling cycle.  Some macromolecular complexes are naturally stable, for example tetrameric hemoglobin, nucleosome, and ribosome. But most macromolecular complexes are formed only transiently, e.g. an enzyme and substrate complex, a growth factor and its receptor interaction, or transcription factors assembled on a promoter.  To determine structures of macromolecular complexes, whether stable or transient, has become a common practice of structural biologists in the 21st century. (Full Article)

Xinhua Ji (NCI):
Lysine Methylation
   
It appears that lysine methylation should be considered a routine step not only in traditional (low-throughput) crystallization trials but also for structural genomics (high-throughput) attempts. Walter and co-workers outlined a detailed protocol with ten examples in their recent article (Structure 14:1617-1622, 2006). The protocol was derived from previously published method by Rayment and co-workers (Science 261:50-58, 1993) and Rayment (Methods Enzymol. 276:171-179, 1997).  A recent success within the NIH X-ray Diffraction Group was reported by Schubot and Waugh (Acta Cryst. D60:1981-1986, 2004), showing that the method was pivotal in the de novo crystallization of a ternary complex that contains three protein molecules!

Click for
Introduction and tips and tricks in Crystallization, Post-crystallization treatments, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Item 3: Topic Discussion

Click for previous discussions on: Low Resolution Crystallography, PHASER, HKL2000, Parallel Protein Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, and Absorption Correction.

 

Item 4: Dr. Zbigniew Dauter's Lectures at the NIH (03/29-31/2005)

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

           with possible use of it for phasing"


This site is maintained by Dr. Xinhua Ji (jix@ncifcrf.gov) on the NCI-CCR-MCL server (http://mcl1.ncifcrf.gov).