Probing protein structure by limited proteolysis

• Autorzy: Fontana A. , Polverino de Laureto P. , Spolaore B. , Frare E. , Picotti P. , Zambonin M.
• Języki publikacji: EN

Abstrakty

EN

Limited proteolysis experiments can be successfully used to probe conformational features of proteins. In a number of studies it has been demonstrated that the sites of limited proteolysis along the polypeptide chain of a protein are characterized by enhanced backbone flexibility, implying that proteolytic probes can pinpoint the sites of local unfolding in a protein chain. Limited proteolysis was used to analyze the partly folded (molten globule) states of several proteins, such as apomyoglobin, a-lactalbumin, calcium-binding lysozymes, cytochrome c and human growth hor­mone. These proteins were induced to acquire the molten globule state under spe­cific solvent conditions, such as low pH. In general, the protein conformational fea­tures deduced from limited proteolysis experiments nicely correlate with those deriv­ing from other biophysical and spectroscopic techniques. Limited proteolysis is also most useful for isolating protein fragments that can fold autonomously and thus be­have as protein domains. Moreover, the technique can be used to identify and pre­pare protein fragments that are able to associate into a native-like and often func­tional protein complex. Overall, our results underscore the utility of the limited pro- teolysis approach for unravelling molecular features of proteins and appear to prompt its systematic use as a simple first step in the elucidation of structure-dynamics- function relationships of a novel and rare protein, especially if available in minute amounts.

Słowa kluczowe

EN

cytochrome C; proteolysis; lysozyme; molten globule; protein structure; growth hormone; protein flexibility; man; limited proteolysis; apomyoglobin; mass spectrometry; alpha-lactalbumin; protein domain

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2004
• Tom: 51
• Numer: 2
• Opis fizyczny: p.299-321,fig.,ref.

Twórcy

autor

Fontana A.

• University of Padua, Viale G.Colombo 3, 35121 Padua, Italy

autor

Polverino de Laureto P.

autor

Spolaore B.

autor

Frare E.

autor

Picotti P.

autor

Zambonin M.

