The Center for Eukaryotic Structural Genomics

Journal of Structural and Functional Genomics

Volumn 10, Issue 2, 2009, Pages 165-179

  Markley, John L ^a   Aceti, David J ^a   Bingman, Craig A ^a   Fox, Brian G ^a   Frederick, Ronnie O ^a   Makino, Shin Ichi ^a   Nichols, Karl W ^a   Phillips Jr , George N ^a   Primm, John G ^a   Sahu, Sarata C ^a   Vojtik, Frank C ^a   Volkman, Brian F ^b   Wrobel, Russell L ^a   Zolnai, Zsolt ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

CESG; LIMS; PepcDB; Plasmid design; Protein production; Protein structure determination; Protein Structure Initiative (PSI); PSI Materials Repository; TEV protease

Indexed keywords

ARABIDOPSIS; BIOINFORMATICS; BIOMEDICINE; EUKARYOTE; HUMAN; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEIN STRUCTURE; REVIEW; STRUCTURAL GENOMICS; TECHNOLOGY; X RAY CRYSTALLOGRAPHY; YEAST;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; GENOMICS; HUMANS; MULTI-INSTITUTIONAL SYSTEMS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; PROTEOMICS;

ARABIDOPSIS THALIANA; CYANIDIOSCHYZON MEROLAE; EUKARYOTA; GALDIERIA SULPHURARIA; HOMO SAPIENS; PLASMODIUM FALCIPARUM; PROKARYOTA; RATTUS; TOBACCO ETCH VIRUS;

EID: 62949196874     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-008-9057-4     Document Type: Review

References (34)

