Ligand binding analysis and screening by chemical denaturation shift

Analytical Biochemistry

Volumn 443, Issue 1, 2013, Pages 52-57

  Schön, Arne ^a   Brown, Richard K ^b   Hutchins, Burleigh M ^b   Freire, Ernesto ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b AVIA Biosystems   (United States)

Author keywords

Chemical denaturation; Ligand binding analysis

Indexed keywords

BINDING ENERGY; CHEMICAL ANALYSIS; DENATURATION; PROTEINS;

ANALYTICAL EQUATIONS; CHEMICAL DENATURATION; DENATURATION TEMPERATURES; INTRINSIC ACTIVITIES; LIGAND BINDING; PHYSIOLOGICAL TEMPERATURE; PROTEIN DENATURATION; PROTEIN STABILIZATION;

LIGANDS;

ARTICLE; BINDING AFFINITY; CONCENTRATION RESPONSE; HUMAN; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SCREENING; TEMPERATURE;

CHEMICAL DENATURATION; LIGAND BINDING ANALYSIS;

ACETAZOLAMIDE; CALORIMETRY; CARBONIC ANHYDRASE I; HIV PROTEASE; HUMANS; HYDROGEN-ION CONCENTRATION; KINETICS; LIGANDS; MESYLATES; OXALATES; PIPERIDINES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; SPECTROMETRY, FLUORESCENCE; TEMPERATURE; THERMODYNAMICS; UREA;

EID: 84884629196     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2013.08.015     Document Type: Article

References (35)