Bibliografia

• Anfinsen CB, Scheraga HA. (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem.; 29: 205-300.
• Arai M, Kuwajima K. (2000) Role of the molten globule state in protein folding. Adv Protein Chem.; 53: 209-82.
• Bond JS. (1990) Commercially available proteases. In Proteolytic Enzymes: A Practical Approach. Beynon RJ, Bond JS, eds, pp 232-40. IRL Press, Oxford.
• Brooks CL. (1992) Characterization of "native" apomyoglobin by molecular dynamics simulation. J Mol Biol.; 227: 375-80.
• Bucciantini M, Giannoni F, Chiti F, Baroni F, Formigli L, Zurdo J, et al. (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature.; 416: 507-11.
• Bychkova VE, Ptitsyn OB. (1995) Folding intermediates are involved in genetic diseases? FEBSLett.; 359: 6-8.
• Campbell D, Downing AK. (1994) Building protein structure and function from modular units. Trends Biotechnol.; 12: 168-74.
• Canet D, Last AM, Tito P, Sunde M, Spencer A, Arche DB, Redfield C, Robinson CV, Dobson CM. (2002) Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme. Nature Struct Biol.; 9: 308-14.
• Cawthern KM, Narayan M, Chaudhuri D, Permyakov EA, Berliner LJ. (1997) Interactions of alpha-lactalbumin with fatty acids and spin label analogs. J Biol Chem.; 272: 30812-6.
• Chamberlain AK, Marqusee S. (2000) Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms. Adv Protein Chem.; 53: 283-327.
• Chrysina ED, Brew K, Acharya KR. (2000) Crystal structures of apo- and holo-bovine alpha- lactalbumin at 2.2-Ä resolution reveal an effect of calcium on inter-lobe interactions. J Biol Chem.; 275: 37021-9.
• Cohen FE, Kelly JW. (2003) Therapeutic approaches to protein-misfolding diseases. Nature.; 426: 905-9.
• Dalzoppo D, Vita C, Fontana A. (1985) Folding of thermolysin fragments: Identification of the minimum size of a carboxyl-terminal fragment that can fold into a stable native like structure. J Mol Biol.; 182: 331-40.
• Darby NJ, Kemmink J, Creighton TE. (1996) Identifying and characterizing a structural domain of protein disulfide isomerase. Biochemistry.; 35: 10517-28.
• de Prat-Gay G. (1996) Association of complementary fragments and the elucidation of protein folding pathways. Protein Eng.; 9: 843-7.
• Dobson CM. (1994) Solid evidence for molten globules. Curr Biol.; 4: 636-40.
• Dobson CM. (1999) Protein misfolding, evolution and disease. Trends Biochem Sci.; 24: 329-32.
• Dobson CM. (2003) Protein folding and disease: A view from the first Horizon Symposium. Nat Rev Drug Discov.; 2: 154-60.
• Dunker AK, Obradovic Z. (2001) The protein trinity: Linking function and disorder. Nat Biotechnol.; 19: 805-6.
• Dunker AK, Brown CJ, Lawson JD, Iakoucheva CM, Obradovic Z. (2002) Intrinsic disorder and protein function. Biochemistry.; 41: 6573-80.
• Eliezer D, Wright PE. (1996) Is apomyoglobin a molten globule? Structural characterization by NMR. JMol Biol.; 263: 531-8.
• Eliezer D, Yao J, Dyson HJ, Wright PE. (1998) Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding. Nature Struct Biol.; 5: 148-55.
• Esmon NL, DeBault LE, Esmon CT. (1983) Proteolytic formation and properties of gamma-carboxyglutamic acid- domainless protein C. J Biol Chem.; 258: 5548-53.
• Evans PA, Radford SE. (1994) Probing the structure of folding intermediates. Curr Opin Struct Biol.; 4: 100-6.
• Falconi M, Parrilli L, Battistoni A, Desideri A. (2002) Flexibility in monomelic Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation. Proteins Struct Funct Genet.; 47: 513-20.
• Fink AL. (1995) Compact intermediate states in protein folding. Annu RevBiophys Biomol Struct.; 24: 495-522.
• Fink AL. (1998) Protein aggregation: Folding intermediates, inclusion bodies and amyloid. FoldDes.; 3: 9-23.
• Fisher A, Taniuchi H. (1992) A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex. Arch Biochem Biophys.; 296: 1-16.
• Fontana A. (1989) Limited proteolysis of globular proteins occur at exposed and flexible loops. In Highlights of Modern Biochemistry. Kotyk A, Skoda J, Pacek V, Kostka W, eds, pp 1711-26. VSP Int Publ, Amsterdam.
• Fontana A, Vita C, Chaiken IM. (1983) Domain characteristics of the carboxyl-terminal fragment 206-316 of thermolysin. Biopolymers.; 22: 69-78.
• Fontana A, Fassina G, Vita C, Dalzoppo D, Zamai M, Zambonin M. (1986) Correlation between sites of limited proteolysis and segmental mobility in thermolysin. Biochemistry.; 25: 1847-51.
• Fontana A, Vita C, Dalzoppo D, Zambonin M. (1989) Limited proteolysis as a tool to detect structure and dynamic features of globular proteins: Studies on thermolysin. In Methods in Protein Sequence Analysis. Wittman- Liebold B, ed, pp 315-24. Springer-Verlag, Berlin.
