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Chapter 13: Calorimetry-based Approaches in Analysis of Protein–Protein Interactions—References

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Bradford M.M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248–254.

Bradshaw J.M. and Waksman G. 1998. Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: Application to the interaction of the Src SH2 domain with a high-affinity tyrosyl phosphopeptide. Biochemistry 37: 15400–15407.

Burrows S.D., Doyle M.L., Murphy K.P., Franklin S.G., White J.R., Brooks I., McNulty D.E., Scott M.O., Knutson J.R., and Porter D. 1994. Determination of the monomer-dimer equilibrium of interleukin-8 reveals it is a monomer at physiological concentrations. Biochemistry 33: 12741–12745.

Caplan M.R. and Erickson H.P. 2003. Apparent cooperative assembly of the bacterial cell division protein FtsZ demonstrated by isothermal titration calorimetry. J. Biol. Chem. 278: 13784–13788.

Cheng Y.S., Patterson C.E., and Staeheli P. 1991. Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and bind GMP in addition to GDP and GTP. Mol. Cell. Biol. 11: 4717–4725.

Covell D.G. and Wallqvist A. 1997. Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope. J. Mol. Biol. 269: 281–297.

de Rooij J., Rehmann H., van Triest M., Cool R.H., Wittinghofer A., and Bos J.L. 2000. Mechanism of regulation of the Epac family of cAMP-dependent RapGEFs. J. Biol. Chem. 275: 20829–20836.

Freire E. 1995a. Differential scanning calorimetry. Methods Mol. Biol. 40: 191–218.

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Freire E. and Murphy K.P. 1991. Molecular basis of co-operativity in protein folding. J. Mol. Biol. 222: 687–698.

Gerstein M. and Chothia C. 1996. Packing at the protein-water interface. Proc. Natl. Acad. Sci. 93: 10167–10172.

Geyer M., Herrmann C., Wohlgemuth S., Wittinghofer A., and Kalbitzer H.R. 1997. Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling. Nat. Struct. Biol. 4: 694–699.

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Gomez J. and Freire E. 1995. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252: 337–350.

Gomez J., Hilser V.J., Xie D., and Freire E. 1995. The heat capacity of proteins. Proteins 22: 404–412.

Guerois R., Nielsen J.E., and Serrano L. 2002. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol. 320: 369–387.

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Heerklotz H.H., Binder H., and Epand R.M. 1999. A "release" protocol for isothermal titration calorimetry. Biophys. J. 76: 2606–2613.

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Herrmann C., Martin G.A., and Wittinghofer A. 1995. Quantitative analysis of the complex between p21ras and the Ras-binding domain of the human Raf-1 protein kinase. J. Biol. Chem. 270: 2901–2905.

Herrmann C., Horn G., Spaargaren M., and Wittinghofer A. 1996. Differential interaction of the ras family GTP-binding proteins H-Ras, Rap1A, and R-Ras with the putative effector molecules Raf kinase and Ral-guanine nucleotide exchange factor. J. Biol. Chem. 271: 6794–6800.

Indyk L. and Fisher H.F. 1998. Theoretical aspects of isothermal titration calorimetry. Methods Enzymol. 295: 350–364.

Janin J. 1999. Wet and dry interfaces: The role of solvent in protein-protein and protein-DNA recognition. Structure Fold. Des. 7: R277–R279.

Jelesarov I. and Bosshard H.R. 1994. Thermodynamics of ferredoxin binding to ferredoxin:NADP+ reductase and the role of water at the complex interface. Biochemistry 33: 13321–13328.

Kaul M., Barbieri C.M., Kerrigan J.E., and Pilch D.S. 2003. Coupling of drug protonation to the specific binding of aminoglycosides to the A site of 16 S rRNA: Elucidation of the number of drug amino groups involved and their identities. J. Mol. Biol. 326: 1373–1387.

Kholodenko V. and Freire E. 1999. A simple method to measure the absolute heat capacity of proteins. Anal. Biochem. 270: 336–338.

Kiel C., Serrano L., and Herrmann C. 2004. A detailed thermodynamic analysis of Ras/effector complex interfaces. J. Mol. Biol. 340: 1039–1058.

Kortemme T. and Baker D. 2002. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. 99: 14116–14121.

Kozlov A.G. and Lohman T.M. 2000. Large contributions of coupled protonation equilibria to the observed enthalpy and heat capacity changes for ssDNA binding to Escherichia coli SSB protein. Proteins (suppl.) 4: 8–22.

Ladbury J.E. 1996. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem. Biol. 3: 973–980.

Ladbury J.E. and Chowdhry B.Z. 1998. Biocalorimetry: Applications of calorimetry in the biological sciences. Wiley, Chichester, United Kingdom.

Ladbury J.E., Wright J.G., Sturtevant J.M., and Sigler P.B. 1994. A thermodynamic study of the trp repressor-operator interaction. J. Mol. Biol. 238: 669–681.

