Newsletter 130
September 11, 2006


The NIH X-Ray Diffraction Interest Group

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

The 2006 International Conference on Structural Genomics

Advances in Protein Crystallography

Item 1: August 2006 Publications by Members:

1:  Esser L, Gong X, Yang S, Yu L, Yu CA, Xia D. 
Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome
bc1 complex.
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13045-50. PMID: 16924113
  
2:  Su HP, Lin DY, Garboczi DN. 
The structure of G4, the poxvirus disulfide oxidoreductase essential for virus maturation and
infectivity.
J Virol. 2006 Aug;80(15):7706-13. PMID: 16840349
  
3:  Shi D, Yu X, Roth L, Morizono H, Tuchman M, Allewell NM. 
Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed
with substrates and substrate analogs imply mechanisms for substrate binding and catalysis.
Proteins. 2006 Aug 1;64(2):532-42. PMID: 16741992
  
4:  Inoue K, Borchers CH, Negishi M. 
Cohesin protein SMC1 represses the nuclear receptor CAR-mediated synergistic activation of
 human P450 gene by xenobiotics.
Biochem J. 2006 Aug 15;398(1):125-33. PMID: 16623664

Item 2: Tips and Tricks - Crystallization

Editorial - The Silver Bullets: At the ACA 2006, Bob Cudney (Hampton Research) and Alexander McPherson (University of California Irvine) presented an alternative stretage for crystallizing macromolecules, as they put it, by searching the silver bullets. Examples of the silver bullets incude hexammine cobalt (III) chloride, 1,3-propanediol, sebacic acid, 4-aminobezonic acid, terephthalic acid, arginine, pentaglycine, glycerol 2-phosphate, trans-aconitic acid, trimesic acid, and putrescine. As you may realize, they are in fact additives. They tested 120 additives in the crystallization experiment of 81 proteins using two fundamental conditions: (1) 30% w/v PEG 3350, 0.1 M HEPES pH 7.0; and (2) 50% TacsimateTM pH 7.0. The succesful rate was very impressive: 65 out of 81 (85%) proteins crystallized. Most significant was that 35 of the 65 (54%) crystallized only in the presence of one or more reagent mixes, but not in control samples lacking any additives!

Crystallization of Protein-Protein Complexes
Peter D. Sun
LI, NIAID, NIH
               As crystallographers zest for larger and larger molecular machinery (spoiled public is part to blame), what used to be a novelty: crystallization of protein-protein complexes, has indeed become a way of life for most of us. Like everyone else, our lab often struggles to obtain that elusive crystal of so-and-so complex. Over the years, it became clear to us that protein complexes often favored certain conditions of crystallizations. Although they were not as well defined as DNA-protein complex crystallizations, these conditions appeared more narrowly distributed than those for general soluble proteins. This lead us to conduct a survey on protein-protein complex crystallizations a few years ago, which resulted in a 48-condition sparse matrix screening kit. More recently, we revisited the survey using a much larger database of published structures and expanded the initial 48-condition to a 96-condition sparse matrix kit (Radaev, Li, and Sun, Acta Cryst. D62:605-612).

Click for Introduction and tips and tricks in Crystallization, Post-crystallization treatments for improving diffraction quality of protein crystals, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Item 3: Topic Discussion - Low Resolution Crystallography

Byron DeLaBarre & Axel Brunger: Considerations for the refinement of low-resolution crystal structures

Click for previous discussions on: 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).