Newsletter 129
Sugust 28, 2006

Item 1: July 2006 Publications by Members:

1:  Zou Z, Sun PD. 
 An improved recombinant mammalian cell expression system for human transforming
growth factor-beta2 and -beta3 preparations.
Protein Expr Purif. 2006 Jul 4; PMID: 16901717
  
2:  Ji X. 
 Structural basis for non-catalytic and catalytic activities of ribonuclease III.
Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):933-40. PMID: 16855311
  
3:  Dauter Z. 
 Estimation of anomalous signal in diffraction data.
Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):867-76. PMID: 16855302
  
4:  Ziolkowska NE, O'Keefe BR, Mori T, Zhu C, Giomarelli B, Vojdani F, Palmer KE, 
McMahon JB, Wlodawer A. 
 Domain-swapped structure of the potent antiviral protein griffithsin and its mode of 
carbohydrate binding.
Structure. 2006 Jul;14(7):1127-35. PMID: 16843894 
  
5:  Fernandez MM, Guan R, Swaminathan CP, Malchiodi EL, Mariuzza RA. 
 Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human MHC 
class II molecule.
J Biol Chem. 2006 Jul 6; [Epub ahead of print] PMID: 16829512
  
6:  Shami PJ, Saavedra JE, Bonifant CL, Chu J, Udupi V, Malaviya S, Carr BI, Kar
S, Wang M, Jia L, Ji X, Keefer LK. 
 Antitumor activity of JS-K [O2-(2,4-dinitrophenyl) 1-[(4-ethoxycarbonyl)piperazin-
1-yl]diazen-1-ium-1,2-diolate] and related O2-aryl diazeniumdiolates in vitro and in vivo.
J Med Chem. 2006 Jul 13;49(14):4356-66. PMID: 16821795

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% Tacsimate^TM 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

Low Resolution Crystallography in the Hurley lab
James Hurley
LMB, NIDDK, NIH

I recently had a visiting seminar speaker in my office, and was describing some of the new structures in the lab to him. I was excited at the time to have the structure of a biggish multiprotein complex and another biggish full-length mammalian signaling protein to show off. The resolution was low in both cases, but for the biological questions being asked about how domains and subunits interacted, the structures were still informative. My visitor commented that “Your lab seems to have a real problem with resolution.” We have had a recent run of low resolution structures, whether due to bad luck, an increased focus on larger proteins and complexes, or both. (Click for the entire article)

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

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"

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