Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

被引：518

作者：

Hura, Greg L. ^{[2
]}

Menon, Angeli L. ^{[3
]}

Hammel, Michal ^{[2
]}

Rambo, Robert P. ^{[2
]}

Poole, Farris L., II ^{[3
]}

Tsutakawa, Susan E. ^{[1
]}

Jenney, Francis E., Jr. ^{[3
,4
]}

Classen, Scott ^{[2
]}

Frankel, Kenneth A. ^{[2
]}

Hopkins, Robert C. ^{[3
]}

Yang, Sung-jae ^{[3
]}

Scott, Joseph W. ^{[3
]}

Dillard, Bret D. ^{[3
]}

Adams, Michael W. W. ^{[3
]}

Tainer, John A. ^{[1
,5
,6
]}

机构：

[1] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Life Sci, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA

[3] Univ Georgia, Dept Biochem & Mol Biol, Athens, GA 30602 USA

[4] Georgia Campus Philadelphia Coll Osteopath Med, Suwanee, GA USA

[5] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA

[6] Scripps Res Inst, Skaggs Inst Chem Biol, La Jolla, CA 92037 USA

来源：

NATURE METHODS | 2009年 / 6卷 / 08期

关键词：

ARCHAEON PYROCOCCUS-FURIOSUS; CRYSTAL-STRUCTURE; BIOLOGICAL MACROMOLECULES; SUPEROXIDE REDUCTASE; ANGSTROM RESOLUTION; PROTEIN; CLASSIFICATION; CONFORMATIONS; RUBREDOXIN; MECHANISM;

D O I：

10.1038/nmeth.1353

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

引用

页码：606 / U83

页数：9

共 42 条

[1] The Southeast Collaboratory for Structural Genomics: A high-throughput gene to structure factory [J].

Adams, MWW ;

Dailey, HA ;

Delucas, LJ ;

Luo, M ;

Prestegard, JH ;

Rose, JP ;

Wang, BC .

ACCOUNTS OF CHEMICAL RESEARCH, 2003, 36 (03) :191-198

[2] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[3] Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd.: Contributions of N-terminal interactions to thermostability [J].

Bau, R ;

Rees, DC ;

Kurtz, DM ;

Scott, RA ;

Huang, HS ;

Adams, MWW ;

Eidsness, MK .

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 1998, 3 (05) :484-493

[4] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[5] Effect of iron-sulfur cluster environment in modulating the thermodynamic properties and biological function of ferredoxin from Pyrococcus furiosus [J].

Brereton, PS ;

Verhagen, MFJM ;

Zhou, ZH ;

Adams, MWW .

BIOCHEMISTRY, 1998, 37 (20) :7351-7362

[6] Reconstruction of protein form with X-ray solution scattering and a genetic algorithm [J].

Chacón, P ;

Díaz, JF ;

Morán, F ;

Andreu, JM .

JOURNAL OF MOLECULAR BIOLOGY, 2000, 299 (05) :1289-1302

[7] ATP ground- and transition states of bacterial enhancer binding AAA plus ATPases support complex formation with their target protein, σ54 [J].

Chen, Baoyu ;

Doucleff, Michaeleen ;

Wemmer, David E. ;

De Carlo, Sacha ;

Huang, Hector H. ;

Nogales, Eva ;

Hoover, Timothy R. ;

Kondrashkina, Elena ;

Guo, Liang ;

Nixon, B. Tracy .

STRUCTURE, 2007, 15 (04) :429-440

[8] Spectroscopic studies of Pyrococcus furiosus superoxide reductase:: Implications for active-site structures and the catalytic mechanism [J].

Clay, MD ;

Jenney, FE ;

Hagedoorn, PL ;

George, GN ;

Adams, MWW ;

Johnson, MK .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2002, 124 (05) :788-805

[9] Structural genomics: from genes to structures with valuable materials and many questions in between [J].

Fox, Brian G. ;

Goulding, Celia ;

Malkowski, Michael G. ;

Stewart, Lance ;

Deacon, Ashley .

NATURE METHODS, 2008, 5 (02) :129-132

[10]

Glatter O. K. O., 1982, Small angle X-ray scattering: London

← 1 2 3 4 5 →