• Fontana A, Polverino de Laureto P, De Filippis V. (1993) Molecular aspects of proteolysis of globular proteins. In Protein Stability and Stabilization. van den Tweel W, Harder A, Buitelear M, eds, pp 101-10. Elsevier Science Publ, Amsterdam.
• Fontana A, Polverino de Laureto P, De Filippis V, Scaramella E, Zambonin M. (1997a) Probing the partly folded states of proteins by limited proteolysis. Fold Des.; 2: R17-26.
• Fontana A, Zambonin M, Polverino de Laureto P, De Filippis V, Clementi A, Scaramella E. (1997b) Probing the conformational state of apomyoglobin by limited proteolysis. J Mol Biol.; 266: 223-30.
• Fontana A, Polverino de Laureto P, De Filippis V, Scaramella E, Zambonin M. (1999) Limited proteolysis in the study of protein conformation. In Proteolytic Enzymes: Tools and Targets. Sterchi EE, Stocker W, eds, pp 257-84. Springer Verlag, Heidelberg.
• Frare E, Polverino de Laureto P, Zurdo J, Dobson CM, Fontana A. (2004) A highly amyloidogenic region of hen lysozyme. J Mol Biol.; in press.
• Frauenfelder H, Petsko GA, Tsernoglou D. (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature.; 280: 558-63.
• Griko YV, Remeta DP. (1999) Energetics of solvent and ligand-induced conformational changes in alpha-lactalbumin. Protein Sci.; 8: 554-61.
• Griko YV, Freire E, Privalov PL. (1994) Energetics of alpha-lactalbumin states: A calorimetric and statistical thermodynamics study. Biochemistry.; 33: 1889-901.
• Hakansson A, Zhivotovsky B, Orrenius S, Sabharwal H, Svanborg C. (1995) Apoptosis induced by a human milk protein. Proc Natl Acad Sci USA.; 92: 8064-8.
• Hakansson A, Andreasson J, Zhivotovsky B, Karpman D, Orrenius S, Svanborg C. (1999) Multimeric alpha-lactalbumin from human milk induces apoptosis through a direct effect on cell nuclei. Exp Cell Res.; 246: 451-60.
• Hakansson A, Svensson M, Mossberg AK, Sabharwal H, Linse S, Lazon I, Lonnerdal B, Svanborg C. (2000) A folding variant of alpha-lactalbumin with bactericidal activity against Streptococcus pneumoniae. Mol Microbiol.; 35: 589-600.
• Herschlag D. (1988) The role of induced fit and conformational changes of enzymes in specificity and catalysis. Bioorganic Chem.; 16: 62-96.
• Hirst JD, Brooks CL. (1995) Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry.; 34: 7614-21.
• Hubbard SJ, Campbell SF, Thornton JM. (1991) Molecular recognition: conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol.; 220: 507-30.
• Hubbard SJ. (1998) The structural aspects of limited proteolysis of native proteins. Biochim Biophys Acta.; 1382: 191-206.
• Hubbard SJ, Eisenmenger F, Thornton JM. (1994) Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Sci.; 3: 757-68.
• Iakoucheva LM., Kimzey AL, Masslon CD, Bruce JE, Garner EC, Brown CJ, Dunker AK, Smith RD, Ackerman EJ. (2001) Identification of intrinsic order and disorder in the DNA repair protein XPA. Protein Sci.; 10: 560-71.
• Janin J, Wodak SJ. (1983) Structural domains in proteins and their role in the dynamics of protein function. Prog Biophys Mol Biol.; 42: 21-78.
• Kataoka M, Kuwajima K, Tokunaga F, Goto Y. (1997) Structural characterization of the molten globule of alpha- lactalbumin by solution X-ray scattering. Protein Sci.; 6: 422-30.
• Klenow H, Henningsen I. (1970) Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc Natl Acad Sci USA.; 65: 168-75.
• Kohler C, Hakansson A, Svanborg C, Orrenius S, Zhivotovsky B. (1999) Protease activation in apoptosis induced by MAL. Exp Cell Res.; 249: 260-8.
• Kohler C, Gogradze V, Hakansson A, Svanborg C, Orrenius S, Zhivotovsky B. (2001) A folding variant of human alpha- lactalbumin induces mitochondrial permeability transition in isolated mitochondria. Eur JBiochem.; 268: 186-91.
• Krebs MR, Wilkins DK, Chung EW, Pitkeathly MC, Chamberlain AK, Zurdo J, Robinson CV, Dobson CM. (2000) Formation and seeding of amyloid fibrils from wild-type hen lysozyme and a peptide fragment from the beta-domain. J MolBiol.; 300: 541-9.
• Krokoszynska I, Otlewski J. (1996) Thermodynamic stability effects of single peptide bond hydrolysis in protein inhibitors of serine proteases. J Mol Biol.; 256: 793-802.
• Kuwajima K. (1989) The molten globule state as a clue for understanding the folding and cooperativity of globular protein structure. Proteins Struct Funct Genet.; 6: 87-103.
• Kuwajima K. (1996) The molten globule state of alpha-lactalbumin. FASEB J; 10: 102-9.