1. JC Norvell AZ Machalek 2000 Structural genomics programs at the US National Institute of General Medical Sciences Nat Struct Biol 7 1 931 10.1038/80694
2. Z Zolnai PT Lee J Li MR Chapman CS Newman GN Phillips Jr I Rayment EL Ulrich BF Volkman JL Markley 2003 Project management system for structural and functional proteomics: Sesame J Struct Funct Genomics 4 11 23 10.1023/A:1024684404761
3. X Pan GE Wesenberg JL Markley BG Fox GN Phillips Jr CA Bingman 2007 A graphical approach to tracking and reporting target status in structural genomics J Struct Funct Genomics 8 209 216 10.1007/s10969-007-9037-0
4. CJ Oldfield EL Ulrich Y Cheng AK Dunker JL Markley 2005 Addressing the intrinsic disorder bottleneck in structural proteomics Proteins 59 444 453 10.1002/prot.20446
5. RM Bannen CA Bingman GN Phillips Jr 2007 Effect of low-complexity regions on protein structure determination J Struct Funct Genomics 8 217 226 10.1007/s10969-008-9039-6
6. PG Blommel PA Martin RL Wrobel E Steffen BG Fox 2006 High efficiency single step production of expression plasmids from cDNA clones using the Flexi Vector cloning system Protein Expr Purif 47 562 570 10.1016/j.pep.2005.11.007
7. S Thao Q Zhao T Kimball E Steffen PG Blommel M Riters CS Newman BG Fox RL Wrobel 2004 Results from high-throughput DNA cloning of Arabidopsis thaliana target genes using site-specific recombination J Struct Funct Genomics 5 267 276 10.1007/s10969-004-7148-4
8. PG Blommel KJ Becker P Duvnjak BG Fox 2007 Enhanced bacterial protein expression during auto-induction obtained by alteration of lac repressor dosage and medium composition Biotechnol Prog 23 585 598 10.1021/bp070011x
9. 15N]-labeled proteins for NMR screening and structure determination Protein Expr Purif 40 268 278 10.1016/j.pep.2004.12.024
10. RO Frederick L Bergeman PG Blommel LJ Bailey JG McCoy J Song L Meske CA Bingman M Riters NA Dillon J Kunert JW Yoon A Lim M Cassidy J Bunge DJ Aceti JG Primm JL Markley GN Phillips Jr BG Fox 2007 Small-scale, semi-automated purification of eukaryotic proteins for structure determination J Struct Funct Genomics 8 153 166 10.1007/s10969-007-9032-5
11. HK Sreenath CA Bingman BW Buchan KD Seder BT Burns HV Geetha WB Jeon FC Vojtik DJ Aceti RO Frederick GN Phillips Jr BG Fox 2005 Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium Protein Expr Purif 40 256 267 10.1016/j.pep.2004.12. 022
12. PG Blommel BG Fox 2007 A combined approach to improving large-scale production of tobacco etch virus protease Protein Expr Purif 55 53 66 10.1016/j.pep.2007.04.013
13. DA Vinarov BL Lytle FC Peterson EM Tyler BF Volkman JL Markley 2004 Cell-free protein production and labeling protocol for NMR-based structural proteomics Nat Methods 1 149 153 10.1038/nmeth716
14. DA Vinarov JL Markley 2005 High-throughput automated platform for nuclear magnetic resonance-based structural proteomics Expert Rev Proteomics 2 49 55 10.1586/14789450.2.1.49
15. Vinarov DA, Loushin Newman CL, Tyler EM, Markley JL (2006) Protein production using the wheat germ cell-free expression system. Curr Protoc Protein Sci 1-18
16. DA Vinarov CL Loushin Newman JL Markley 2006 Wheat germ cell-free platform for eukaryotic protein production FEBS J 273 4160 4169 10.1111/j.1742-4658.2006.05434.x
17. RC Tyler DJ Aceti CA Bingman CC Cornilescu BG Fox RO Frederick WB Jeon MS Lee CS Newman FC Peterson GN Phillips Jr MN Shahan S Singh J Song HK Sreenath EM Tyler EL Ulrich DA Vinarov FC Vojtik BF Volkman RL Wrobel Q Zhao JL Markley 2005 Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies Proteins 59 633 643 10.1002/prot.20436
18. WB Jeon DJ Aceti CA Bingman FC Vojtik AC Olson JM Ellefson JE McCombs HK Sreenath PG Blommel KD Seder BT Burns HV Geetha AC Harms G Sabat MR Sussman BG Fox GN Phillips Jr 2005 High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics J Struct Funct Genomics 6 143 147 10.1007/s10969-005-1908-7
19. EJ Levin DA Kondrashov GE Wesenberg GN Phillips Jr 2007 Ensemble refinement of protein crystal structures: validation and application Structure 15 1040 1052 10.1016/j.str.2007.06.019
20. F DiMaio DA Kondrashov E Bitto A Soni CA Bingman GN Phillips Jr JW Shavlik 2007 Creating protein models from electron-density maps using particle-filtering methods Bioinformatics 23 2851 2858 10.1093/bioinformatics/ btm480
21. HR Eghbalnia A Bahrami M Tonelli K Hallenga JL Markley 2005 High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection J Am Chem Soc 127 12528 12536 10.1021/ja052120i
22. G Cornilescu A Bahrami M Tonelli JL Markley HR Eghbalnia 2007 HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections J Biomol NMR 38 341 351 10.1007/s10858-007-9173-7
23. HR Eghbalnia A Bahrami L Wang A Assadi JL Markley 2005 Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO) J Biomol NMR 32 219 233 10.1007/s10858-005-7944- 6
24. L Wang HR Eghbalnia A Bahrami JL Markley 2005 Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications J Biomol NMR 32 13 22 10.1007/s10858-005-1717-0
25. L Wang HR Eghbalnia JL Markley 2006 Probabilistic approach to determining unbiased random-coil carbon-13 chemical shift values from the protein chemical shift database J Biomol NMR 35 155 165 10.1007/s10858-006-9022-0
26. L Wang HR Eghbalnia JL Markley 2007 Nearest-neighbor effects on backbone alpha and beta carbon chemical shifts in proteins J Biomol NMR 39 247 257 10.1007/s10858-007-9193-3
27. HR Eghbalnia L Wang A Bahrami A Assadi JL Markley 2005 Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements J Biomol NMR 32 71 81 10.1007/s10858-005-5705-1
28. Bahrami A, Markley JL, Assadi A, Eghbalnia HR (2009) Probabilistic interaction network of evidence: application to key steps in the automation of protein structure determination by NMR spectroscopy. PLoS Comp Biol (in press)
29. M Takeda N Sugimori T Torizawa T Terauchi AM Ono H Yagi Y Yamaguchi K Kato T Ikeya JP Jee P Güntert DJ Aceti JL Markley M Kainosho 2008 Structure of the putative 32 kDa myrosinase binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR FEBS J 275 5873 5884 10.1111/j.1742-4658. 2008.06717.x
30. BA Griffin SR Adams J Jones RY Tsien 2000 Fluorescent labeling of recombinant proteins in living cells with FlAsH Methods Enzymol 327 565 578 10.1016/S0076-6879(00)27302-3
31. HE Klock EJ Koesema MW Knuth SA Lesley 2008 Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts Proteins 71 982 994 10.1002/prot.21786
32. FW Studier 2005 Protein production by auto-induction in high-density shaking cultures Protein Expr Purif 41 207 234 10.1016/j.pep.2005.01.016
33. T Borggrefe R Davis H Erdjument-Bromage P Tempst RD Kornberg 2002 A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast J Biol Chem 277 44202 44207 10.1074/jbc.M207195200
34. P Sobrado MA Goren D James CK Amundson BG Fox 2008 A protein structure initiative approach to expression, purification, and in situ delivery of human cytochrome b5 to membrane vesicles Protein Expr Purif 58 229 241 10.1016/j.pep.2007.11.018