Lafitte D., Lamour V., Tsvetkov P.O., Makarov A.A., Klich M., Deprez P., Moras D., Briand C., and Gilli R. 2002. DNA gyrase interaction with coumarin-based inhibitors: The role of the hydroxybenzoate isopentenyl moiety and the 5´-methyl group of the noviose. Biochemistry 41: 7217–7223.

Lassalle M.W., Hinz H.J., Wenzel H., Vlassi M., Kokkinidis M., and Cesareni G. 1998. Dimer-to-tetramer transformation: Loop excision dramatically alters structure and stability of the ROP four α-helix bundle protein. J. Mol. Biol. 279: 987–1000.

Leavitt S. and Freire E. 2001. Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol. 11: 560–566.

Lin S.H. and Lee J.C. 2002. Communications between the high-affinity cyclic nucleotide binding sites in E. coli cyclic AMP receptor protein: Effect of single site mutations. Biochemistry 41: 11857–11867.

Lobo B.A., Koe G.S., Koe J.G., and Middaugh C.R. 2003. Thermodynamic analysis of binding and protonation in DOTAP/DOPE (1:1): DNA complexes using isothermal titration calorimetry. Biophys. Chem. 104: 67–68.

Luque I. and Freire E. 1998. Structure-based prediction of binding affinities and molecular design of peptide ligands. Methods Enzymol. 295: 100–127.

Luque I. and Freire E. 2002. Structural parameterization of the binding enthalpy of small ligands. Proteins 49: 181–190.

Luque I., Gomez J., Semo N., and Freire E. 1998. Structure-based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin. Proteins 30: 74–85.

Martinez J.C., Filimonov V.V., Mateo P.L., Schreiber G., and Fersht A.R. 1995. A calorimetric study of the thermal stability of barstar and its interaction with barnase. Biochemistry 34: 5224–5233.

Morton C.J. and Ladbury J.E. 1996. Water-mediated protein-DNA interactions: The relationship of thermodynamics to structural detail. Protein Sci. 5: 2115–2118.

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Murphy K.P. and Freire E. 1992. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv. Protein Chem. 43: 313–361.

Nassar N., Horn G., Herrmann C., Scherer A., McCormick F., and Wittinghofer A. 1995. The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375: 554–560.

O'Brien R., De Decker B., Fleming K.G., Sigler P.B., and Ladbury J.E. 1998. The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archaeon. J. Mol. Biol. 279: 117–125.

Ohtaka H., Velazquez-Campoy A., Xie D., and Freire E. 2002. Overcoming drug resistance in HIV-1 chemotherapy: The binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease. Protein Sci. 11: 1908–1916.

Pacold M.E., Suire S., Perisic O., Lara-Gonzalez S., Davis C.T., Walker E.H., Hawkins P.T., Stephens L., Eccleston J.F., and Williams R.L. 2000. Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase γ. Cell 103: 931–943.

Paula S., Süs W., Tuchtenhagen J., and Blume A. 1995. Thermodynamics of micelle formation as a function of temperature: A high sensitivity titration calorimetry study. J. Phys. Chem. 99: 11742–11751.

Pierce M.M., Raman C.S., and Nall B.T. 1999. Isothermal titration calorimetry of protein-protein interactions. Methods 19: 213–221.

Praefcke G.J., Geyer M., Schwemmle M., Robert Kalbitzer H., and Herrmann C. 1999. Nucleotide-binding characteristics of human guanylate-binding protein 1 (hGBP1) and identification of the third GTP-binding motif. J. Mol. Biol. 292: 321–332.

Prakash B., Praefcke G.J., Renault L., Wittinghofer A., and Herrmann C. 2000. Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. Nature 403: 567–571.

Privalov G., Kavina V., Freire E., and Privalov P.L. 1995. Precise scanning calorimeter for studying thermal properties of biological macromolecules in dilute solution. Anal. Biochem. 232: 79–85.

Rudolph M.G., Linnemann T., Grunewald P., Wittinghofer A., Vetter I.R., and Herrmann C. 2001. Thermodynamics of Ras/effector and Cdc42/effector interactions probed by isothermal titration calorimetry. J. Biol. Chem. 276: 23914–23921.

Scheffzek K., Grunewald P., Wohlgemuth S., Kabsch W., Tu H., Wigler M., Wittinghofer A., and Herrmann C. 2001. The Ras-Byr2RBD complex: Structural basis for Ras effector recognition in yeast. Structure 9: 1043–1050.

Schreiber G., Frisch C., and Fersht A.R. 1997. The role of Glu73 of barnase in catalysis and the binding of barstar. J. Mol. Biol. 270: 111–122.

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Swaminathan C.P., Nandi A., Visweswariah S.S., and Surolia A. 1999. Thermodynamic analyses reveal role of water release in epitope recognition by a monoclonal antibody against the human guanylyl cyclase C receptor. J. Biol. Chem. 274: 31272–31278.

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Xie D., Gulnik S., Collins L., Gustchina E., Suvorov L., and Erickson J.W. 1997. Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: Direct measurement of the protonation states of the catalytic aspartic acid residues. Biochemistry 36: 16166–16172.

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