Energetics-based discovery of protein-ligand interactions on a proteomic scale

Journal of Molecular Biology

Volumn 408, Issue 1, 2011, Pages 147-162

  Liu, Pei Fen ^a,b   Kihara, Daisuke ^b,c   Park, Chiwook ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

ATP; protein stability; protein ligand interaction; proteolysis; target identification

Indexed keywords

6 PHOSPHOFRUCTOKINASE 1; ADENOSINE TRIPHOSPHATE; BACTERIAL PROTEIN; CHAPERONIN; DIHYDROLIPOAMIDE DEHYDROGENASE; GLUTAMINE TRANSFER RNA LIGASE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; LIGAND; PERIPLASMIC BINDING PROTEIN; PHENYLALANINE TRANSFER RNA LIGASE; PROTEIN; PROTEOME; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; SUCCINYL COENZYME A SYNTHETASE ALPHA; UNCLASSIFIED DRUG; UREA; YNCE PROTEIN;

ARTICLE; BINDING SITE; CELL LYSATE; CELL METABOLISM; ENERGY TRANSFER; ESCHERICHIA COLI; LIGAND BINDING; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS;

ESCHERICHIA COLI;

EID: 79953237284     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.02.026     Document Type: Article

References (61)

1. Mercier K.A., Baran M., Ramanathan V., Revesz P., Xiao R., Montelione G.T., and Powers R. FAST-NMR: functional annotation screening technology using NMR spectroscopy J. Am. Chem. Soc. 128 2006 15292 15299 (Pubitemid 44853540)
2. Luesch H., Chanda S.K., Raya R.M., DeJesus P.D., Orth A.P., and Walker J.R. A functional genomics approach to the mode of action of apratoxin A Nat. Chem. Biol. 2 2006 158 167 (Pubitemid 44323868)
3. Bantscheff M., Eberhard D., Abraham Y., Bastuck S., Boesche M., and Hobson S. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors Nat. Biotechnol. 25 2007 1035 1044 (Pubitemid 47517638)
4. Hantschel O., Rix U., Schmidt U., Burckstummer T., Kneidinger M., and Schutze G. The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib Proc. Natl Acad. Sci. USA 104 2007 13283 13288 (Pubitemid 47293937)
5. Missner E., Bahr I., Badock V., Lucking U., Siemeister G., and Donner P. Off-target decoding of a multitarget kinase inhibitor by chemical proteomics ChemBioChem 10 2009 1163 1174
6. Burdine L., and Kodadek T. Target identification in chemical genetics: the (often) missing link Chem. Biol. 11 2004 593 597 (Pubitemid 38708828)
7. Terstappen G.C., Schlupen C., Raggiaschi R., and Gaviraghi G. Target deconvolution strategies in drug discovery Nat. Rev. Drug Discov. 6 2007 891 903 (Pubitemid 350042397)
8. Ong S.E., Schenone M., Margolin A.A., Li X., Do K., and Doud M.K. Identifying the proteins to which small-molecule probes and drugs bind in cells Proc. Natl Acad. Sci. USA 106 2009 4617 4622
9. Chan J.N., Nislow C., and Emili A. Recent advances and method development for drug target identification Trends Pharmacol. Sci. 31 2009 82 88
10. Godl K., Wissing J., Kurtenbach A., Habenberger P., Blencke S., and Gutbrod H. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors Proc. Natl Acad. Sci. USA 100 2003 15434 15439 (Pubitemid 38021007)
11. Rix U., and Superti-Furga G. Target profiling of small molecules by chemical proteomics Nat. Chem. Biol. 5 2009 616 624
12. Sleno L., and Emili A. Proteomic methods for drug target discovery Curr. Opin. Chem. Biol. 12 2008 46 54
13. Giaever G., Flaherty P., Kumm J., Proctor M., Nislow C., and Jaramillo D.F. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast Proc. Natl Acad. Sci. USA 101 2004 793 798 (Pubitemid 38121037)
14. Parsons A.B., Lopez A., Givoni I.E., Williams D.E., Gray C.A., and Porter J. Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast Cell 126 2006 611 625 (Pubitemid 44163601)
15. Hoon S., Smith A.M., Wallace I.M., Suresh S., Miranda M., and Fung E. An integrated platform of genomic assays reveals small-molecule bioactivities Nat. Chem. Biol. 4 2008 498 506
16. Lomenick B., Hao R., Jonai N., Chin R.M., Aghajan M., and Warburton S. Target identification using Drug Affinity Responsive Target Stability (DARTS) Proc. Natl Acad. Sci. USA 106 2009 21984 21989
