Research Article
Thermal unfolding of small proteins with SH3 domain folding pattern
Stefan Knapp,
Pekka T. Mattson,
Petya Christova,
Kurt D. Berndt,
Andrej Karshikoff,
Mauno Vihinen,
C.I. Edvard Smith,
Rudolf Ladenstein,
Stefan Knapp
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Search for more papers by this authorPekka T. Mattson
Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
Center for Biotechnology, Department of Clinical Immunology, Karolinska Institute, NOVUM, Huddinge, Sweden
Search for more papers by this authorPetya Christova
Institute of Organic Chemistry, Biophysical Chemistry Laboratory, Bulgarian Academy of Science, Sofia, Bulgaria
Search for more papers by this authorKurt D. Berndt
Medical Nobel Institute for Biochemistry, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
Search for more papers by this authorAndrej Karshikoff
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Search for more papers by this authorMauno Vihinen
Department of Bioscience, Division of Biochemistry, University of Helsinki, Helsinki, Finland
Search for more papers by this authorC.I. Edvard Smith
Center for Biotechnology, Department of Clinical Immunology, Karolinska Institute, NOVUM, Huddinge, Sweden
Search for more papers by this authorCorresponding Author
Rudolf Ladenstein
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, S-14157 Huddinge, Sweden===Search for more papers by this authorStefan Knapp,
Pekka T. Mattson,
Petya Christova,
Kurt D. Berndt,
Andrej Karshikoff,
Mauno Vihinen,
C.I. Edvard Smith,
Rudolf Ladenstein,
Stefan Knapp
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Search for more papers by this authorPekka T. Mattson
Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
Center for Biotechnology, Department of Clinical Immunology, Karolinska Institute, NOVUM, Huddinge, Sweden
Search for more papers by this authorPetya Christova
Institute of Organic Chemistry, Biophysical Chemistry Laboratory, Bulgarian Academy of Science, Sofia, Bulgaria
Search for more papers by this authorKurt D. Berndt
Medical Nobel Institute for Biochemistry, Department of Molecular Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
Search for more papers by this authorAndrej Karshikoff
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Search for more papers by this authorMauno Vihinen
Department of Bioscience, Division of Biochemistry, University of Helsinki, Helsinki, Finland
Search for more papers by this authorC.I. Edvard Smith
Center for Biotechnology, Department of Clinical Immunology, Karolinska Institute, NOVUM, Huddinge, Sweden
Search for more papers by this authorCorresponding Author
Rudolf Ladenstein
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
Center for Structural Biochemistry, Karolinska Institutet, NOVUM, S-14157 Huddinge, Sweden===Search for more papers by this authorFirst published: 07 December 1998
Citations: 49
Abstract
The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy. The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 < pH < 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec). At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12–16 kJ/mol but show quite high melting temperatures.
Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities. Proteins 31:309–319, 1998. © 1998 Wiley-Liss, Inc.
References
- 1 Mayer, B.J., Hamaguchi, M., Hanafusa, H. A novel viral oncogene with structural similarity to phospholipase C. Nature 332: 272–275, 1988.
- 2 Sahr, K.E., Laurila, P., Kotula, L., et al. The complete cDNA and polypeptide sequences of human erythroid alpha-spectrin. J. Biol. Chem. 265: 4434–4443, 1990.
- 3 Wasenius, V.M., Saraste, M., Salven, P., Erämaa, M., Holm, L., Lehto, V.P. Primary structure of the brain alpha-spectrin. J. Cell Biol. 108: 79–93, 1989.
- 4 Jung, G., Korn, E.D., Hammer, J.A. The heavy chain of Acanthamoeba myosin IB is a fusion of myosin-like and non myosin like sequences. Proc. Natl. Acad. Sci. USA 84: 6720–6724, 1987.
- 5 Drubin, D.G., Miller, K.G., Botstein, D.J. Yeast actin-binding proteins: Evidence for a role in morphogenesis. J. Cell Biol. 107: 2551–2561, 1988.
- 6 Drubin, D.G., Mulholland, J., Zhu, Z.M., Botstein, D. Homology of a yeast actin-binding protein to signal transduction proteins and myosins-I. Nature 343: 288–290, 1990.
- 7 Bustelo, X.R., Ledbetter, J.A., Barbacid, M. Product of vav proto-oncogene defines a new class of tyrosine protein kinase substrates. Nature 356: 68–71, 1992.
