SAD phasing using iodide ions in a high-throughput structural genomics environment
详细信息 查看全文
- 作者：Jan Abendroth (1) (4)
Anna S. Gardberg (1) (4)
John I. Robinson (1) (4)
Jeff S. Christensen (1) (4)
Bart L. Staker (1) (4)
Peter J. Myler (2) (3) (4)
Lance J. Stewart (1) (4)
Thomas E. Edwards (1) (4) - 关键词：Experimental phasing ; Iodide ions ; SAD ; Selenomethionine ; Structural genomics ; Structure determination
- 刊名：Journal of Structural and Functional Genomics
- 出版年：2011
- 出版时间：July 2011
- 年：2011
- 卷：12
- 期：2
- 页码：83-95
- 全文大小：971KB
- 参考文献：1. Myler PJ, Stacy R, Stewart L, Staker BL, Van Voorhis WC et al (2009) The Seattle Structural Genomics Center for Infectious Disease (SSGCID). Infect Disord Drug Targets 9:493鈥?06 CrossRef
2. Van Voorhis WC, Hol WG, Myler PJ, Stewart LJ (2009) The role of medical structural genomics in discovering new drugs for infectious diseases. PLoS Comput Biol 5:e1000530 CrossRef
3. Anderson WF (2009) Structural genomics and drug discovery for infectious diseases. Infect Disord Drug Targets 9:507鈥?17 CrossRef
4. Dauter M, Dauter Z (2007) Phase determination using halide ions. Methods Mol Biol 364:149鈥?58
5. Dauter Z, Dauter M, Rajashankar KR (2000) Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. Acta Crystallogr D Biol Crystallogr 56:232鈥?37 CrossRef
6. Abendroth J, Mitchell DD, Korotkov KV, Johnson TL, Kreger A et al (2009) The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of / Vibrio cholerae. J Struct Biol 166:303鈥?15 CrossRef
7. Edwards TE, Phan I, Abendroth J, Dieterich SH, Masoudi A et al (2010) Structure of a / Burkholderia pseudomallei trimeric autotransporter adhesin head. PLoS One 5:e12803 CrossRef
8. Yogavel M, Gill J, Mishra PC, Sharma A (2007) SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution. Acta Crystallogr D Biol Crystallogr 63:931鈥?34 CrossRef
9. Yogavel M, Gill J, Sharma A (2009) Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly protein. Acta Crystallogr D Biol Crystallogr 65:618鈥?22 CrossRef
10. Yogavel M, Khan S, Bhatt TK, Sharma A (2010) Structure of d -tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states. Acta Crystallogr D Biol Crystallogr 66:584鈥?92 CrossRef
11. Kostrewa D, Winkler FK, Folkers G, Scapozza L, Perozzo R (2005) The crystal structure of PfFabZ, the unique beta-hydroxyacyl-ACP dehydratase involved in fatty acid biosynthesis of / Plasmodium falciparum. Protein Sci 14:1570鈥?580 CrossRef
12. Dauter Z, Dauter M, Dodson E (2002) Jolly SAD. Acta Crystallogr D Biol Crystallogr 58:494鈥?06 CrossRef
13. Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ (2010) Structural characterization of / Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 鈥榦pen鈥?state. Biochem Biophys Res Commun 394:1012鈥?017 CrossRef
14. Yamada S, Hatta M, Staker BL, Watanabe S, Imai M et al (2010) Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 6:e1001034 CrossRef
15. Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18:6069鈥?074 CrossRef
16. Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A et al (2009) Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol 9:36 CrossRef
17. Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M et al (2009) Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using gene composer. BMC Biotechnol 9:37 CrossRef
18. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207鈥?34 CrossRef
19. Newman J, Egan D, Walter TS, Meged R, Berry I et al (2005) Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy. Acta Crystallogr D Biol Crystallogr 61:1426鈥?431 CrossRef
20. Gerdts CJ, Elliott M, Lovell S, Mixon MB, Napuli AJ et al (2008) The plug-based nanovolume microcapillary protein crystallization system (MPCS). Acta Crystallogr D Biol Crystallogr 64:1116鈥?122 CrossRef
21. Gerdts CJ, Stahl GL, Napuli A, Staker B, Abendroth J et al (2010) Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system. J Appl Crsyt 43:1078 CrossRef
22. Wernimont A, Edwards A (2009) In situ proteolysis to generate crystals for structure determination: an update. PLoS One 4:e5094 CrossRef
23. Thakur AS, Robin G, Guncar G, Saunders NF, Newman J et al (2007) Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents. PLoS One 2:e1091 CrossRef
24. Kabsch W (2010) Xds. Acta Crystallogr D Biol Crystallogr 66:125鈥?32 CrossRef
25. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW et al (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213鈥?21 CrossRef
26. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112鈥?22 CrossRef
27. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC et al (2007) Phaser crystallographic software. J Appl Crystallogr 40:658鈥?74 CrossRef
28. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760鈥?63
29. Cowtan K (2010) Recent developments in classical density modification. Acta Crystallogr D Biol Crystallogr 66:470鈥?78 CrossRef
30. Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 62:1002鈥?011 CrossRef
31. Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171鈥?179 CrossRef
32. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240鈥?55 CrossRef
33. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126鈥?132 CrossRef
34. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375鈥揥383 CrossRef
35. Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM et al (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12鈥?1 CrossRef
36. Cianci M, Helliwell JR, Suzuki A (2008) The interdependence of wavelength, redundancy and dose in sulfur SAD experiments. Acta Crystallogr D Biol Crystallogr 64:1196鈥?209 CrossRef
37. Dauter Z (2010) Carrying out an optimal experiment. Acta Crystallogr D Biol Crystallogr 66:389鈥?92 CrossRef
38. Schneider TR, Sheldrick GM (2002) Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 58:1772鈥?779 CrossRef
39. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491鈥?97 CrossRef
40. Hunfeld KP, Hildebrandt A, Gray JS (2008) Babesiosis: recent insights into an ancient disease. Int J Parasitol 38:1219鈥?237 CrossRef
41. Santos JM, Freire P, Vicente M, Arraiano CM (1999) The stationary-phase morphogene bolA from / Escherichia coli is induced by stress during early stages of growth. Mol Microbiol 32:789鈥?98 CrossRef
42. Kasai T, Inoue M, Koshiba S, Yabuki T, Aoki M et al (2004) Solution structure of a BolA-like protein from Mus musculus. Protein Sci 13:545鈥?48 CrossRef
43. Tuinstra RL, Peterson FC, Elgin ES, Pelzek AJ, Volkman BF (2007) An engineered second disulfide bond restricts lymphotactin/XCL1 to a chemokine-like conformation with XCR1 agonist activity. Biochemistry 46:2564鈥?573 CrossRef
44. Chen YW, Dodson EJ, Kleywegt GJ (2000) Does NMR mean 鈥渘ot for molecular replacement鈥? Using NMR-based search models to solve protein crystal structures. Structure聽8:R213鈥揜220 CrossRef
45. Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256鈥?268 CrossRef
46. Hector RF, Laniado-Laborin R (2005) Coccidioidomycosis鈥攁 fungal disease of the Americas. PLoS Med 2:e2 CrossRef
47. Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR et al (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19:1722鈥?731 CrossRef
48. Galkin A, Kulakova L, Melamud E, Li L, Wu C et al (2007) Characterization, kinetics, and crystal structures of fructose-1, 6-bisphosphate aldolase from the human parasite, / Giardia lamblia. J Biol Chem 282:4859鈥?867 CrossRef
49. Roversi P, Johnson S, Lea SM (2010) With phases: how two wrongs can sometimes make a right. Acta Crystallogr D Biol Crystallogr 66:420鈥?25 CrossRef
50. Walden H (2010) Selenium incorporation using recombinant techniques. Acta Crystallogr D Biol Crystallogr 66:352鈥?57 CrossRef
51. Morton S, Glossinger J, Smith-Baumann A, McKean JP, Trame C et al (2007) Recent major improvements to the ALS sector 5 macromolecular crystallography beamlines. Sync Rad News 20:23鈥?0 CrossRef
52. Terwilliger TC, Berendzen J (1999) Exploring structure space. A protein structure initiative. Genetica 106:141鈥?47 CrossRef
53. Stols L, Millard CS, Dementieva I, Donnelly MI (2004) Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J Struct Funct Genomics 5:95鈥?02 CrossRef
54. Joyce MG, Radaev S, Sun PD (2010) A rational approach to heavy-atom derivative screening. Acta Crystallogr D Biol Crystallogr 66:358鈥?65 CrossRef
55. Ravelli RB, Leiros HK, Pan B, Caffrey M, McSweeney S (2003) Specific radiation damage can be used to solve macromolecular crystal structures. Structure聽11:217鈥?24 CrossRef
56. Miyatake H, Hasegawa T, Yamano A (2006) New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL). Acta Crystallogr D Biol Crystallogr 62:280鈥?89 CrossRef
57. Beck T, Krasauskas A, Gruene T, Sheldrick GM (2008) A magic triangle for experimental phasing of macromolecules. Acta Crystallogr D Biol Crystallogr 64:1179鈥?182 CrossRef
58. Gilchrist CA, Baba DJ, Zhang Y, Crasta O, Evans C et al (2008) Targets of the Entamoeba histolytica transcription factor URE3-BP. PLoS Negl Trop Dis 2:e282 CrossRef
59. Brennan S, Cowan PL (1992) A suite of programs for calculating x-ray absorption, reflection and diffraction performance for a variety of materials at arbitrary wavelengths. Rev Sci Instrum 63:850 CrossRef
60. Buchko GW, Phan I, Myler PJ, Terwilliger TC, Kim YC (2011) Inaugural structure from the DUF3349 superfamily of proteins, / Mycobacterium tuberculosis Rv0543c. Arch Biochem Biophys 506(2):150鈥?56 - 作者单位：Jan Abendroth (1) (4)
Anna S. Gardberg (1) (4)
John I. Robinson (1) (4)
Jeff S. Christensen (1) (4)
Bart L. Staker (1) (4)
Peter J. Myler (2) (3) (4)
Lance J. Stewart (1) (4)
Thomas E. Edwards (1) (4)
1. Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA, 98110, USA
4. Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
2. Seattle Biomedical Research Institute, Seattle, WA, 98109, USA
3. Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA, 98195, USA
文摘
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.