Applications of isothermal titration calorimetry in protein science
Corresponding Author
Yi Liang
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
*Corresponding author: Tel/Fax, 86-27-68754902; E-mail, [email protected]Search for more papers by this authorCorresponding Author
Yi Liang
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
*Corresponding author: Tel/Fax, 86-27-68754902; E-mail, [email protected]Search for more papers by this authorThis work was supported by grants from the National Key Basic Research Foundation of China (No. 2006CB910301), the National Natural Science Foundation of China (No. 30770421) and the Program for New Century Excellent Talents in University (No. NCET-04-0670)
Abstract
During the past decade, isothermal titration calorimetry (ITC) has developed from a specialist method for understanding molecular interactions and other biological processes within cells to a more robust, widely used method. Nowadays, ITC is used to investigate all types of protein interactions, including protein-protein interactions, protein-DNA/RNA interactions, protein-small molecule interactions and enzyme kinetics; it provides a direct route to the complete thermodynamic characterization of protein interactions. This review concentrates on the new applications of ITC in protein folding and misfolding, its traditional application in protein interactions, and an overview of what can be achieved in the field of protein science using this method and what developments are likely to occur in the near future. Also, this review discusses some new developments of ITC method in protein science, such as the reverse titration of ITC and the displacement method of ITC.
References
- 1 Cliff MJ, Gutierrez A, Ladbury JE. A survey of the year 2003 literature on applications of isothermal titration calorimetry. J Mol Recognit 2004, 17: 513–523.
- 2 Ababou A, Ladbury JE. Survey of the year 2004: literature on applications of isothermal titration calorimetry. J Mol Recognit 2006, 19: 79–89.
- 3 Ababou A, Ladbury JE. A survey of the year 2005 literature on applications of isothermal titration calorimetry. J Mol Recognit 2007, 20: 4–14.
- 4 Okhrimenkoa O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008, 21: 1–19.
- 5 Baker BM, Murphy KP. Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry. Biophys J 1996, 71: 2049–2055.
- 6 Connelly PR, Varadarajan R, Sturtevant JM, Richards FM. Thermodynamics of protein-peptide interactions in the ribonuclease S system studied by titration calorimetry. Biochemistry 1990, 29: 6108–6114.
- 7 Spolar RS, Record MT Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994, 263: 777–784.
- 8 Anfinsen CB. Principles that govern the folding of protein chains. Science 1973, 181: 223–230.
- 9 Liang Y, Du F, Sanglier S, Zhou BR, Xia Y, Va n Dorsselaer A, Maechling C et al. Unfolding of rabbit muscle creatine kinase induced by acid. A study using electrospray ionization mass spectrometry, isothermal titration calorimetry, and fluorescence spectroscopy. J Biol Chem 2003, 278: 30098–30105.
- 10 Fan YX, Zhou JM, Kihara H, Tsou CL. Unfolding and refolding of dimeric creatine kinase equilibrium and kinetic studies. Protein Sci 1998, 7: 2631–2641.
- 11 Nakamura S, Kidokoro S. Direct observation of the enthalpy change accompanying the native to molten-globule transition of cytochrome c by using isothermal acid-titration calorimetry. Biophys Chem 2005, 113: 161–168.
- 12 Luke K, Wittung-Stafshede P. Folding and assembly pathways of co-chaperonin proteins 10: Origin of bacterial thermostability. Arch Biochem Biophys 2006, 456: 8–18.
- 13 Yang F Jr, Zhang M, Zhou BR, Chen J, Liang Y. Oleic acid inhibits amyloid formation of the intermediate of α-lactalbumin at moderately acidic pH. J Mol Biol 2006, 362: 821–834.
- 14 Kardos J, Yamamoto K, Hasegawa K, Naiki H, Goto Y. Direct measurement of the thermodynamic parameters of amyloid formation by isothermal titration calorimetry. J Biol Chem 2004, 279: 55308–55314.
- 15 Zhou BR, Liang Y, Du F, Zhou Z, Chen J. Mixed macromolecular crowding accelerates the oxidative refolding of reduced, denatured lysozyme: implications for protein folding in intracellular environments. J Biol Chem 2004, 279: 55109–55116.
- 16 Du F, Zhou Z, Mo ZY, Shi JZ, Chen J, Liang Y. Mixed macromolecular crowding accelerates the refolding of rabbit muscle creatine kinase: implications for protein folding in physiological environments. J Mol Biol 2006, 364: 469–482.
- 17 Zhou BR, Zhou Z, Hu QL, Chen J, Liang Y. Mixed macromolecular crowding inhibits amyloid formation of hen egg white lysozyme. Biochim Biophys Acta 2008, 1784: 472–480.
- 18 Ahmad MF, Ramakrishna T, Raman B, Rao Ch M. Fibrillogenic and non-fibrillogenic ensembles of SDS-bound human α-synuclein. J Mol Biol 2006, 364: 1061–1072.
- 19 Groenning M, Norrman M, Flink JM, Van De Weert M, Bukrinsky JT, Schluckebier G, Frokjaer S. Binding mode of thioflavin T in insulin amyloid fibrils. J Struct Biol 2007, 159: 483–497.
- 20 Zhou YL, Liao JM, Chen J, Liang Y. Macromolecular crowding enhances the binding of superoxide dismutase to xanthine oxidase: implications for protein-protein interactions in intracellular environments. Int J Biochem Cell Biol 2006, 38: 1986–1994.