- 8 Kitamura, D., Kaneko, H., Miyagoe, Y., Ariyasu, T., Watanabe, T. Isolation and characterization of a novel human gene expressed specifically in the cells of hematopoietic lineage. Nucleic Acids Res. 17: 9367–9379, 1989.
- 9 Kohda, D., Hatanaka, H., Odaka, M., et al. Solution structure of the SH3 domain of phospholipase C-gamma. Cell 72: 953–960, 1993.
- 10 Volpp, B.D., Nauseef, W.M., Donelson, J.E., Moser, D.R., Clark, R.A. Cloning of the cDNA and functional expression of the 47-kilodalton cytosolic component of human neutrophil respiratory burst oxidase. Proc. Natl. Acad. Sci. USA 86: 7195–7199, 1989.
- 11 Leto, T.L., Lomax, K.J., Volpp, B.D., et al. Cloning of a 67-kD neutrophil oxidase factor with similarity to a noncatalytic region of p60c-src. Science 248: 727–730, 1990.
- 12 Broek, D., Toda, T., Michaeli, T., et al. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell 48: 789–799, 1987.
- 13 Hughes, D.A., Fukui, Y., Yamamoto, M. Homologous activators of ras in fission and budding yeast. Nature 344: 355–357, 1990.
- 14 Musacchio, A., Gibson, T., Lehto, V.P., Saraste, M. SH3—an abundant protein domain in search of a function. FEBS Lett. 307: 55–61, 1992.
- 15 Yu, H., Rosen, M.K., Shin, T.B., Seidel-Dugan, C., Brugge, J.S., Schreiber, S.L. Solution structure of the SH3 domain of Src and identification of its ligand-binding site. Science 258: 1665–1668, 1992.
- 16 Booker, G.W., Gout, I., Downing, A.K., et al. Solution structure and ligand-binding site of the SH3 domain of the p85 alpha-subunit of phosphatidylinositol 3-kinase. Cell 73: 813–822, 1993.
- 17 Koyama, S., Yu, H., Dalgarno, D.C., Shin, T.B., Zydowsky, L.D., Schreiber, S.L. Structure of the PI3K SH3 domain and analysis of the SH3 family. Cell 72: 945–952, 1993.
- 18 Yang, Y.S., Garbay, C., Duchesne, M., et al. Solution structure of GAP SH3 domain by 1H NMR and spatial arrangement of essential Ras signaling-involved sequences. EMBO J. 13: 1270–1279, 1994.
- 19 Andreotti, A.H., Bunnell, S.C., Feng, S., Berg, L., Schreiber, S.L. Regulatory intramolecular association in a tyrosine kinase of the Tec family. Nature 385: 93–97, 1997.
- 20 Musacchio, A., Noble, M., Pauptit, R., Wierenga, R., Saraste, M. Crystal structure of a Src-homology 3 (SH3) domain. Nature 359: 851–855, 1992.
- 21 Borchert, T.V., Mathieu, M., Zeelen, J.P., Courtneidge, S.A., Wierenga, R.K. The crystal structure of human CskSH3: Structural diversity near the RT-Src and n-Src loop. FEBS Lett. 341: 79–85, 1994.
- 22 Noble, M.E., Musacchio, A., Saraste, M., Courtneidge, S.A., Wierenga, R.K. Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinase and spectrin. EMBO J. 12: 2617–2624, 1993.
- 23 Musacchio, A., Saraste, M., Wilmanns, M. High resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nat. Struct. Biol. 1: 546–551, 1994.
- 24 Liang, J., Chen, J.K., Schreiber, S.L., Clardy, J. Crystal structure of PI3K SH3 domain at 2.0 Å resolution. J. Mol. Biol. 257: 632–643, 1996.
- 25 Eck, M.J., Atwell, S.K., Shoelson, S.E., Harrison, S.C. Structure of the regulatory domains of the Src-family tyrosine kinase Lck. Nature 368: 764–769, 1994.
- 26 Sicheri, F., Moarefi, I., Kuriyan, J. Crystal structure of the Src family tyrosine kinase Hck. Nature 385: 602–609, 1997.