1. J. Wyman Heme proteins Adv. Protein Chem. 4 1948 407 531
2. J. Wyman, and S.J. Gill Binding and Linkage: The Functional Chemistry of Biological Macromolecules 1990 University Science Books Sausalito, CA
3. J.F. Brandts, R.J. Oliveira, and C. Westort Thermodynamics of protein denaturation: effect of pressure on the denaturation of ribonuclease A Biochemistry 9 1970 1038 1047
4. P.L. Privalov Stability of proteins: small globular proteins Adv. Protein Chem. 33 1979 167 239
5. R.F. Greene Jr., and C.N. Pace Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, α-chymotrypsin, and β-lactoglobulin J. Biol. Chem. 249 1974 5388 5393
6. I.M. Plaza del Pino, C.N. Pace, and E. Freire Temperature and guanidine hydrochloride dependence of the structural stability of ribonuclease T1 Biochemistry 31 1992 11196 11202
7. E. Freire The thermodynamic linkage between protein structure, stability, and function K.P. Murphy, Methods in Molecular Biology vol. 168 2001 Humana Totowa, NJ 37 68
8. C.N. Pace, D.V. Laurents, and R.E. Erickson Urea denaturation of barnase: pH dependence and characterization of the unfolded state Biochemistry 31 1992 2728 2734
9. M.M. Santoro, and D.W. Bolen Unfolding free energy changes determined by the linear extrapolation method: 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants Biochemistry 27 1998 8063 8068
10. D.W. Bolen, and M.M. Santoro Unfolding free energy changes determined by the linear extrapolation method: 2. Incorporation of DGN-U values in a thermodynamic cycle Biochemistry 27 1988 8069 8074
11. J.K. Myers, C.N. Pace, and J.M. Scholtz Denaturant m values and heat capacity changes: relation to changes in accessible surface area of protein unfolding Protein Sci. 4 1995 2138 2148
12. E. Freire, A. Schön, B.M. Hutchins, R.K. Brown, Chemical denaturation as a tool in the formulation optimization of biologics, Drug Discov. Today (in press), http://dx.doi.org/10.1016/j.drudis.2013.06.005.
13. I. Luque, S.A. Leavitt, and E. Freire The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu. Rev. Biophys. Biomol. Struct. 31 2002 235 256 (Pubitemid 34666832)
14. U.B. Ericsson, B.M. Hallberg, G.T. Detitta, N. Dekker, and P. Nordlund ThermoFluor-based high-throughput stability optimization of proteins for structural studies Anal. Biochem. 357 2006 289 298 (Pubitemid 44430091)
15. M.C. Lo, A. Aulabaugh, G. Jin, R. Cowling, J. Bard, M. Malamas, and G. Ellestad Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery Anal. Biochem. 332 2004 153 159 (Pubitemid 39099482)
16. D. Matulis, J.K. Kranz, F.R. Salemme, and M.J. Todd Thermodynamic stability of carbonic anhydrase: measurements of binding affinity and stoichiometry using ThermoFluor Biochemistry 44 2005 5258 5266 (Pubitemid 40471238)
17. M.W. Pantoliano, E.C. Petrella, J.D. Kwasnoski, V.S. Lobanov, J. Myslik, E. Graf, T. Carver, E. Asel, B.A. Springer, P. Lane, and F.R. Salemme High-density miniaturized thermal shift assays as a general strategy for drug discovery J. Biomol. Screening 6 2001 429 440 (Pubitemid 34052847)
18. J.F. Brandts, and L.N. Lin Study of strong to ultratight protein interactions using differential scanning calorimetry Biochemistry 29 1990 6927 6940 (Pubitemid 20225495)
19. M. Straume, and E. Freire Two-dimensional differential scanning calorimetry: simultaneous resolution of intrinsic protein structural energetics and ligand binding interactions by global linkage analysis Anal. Biochem. 203 1992 259 268
20. C.N. Pace, and T. McGrath Substrate stabilization of lysozyme to thermal and guanidine hydrochloride denaturation J. Biol. Chem. 255 1990 3862 3865
21. M. Gaudet, N. Remtulla, S.E. Jackson, E.R.G. Main, D.G. Bracewell, G. Aeppli, and P.A. Dalby Protein denaturation and protein:drug interactions from intrinsic protein fluorescence measurements at the nanolitre scale Protein Sci. 19 2010 1544 1554
22. K. Mahendrarajah, P.A. Dalby, B. Wilkinson, S.E. Jackson, and E.R. Main A high-throughput fluorescence chemical denaturation assay as a general screen for protein-ligand binding Anal. Biochem. 411 2011 155 157
23. T. Wiseman, S. Williston, J.F. Brandts, and L.N. Lin Rapid measurement of binding constants and heats of binding using a new titration calorimeter Anal. Biochem. 179 1989 131 135
24. D. Sali, M. Bycroft, and A.R. Fersht Surface electrostatic interactions contribute little to stability of barnase J. Mol. Biol. 220 1991 779 788
25. F. Chiti, M. Calamai, N. Taddei, M. Stefani, G. Ramponi, and C.M. Dobson Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases Proc. Natl. Acad. Sci. U.S.A. 99 2002 16419 16426 (Pubitemid 35470988)
26. T.N. Bhat, E.T. Baldwin, B. Liu, Y.S. Cheng, and J.W. Erickson Crystal structure of a tethered dimer of HIV-1 proteinase complexed with an inhibitor Nat. Struct. Biol. 1 1994 552 556
27. I. Luque, M.J. Todd, J. Gómez, N. Semo, and E. Freire Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis Biochemistry 37 1998 5791 5797 (Pubitemid 28196730)
28. M.J. Todd, I. Luque, A. Velazquez-Campoy, and E. Freire Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant Biochemistry 39 2000 11876 11883
29. E.T. Brower, A. Schön, and E. Freire Naturally occurring variability in the envelope glycoprotein of HIV-1 and development of cell entry inhibitors Biochemistry 49 2010 2359 2367
30. A. Schon, N. Madani, J.C. Klein, A. Hubicki, D. Ng, X. Yang, A.B. Smith 3rd, J. Sodroski, and E. Freire Thermodynamics of binding of a low-molecular-weight CD4 mimetic to HIV-1 gp120 Biochemistry 45 2006 10973 10980 (Pubitemid 44360167)
31. Y. Kawasaki, E.E. Chufan, V. Lafont, K. Hidaka, Y. Kiso, L. Mario Amzel, and E. Freire How much binding affinity can be gained by filling a cavity? Chem. Biol. Drug Des. 75 2010 143 151
32. S. D'Auria, M. Staiano, I.M. Kuznetsova, and K.K. Turoverov The combined use of fluorescence spectroscopy and X-ray crystallography greatly contributes to elucidating structure and dynamics of proteins C.D. Geddes, J.R. Lakowicz, Reviews in Fluorescence vol. 2005 2005 Springer New York 25 61
33. A. Hawe, M. Sutter, and W. Jiskoot Extrinsic fluorescent dyes as tools for protein characterization Pharm. Res. 25 2008 1487 1499
34. C. Temperini, A. Cecchi, A. Scozzafava, and C.T. Supuran Carbonic anhydrase inhibitors: comparison of chlorthalidone, indapamide, trichloromethiazide, and furosemide X-ray crystal structures in adducts with isozyme II, when several water molecules make the difference Bioorg. Med. Chem. 17 2009 1214 1221
35. Q. Zhao, L. Ma, S. Jiang, H. Lu, S. Liu, Y. He, N. Strick, N. Neamati, and A.K. Debnath Identification of N-phenyl-N'-(2,2,6,6-tetramethyl-piperidin-4- yl)-oxalamides as a new class of HIV-1 entry inhibitors that prevent gp120 binding to CD4 Virology 339 2005 213 225 (Pubitemid 41169789)