- 21 Zhou YL, Liao JM, Chen J, Liang Y. Thermodynamics of the interaction of xanthine oxidase with superoxide dismutase by isothermal titration calorimetry and fluorescence spectroscopy. Thermochim Acta 2005, 426: 173–178.
- 22 Jin R, Rummel A, Binz T, Brunger AT. Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity. Nature 2006, 444: 1092–1095.
- 23 Knipscheer P, Van Dijk WJ, Olsen JV, Mann M, Sixma TK. Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation. EMBO J 2007, 26: 2797–2807.
- 24 Chen Y, Xu Y, Bao Q, Xing Y, Li Z, Lin Z, Stock JB et al. Structural and biochemical insights into the regulation of protein phosphatase 2A by small t antigen of SV40. Nat Struct Mol Biol 2007, 14: 527–534.
- 25 Rainaldi M, Yamniuk AP, Murase T, Vogel HJ. Calcium-dependent and -independent binding of soybean calmodulin isoforms to the calmodulin binding domain of tobacco MAPK phosphatase-1. J Biol Chem 2007, 282: 6031–6042.
- 26 Kiel C, Selzer T, Shaul Y, Schreiber G, Herrmann C. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc Natl Acad Sci U S A 2004, 101: 9223–9228.
- 27 Siligardi G, Hu B, Panaretou B, Piper PW, Pearl LH, Prodromou C. Co-chaperone regulation of conformational switching in the Hsp90 ATPase cycle. J Biol Chem 2004, 279: 51989–51998.
- 28 Yokota A, Tsumoto K, Shiroishi M, Kondo H, Kumagai I. The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction. J Biol Chem 2003, 278: 5410–5418.
- 29 Minetti CA, Remeta DP, Zharkov DO, Plum GE, Johnson F, Grollman AP, Breslauer KJ. Characterization of formamidopyrimidine-glycosylase(Fpg) interactions with damaged DNA duplexes. J Mol Biol 2003, 328: 1047–1060.
- 30 Buczek P, Horvath MP. Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain. J Mol Biol 2006, 359: 1217–1234.
- 31 Ziegler A, Seelig J. High affinity of the cell-penetrating peptide HIV-1 Tat-PTD for DNA. Biochemistry 2007, 46: 8138–8145.
- 32 Loregian A, Sinigalia E, Mercorelli B, Palù G, Coen DM. Binding parameters and thermodynamics of the interaction of the human cytomegalovirus DNA polymerase accessory protein, UL44, with DNA: implications for the processivity mechanism. Nucleic Acids Res 2007, 35: 4779–4791.
- 33 Recht MI, Williamson JR. RNA tertiary structure and cooperative assembly of a large ribonucleoprotein complex. J Mol Biol 2004, 344: 395–407.
- 34 Volpon L, D'Orso I, Young CR, Frasch AC, Gehring K. NMR structural study of TcUBP1, a single RRM domain protein from Trypanosoma cruzi: contribution of a β hairpin to RNA binding. Biochemistry 2005, 44: 3708–3717.
- 35 Yang F, Zhou BR, Zhang P, Zhao YF, Chen J, Liang Y. Binding of ferulic acid to cytochrome c enhances stability of the protein at physiological pH and inhibits cytochrome c-induced apoptosis. Chem Biol Interact. 2007, 170: 231–243.
- 36 Brogan AP, Widger WR, Bensadek D, Riba-Garcia I, Gaskell SJ, Kohn H. Development of a technique to determine bicyclomycinrho binding and stoichiometry by isothermal titration calorimetry and mass spectrometry. J Am Chem Soc 2005, 127: 2741–2751.
- 37 Engel M, Hindie V, Lopez-Garcia LA, Stroba A, Schaeffer F, Adrian I, Imig J et al. Allosteric activation of the protein kinase PDK1 with low molecular weight compounds. EMBO J 2006, 25: 5469–5480.
- 38 Burnett JC, Ruthel G, Stegmann CM, Panchal RG., Nguyen TL, Hermone AR, Stafford RG et al. Inhibition of metalloprotease botulinum serotype A from a pseudo-peptide binding mode to a small molecule that is active in primary neurons. J Biol Chem 2007, 282: 5004–5014.
- 39 Lorca GL, Ezersky A, Lunin VV, Walker JR, Altamentova S, Evdokimova E, Vedadi M et al. Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator. J Biol Chem 2007, 282: 16476–16491.
- 40 Wilcox DE. Isothermal titration calorimetry of metal ions binding to proteins: an overview of recent studies. Inorganica Chim Acta 2008, 361: 857–867.
- 41 Thompsett AR, Abdelraheim SR, Daniels M, Brown DR. High affinity binding between copper and full-length prion protein identified by two different techniques. J Biol Chem 2005, 280: 42750–42758.
- 42 Velazquez-Campoy A, Freire E. Isothermal titration calorimetry to determine association constants for high-affinity ligands. Nat Protoc 2006, 1: 186–191.
- 43 Vander Meulen KA, Saecker RM, Record MT Jr. Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA. J Mol Biol 2008, 377: 9–27.
- 44 Fisher RJ, Fivash MJ, Stephen AG, Hagan NA, Shenoy SR, Medaglia MV, Smith LR et al. Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res 2006, 34: 472–484.
- 45 Velázquez Campoy A, Freire E. ITC in the post-genomic era Priceless. Biophys Chem 2005, 115: 115–124.
- 46 Andújar-Sánchez M, Jara-Pérez V, Cámara-Artigas A. Thermodynamic determination of the binding constants of angiotensin-converting enzyme inhibitors by a displacement method. FEBS Lett 2007, 581: 3449–3454.