- 27 Maignan, S., Guilloteau, J.P., Fromage, N., Arnoux, B., Becquart, J., Ducruix, A. Crystal structure of the mammalian Grb2 adaptor. Science 268: 291–293, 1995.
- 28 Yu, H., Chen, J.K., Feng, S., Dalgarno, D.C., Brauer, A.W., Schreiber, S.L. Structural basis for the binding of proline-rich peptides to SH3 domains. Cell 76: 933–945, 1994.
- 29 Feng, S., Chen, J.K., Yu, H., Simon, J.A., Schreiber, S.L. Two binding orientations for peptides to the Src SH3 domain: Development of a general model for SH3-ligand interactions. Science 266: 1241–1247, 1994.
- 30 Terasawa, H., Kohda, D., Hatanaka, H., et al. Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factors Sos. Nat. Struct. Biol. 1: 891–897, 1994.
- 31 Wittekind, M., Mapelli, C., Farmer, B.T., et al. Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. Biochemistry 33: 13531–13539, 1994.
- 32 Lim, W.A., Richards, F.M., Fox, R.O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372: 375–379, 1994.
- 33 Wu, X., Knudsen, B., Feller, S.M., et al. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure 3: 215–226, 1995.
- 34 Chen, J.K., Lane, W.S., Brauer, A.W., Tanaka, K., Schreiber, S.L. Biased combinatorial libraries; novel ligands for the SH3 domain of phosphatidyl inositol 3-kinase. J. Am. Chem. Soc. 115: 12591–12592, 1993.
- 35 Rickles, R.J., Botfield, M.C., Weng, Z., et al. Identification of Src, Fyn, Lyn, PI3K and Abl SH3 domain ligands using phage display libraries. EMBO J. 13: 5598–5604, 1994.
- 36 Falzone, C.J., Kao, Y.H., Zhao, J., Bryant, D.A., Lecomte, J.T. Three dimensional solution structure of PsaE from the cyanobacterium Synechoccus sp. strain PCC 7002, a photosystem I protein that shows structural homology with SH3 domains. Biochemistry 33: 6052–6062, 1994.
- 37 Wilson, K.P., Shewchuk, L.M., Brennan, R.G., Otsuka, A.J., Matthews, B.W. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc. Natl. Acad. Sci. USA 89: 9257–9261, 1992.
- 38 Baumann, H., Knapp, S., Lundbäck, T., Ladenstein, R., Härd, T. Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus. Nat. Struct. Biol. 1: 808–819, 1994.
- 39 Edmondson, S.P., Qiu, L., Shriver, J.W. Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry 34: 13289–13304, 1995.
- 40 Viguera, A.R., Martinez, J.C., Filimonov, V.V., Mateo, P.L., Serrano, L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 33: 2142–2159, 1994.
- 41 Knapp, S., Karshikoff, A., Berndt, K.D., Christova, P., Atanasov, B., Ladenstein, R. Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile Sulfolobus solfataricus. J. Mol. Biol. 264: 1132–1144, 1996.
- 42 Desiderio, S., Siliciano, J.D. The Itk/Btk/Tec family of protein-tyrosine kinases. Chem. Immunol. 59: 191–210, 1994.
- 43 Sideras, P., Smith, C.I. Molecular and cellular aspects of X-linked agammaglobulinemia. Adv. Immunol. 59: 135–223, 1995.
- 44 Mattsson, P.T., Vihinen, M., Smith, S.I. X-linked agammaglobulinemia (XLA): A genetic tyrosine kinase (Btk) disease. Bioessays 18: 825–834, 1996.
- 45 Brinkmann, U., Mattes, R.E., Buckel, P. High-level expression of recombinant genes in Escherichia coli is dependent on the availibility of the dnaY gene product. Gene 85: 109–114, 1989.
- 46 Gill, S.C., von Hippel, P.H. Calculation of protein extinction coefficients from amino acid sequence data. Analyt. Biochem. 182: 319–326, 1989.
- 47 Swint, L., Robertson, A.D. Thermodynamics of unfolding for turkey ovomucoid third domain: Thermal and chemical denaturation. Prot. Sci. 2: 2037–2049, 1993.
- 48 Santoro, M.M., Bolen, D.W. Unfolding free energy changes by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27: 8063–8068, 1988.
- 49 McAfee, J.G., Edmondson, S.P., Datta, P.K., Shriver, J.W., Gupta, R. Gene cloning, expression, and characterization of the Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry 34: 10063–10077, 1995.