17. West G.M., Tucker C.L., Xu T., Park S.K., Han X., Yates J.R. III, and Fitzgerald M.C. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements Proc. Natl Acad. Sci. USA 107 2010 9078 9082
18. Park C., and Marqusee S. Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding Nat. Methods 2 2005 207 212 (Pubitemid 41122128)
19. Na Y.R., and Park C. Investigating protein unfolding kinetics by pulse proteolysis Protein Sci. 18 2009 268 276
20. Kim M.S., Song J., and Park C. Determining protein stability in cell lysates by pulse proteolysis and Western blotting Protein Sci. 18 2009 1051 1059
21. Schlebach J.P., Kim M.-S., Joh N.H., Bowie J.U., and Park C. Probing membrane protein unfolding with pulse proteolysis J. Mol. Biol. 406 2011 545 551
22. Dunn S.D., and Futai M. Reconstitution of a functional coupling factor from the isolated subunits of Escherichia coli F1 ATPase J. Biol. Chem. 255 1980 113 118 (Pubitemid 10146035)
23. Bhattacharyya T., Bhattacharyya A., and Roy S. A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism Eur. J. Biochem. 200 1991 739 745
24. Kosakowski H.M., and Holler E. Phenylalanyl-tRNA synthetase from Escherichia coli K10. Synergistic coupling between the sites for binding of l-phenylalanine and ATP Eur. J. Biochem. 38 1973 274 282
25. Johnson J.L., and Reinhart G.D. MgATP and fructose 6-phosphate interactions with phosphofructokinase from Escherichia coli Biochemistry 31 1992 11510 11518
26. Joyce M.A., Fraser M.E., Brownie E.R., James M.N., Bridger W.A., and Wolodko W.T. Probing the nucleotide-binding site of Escherichia coli succinyl-CoA synthetase Biochemistry 38 1999 7273 7283
27. Martin J., Geromanos S., Tempest P., and Hartl F.U. Identification of nucleotide-binding regions in the chaperonin proteins GroEL and GroES Nature 366 1993 279 282 (Pubitemid 23359713)
28. Keseler I.M., Collado-Vides J., Gama-Castro S., Ingraham J., Paley S., and Paulsen I.T. EcoCyc: a comprehensive database resource for Escherichia coli Nucleic Acids Res. 33 2005 D334 D337
29. Hulo N., Bairoch A., Bulliard V., Cerutti L., De Castro E., and Langendijk-Genevaux P.S. The PROSITE database Nucleic Acids Res. 34 2006 D227 D230
30. Park C., and Marqusee S. Analysis of the stability of multimeric proteins by effective ΔG and effective m-values Protein Sci. 13 2004 2553 2558 (Pubitemid 39128877)
31. Pettit F.H., and Reed L.J. Alpha-keto acid dehydrogenase complexes: 8. Comparison of dihydrolipoyl dehydrogenases from pyruvate and alpha-ketoglutarate dehydrogenase complexes of Escherichia coli Proc. Natl Acad. Sci. USA 58 1967 1126 1130
32. Guest J.R., and Creaghan I.T. Lipoamide dehydrogenase mutants of Escherichia coli K 12 Biochem. J. 130 1972 8P
33. Steiert P.S., Stauffer L.T., and Stauffer G.V. The lpd gene product functions as the L protein in the Escherichia coli glycine cleavage enzyme system J. Bacteriol. 172 1990 6142 6144 (Pubitemid 20317163)
34. Lindsay H., Beaumont E., Richards S.D., Kelly S.M., Sanderson S.J., Price N.C., and Lindsay J.G. FAD insertion is essential for attaining the assembly competence of the dihydrolipoamide dehydrogenase (E3) monomer from Escherichia coli J. Biol. Chem. 275 2000 36665 36670 (Pubitemid 32002069)
35. Pieper U., Eswar N., Davis F.P., Braberg H., Madhusudhan M.S., and Rossi A. MODBASE: a database of annotated comparative protein structure models and associated resources Nucleic Acids Res. 34 2006 D291 D295
36. Laskowski R.A., Watson J.D., and Thornton J.M. ProFunc: a server for predicting protein function from 3D structure Nucleic Acids Res. 33 2005 W89 W93
37. Baba-Dikwa A., Thompson D., Spencer N.J., Andrews S.C., and Watson K.A. Overproduction, purification and preliminary X-ray diffraction analysis of YncE, an iron-regulated Sec-dependent periplasmic protein from Escherichia coli Acta Crystallogr. Sect. F 64 2008 966 969
38. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., and Weissig H. The Protein Data Bank Nucleic Acids Res. 28 2000 235 242 (Pubitemid 30047768)
39. Yang, Y. D., Spratt, P., Chen, H., Park, C. & Kihara, D. Sub-AQUA: real-value quality assessment of protein structure models. Protein Eng. Des. Sel. 23, 617-632.
40. Ünlü M., Morgan M.E., and Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts Electrophoresis 18 1997 2071 2077 (Pubitemid 27501267)
41. Aebersold R., and Mann M. Mass spectrometry-based proteomics Nature 422 2003 198 207 (Pubitemid 36362757)
42. Mann M. Functional and quantitative proteomics using SILAC Nat. Rev. Mol. Cell Biol. 7 2006 952 958 (Pubitemid 44871421)
43. Leung D., Hardouin C., Boger D.L., and Cravatt B.F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes Nat. Biotechnol. 21 2003 687 691 (Pubitemid 36638097)
44. Evans M.J., Saghatelian A., Sorensen E.J., and Cravatt B.F. Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling Nat. Biotechnol. 23 2005 1303 1307 (Pubitemid 41486859)
45. Senda M., Kanazawa H., Tsuchiya T., and Futai M. Conformational change of the α subunit of Escherichia coli F1 ATPase: ATP changes the trypsin sensitivity of the subunit Arch. Biochem. Biophys. 220 1983 398 404 (Pubitemid 13119457)
46. Perlin D.S., Latchney L.R., Wise J.G., and Senior A.E. Specificity of the proton adenosinetriphosphatase of Escherichia coli for adenine, guanine, and inosine nucleotides in catalysis and binding Biochemistry 23 1984 4998 5003
47. Myers J.A., and Boyer P.D. Catalytic properties of the ATPase on submitochondrial particles after exchange of tightly bound nucleotides under different steady state conditions FEBS Lett. 162 1983 277 281
48. Hunt J.F., Weaver A.J., Landry S.J., Gierasch L., and Deisenhofer J. The crystal structure of the GroES co-chaperonin at 2.8 Å resolution Nature 379 1996 37 45
49. Schneider D.A., and Gourse R.L. Relationship between growth rate and ATP concentration in Escherichia coli: a bioassay for available cellular ATP J. Biol. Chem. 279 2004 8262 8268 (Pubitemid 38294718)
50. Park C., Zhou S., Gilmore J., and Marqusee S. Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis J. Mol. Biol. 368 2007 1426 1437 (Pubitemid 46617598)
51. Xia K., Manning M., Hesham H., Lin Q., Bystroff C., and Colon W. Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE Proc. Natl Acad. Sci. USA 104 2007 17329 17334 (Pubitemid 350219842)
52. Hubbard S.J. The structural aspects of limited proteolysis of native proteins Biochim. Biophys. Acta 1382 1998 191 206 (Pubitemid 28130392)
53. Park C., and Marqusee S. Probing the high energy states in proteins by proteolysis J. Mol. Biol. 343 2004 1467 1476 (Pubitemid 39387837)
54. Chang Y., and Park C. Mapping transient partial unfolding by protein engineering and native-state proteolysis J. Mol. Biol. 393 2009 543 556
55. Grimsley G.R., and Pace C.N. Spectrophotometric determination of protein concentration Curr. Protoc. Protein Sci. 2004 Unit 3.1
56. Mach H., Middaugh C.R., and Denslow N. Determining the identity and purity of recombinant proteins by UV absorption spectroscopy Curr. Protoc. Protein Sci. 2001 Unit 7.2
57. Park C., and Marqusee S. Quantitative determination of protein stability and ligand binding by pulse proteolysis Curr. Protoc. Protein Sci. 46 2006 20.11.14 20.11.21
58. Wildes D., Anderson L.M., Sabogal A., and Marqusee S. Native state energetics of the Src SH2 domain: evidence for a partially structured state in the denatured ensemble Protein Sci. 15 2006 1769 1779
59. Dahlquist F.W., Long J.W., and Bigbee W.L. Role of calcium in the thermal stability of thermolysin Biochemistry 15 1976 1103 1111
60. Neuhoff V., Arold N., Taube D., and Ehrhardt W. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie brilliant blue G-250 and R-250 Electrophoresis 9 1988 255 262
61. Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567 (Pubitemid 30007252)