Newsletter 123
June 5, 2006

Item 1: May 2006 Publications by Members:

1: Shi H, Rojas R, Bonifacino JS, Hurley JH.
The retromer subunit Vps26 has an arrestin fold and binds Vps35 through its C-terminal domain.
Nat Struct Mol Biol. 2006 May 28; [Epub ahead of print] PMID: 16732284

2: Bell JK, Askins J, Hall PR, Davies DR, Segal DM.
The dsRNA binding site of human Toll-like receptor 3.
Proc Natl Acad Sci U S A. 2006 May 23; [Epub ahead of print] PMID: 16720699

3: Shi D, Morizono H, Cabrera-Luque J, Yu X, Roth L, Malamy MH, Allewell NM, Tuchman M.
Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis.
J Biol Chem. 2006 May 16; [Epub ahead of print] PMID: 16704984

4: Radaev S, Li S, Sun PD.
A survey of protein-protein complex crystallizations.
Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):605-12. Epub 2006 May 12. PMID: 16699187

5: Xu Q, Guo H, Wlodawer A, Guo H.
The Importance of Dynamics in Substrate-Assisted Catalysis and Specificity.
J Am Chem Soc. 2006 May 10;128(18):5994-5995. PMID: 16669642

6: Guan R, Brown PH, Swaminathan CP, Roychowdhury A, Boons GJ, Mariuzza RA.
Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria.
Protein Sci. 2006 May;15(5):1199-206. PMID: 16641493

Item 2: Tips and Tricks - Crystallization

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"

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