- 50 Vihinen, M., Vetrie, D., Maniar, H.S., et al. Structural basis for chromosome X-linked agamma globulinemia: A tyrosine kinase disease. Proc. Natl. Acad. Sci. USA 91: 12803–12807, 1994.
- 51 Hansson, H., Allard, P., Mattson, P.T., Vihinen, M., Smith, C.I., Härd, T. Solution structure of the SH3 domain in Bruton's tyrosine kinase. Biochemistry, in press.
- 52 Freskgård, P.O., Mårtensson, L.G., Jonasson, P., Jonsson, B.H., Carlsson, U. Assignment of the contribution of the tryptophan residues to the circular dichroism spectrum of human carbonic anhydrase II. Biochemistry 33: 14281–14288, 1994.
- 53 Liu, Y., Sturtevant, J.M. The observed change in heat capacity accompanying the thermal unfolding of proteins depends on the composition of the solution and on the method employed to change the temperature of unfolding. Biochemistry 35: 3059–3062, 1996.
- 54 Alexander, P., Fahnestock, S., Lee, T., Orban, J., Bryan, P. Thermodynamic analysis of the folding of the Streptococcal protein G IgG-binding domains B1 and B2: Why small proteins tend to have high denaturation temperatures. Biochemistry 31: 3597–3603, 1992.
- 55 Varley, P., Gronenborn, A.M., Christensen, H., Wingfield, P.T., Pain, R.H., Clore, G.M. Kinetics of folding of the all-beta sheet protein interleukin-1 beta. Science 260: 111–1113, 1993.
- 56 Privalov, P.L., Gill, S.J. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39: 191–234, 1988.
- 57
Chen, Y.J.,
Lin, S.C.,
Tzeng, S.R.,
Patel, H.V.,
Lyu, P.C.,
Cheng, J.W.
Stability and folding of the SH3 domain of Bruton's tyrosine kinase.
Proteins
26: 465–471,
1996.
10.1002/(SICI)1097-0134(199612)26:4<465::AID-PROT7>3.0.CO;2-A CAS PubMed Web of Science® Google Scholar
- 58 Bae, S.J., Sturtevant, J.M. Thermodynamics of the thermal unfolding of eglin c in the presence and absence of guanidinium chloride. Biophys. Chem. 55: 247–252, 1995.
- 59 Jackson, S.E., Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30: 10428–10435, 1991.
- 60 Murphy, K.P., Bhakuni, V., Xie, D., Freire, E. Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates. J. Mol. Biol. 227: 293–306, 1992.
- 61 Rao, S.T., Rossmann, M.G. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76: 241–256, 1973.
- 62 Richardson, J.S. Beta-sheet topology and the relatedness of proteins. Nature 268: 495–500, 1977.
- 63 Schulz, G.E. Structural rules for globular proteins. Angew. Chem. Int. Ed. 16: 23–32, 1977.
- 64 Ptitsyn, O.B., Finkelstein, A.V. Similarities of protein topologies: Evolutionary divergence, functional convergence or principles of folding? Q. Rev. Biophys. 13: 339–386, 1980.
- 65
Wang, Z.X.
How many fold types of protein are there in nature?
Proteins
26: 186–191,
1996.
10.1002/(SICI)1097-0134(199610)26:2<186::AID-PROT8>3.0.CO;2-E CAS PubMed Web of Science® Google Scholar
- 66 Li, H., Helling, R., Tang, C., Wingreen, N. Emergence of preferred structures in a simple model of protein folding. Science 273: 666–669, 1996.
- 67 McCrary, B.S., Edmondson, S.P., Shriver, J.W. Hyperthermophile protein folding thermodynamics: Differential scanning calorimetry and chemical denaturation of Sac7d. J. Mol. Biol. 264: 784–805, 1996.
- 68 Vihinen, M. Relationship of protein flexibility to thermostability. Protein Eng. 1: 477–480, 1987.
- 69 Zhu, Q., Zhang, M., Rawlings, D.J., et al. Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA). J. Exp. Med. 180: 461–470, 1994.
- 70 Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946–950, 1991.
- 71 Merrit, E.A., Murphy, M.E. Raster3D Version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr. D50: 869–873, 1994.
Citing Literature