• Lebherz HG, Burke T, Shackelford JE, Strickler JE, Wilson KJ. (1986) Specific proteolytic modification of creatine kinase isoenzymes. Implication of C-terminal involvement in enzymic activity but not in subunit-subunit recognition. Biochem J.; 233: 51-6.
• Lecomte JTJ, Kao YH, Cocco MJ. (1996) The native state of apomyoglobin described by proton NMR spectroscopy: The A-B-G-H interface of wild-type sperm whale apomyoglobin. Proteins Struct Funct Genet.; 25: 267-85.
• Lecomte JTJ, Sukits SF, Bhattacharya S, Falzone CJ. (1999) Conformational properties of native sperm whale apomyoglobin in solution. Protein Sci.; 8: 1484-91.
• Mihalyi E. (1978) Application of Proteolytic Enzymes to Protein Structure Studies. CRC Press, Boca Raton, FL.
• Musi V, Spolaore B, Picotti P, Zambonin M, De Filippis V, Fontana A. (2004) Nicked apomyoglobin: A noncovalent complex of two polypeptide fragments comprising the entire protein chain. Biochemistry.; 43: 6230-40.
• Neurath H. (1980) Limited proteolysis, protein folding and physiological regulation. In Protein Folding. Jaenicke R, ed, pp 501-4. Elsevier/North Holland Biomedical Press, Amsterdam-New York.
• Novotny J, Bruccoleri RE. (1987) Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility. FEBS Lett; 211: 185-9.
• Ohgushi M, Wada A. (1983) Molten globule state: A compact form of globular proteins with mobile side-chain. FEBS Lett.; 164: 21-4.
• Onufriev A, Case DA, Bashford D. (2003) Structural details, pathways and energetics of unfolding apomyoglobin. J Mol Biol.; 325: 555-67.
• Patthy L, Trexler M, Vali Z, Banyai L, Varadi A. (1984) Kringles, modules specialized for protein binding: Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases. FEBS Lett.; 171: 131-6.
• Peng ZY, Kim PS. (1994) A protein dissection study of a molten globule. Biochemistry.; 33: 2136-41.
• Peng ZY, Wu LC. (2000) Autonomous protein folding units. Adv Protein Chem.; 53: 1-47.
• Permyakov EA, Berliner LJ. (2000) alpha-Lactalbumin: structure and function. FEBSLett.; 473: 269-74.
• Permyakov EA, Permyakov SE, Berliner LJ. (2003) a-Lactalbumin: Ca2+-binding protein with multiple functions. In Protein Structures: Kaleidoscope ofStructural Properties and Functions. Uversky VN, ed, pp 475-97. Research Signpost, Kerala, India.
• Picotti P, Marabotti A, Negro A, Musi V, Spolaore B, Zambonin M, Fontana A. (2004) Modulation of the structural integrity of helix F in apomyoglobin by single amino acid replacements. Protein Sci.; 13: 1572-85.
• Pike ACW, Brew K, Acharya KR. (1996) Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase. Structure.; 4: 691-703.
• Polverino de Laureto P, De Filippis V, Di Bello M, Zambonin M, Fontana A. (1995) Probing the molten globule state of alpha-lactalbumin by limited proteolysis. Biochemistry.; 34: 12596-604.
• Polverino de Laureto P, Vinante D, Scaramella E, Frare E, Fontana A. (2001) Stepwise proteolytic removal of the beta subdomain in alpha-lactalbumin: The protein remains folded and can form the molten globule in acid solution. Eur J Biochem.; 268: 4324-33.
• Polverino de Laureto P, Frare E, Gottardo R, van Dael H, Fontana A. (2002a) Partly folded states of members of the lysozyme/lactalbumin superfamily: A comparative study by circular dichroism spectroscopy and limited proteolysis. Protein Sci.; 11: 2932-46.
• Polverino de Laureto P, Frare E, Gottardo R, Fontana A. (2002b) Molten globule of bovine alpha-lactalbumin at neutral pH induced by heat, trifluoroethanol and oleic acid: a comparative analysis by circular dichroism and limited proteolysis. Proteins Struct Funct Genet. ; 49: 385-97.
• Polverino de Laureto P, Taddei N, Frare E, Capanni C, Costantini S, Zurdo J, Chiti F, Dobson CM, Fontana A. (2003) Protein aggregation and amyloid fibril formation by an SH3 domain probed by limited proteolysis. J Mol Biol.; 334: 129-41.
• Price NC, Johnson CM. (1990) Proteinases as probes of conformation of soluble proteins. In Proteolytic Enzymes: A Practical Approach. Beynon RJ, Bond, JS, eds, pp 163-80. IRL Press, Oxford.
• Ptitsyn OB. (1987) Protein folding: hypotheses and experiments. J Protein Chem.; 6: 273-93.
• Ptitsyn OB. (1995) Molten globule and protein folding. Adv Protein Chem.; 47: 83-229.
• Ptitsyn OB, Pain RH, Semisotnov GV, Zerovnik E, Razgulgaev OI. (1990) Evidence for a molten globule state as a general intermediate in protein folding. FEBS Lett.; 262: 20-4.
• Rico M, Jimenez MA, Gonzalez C, De Filippis V, Fontana A. (1994) NMR solution structure of the C-terminal fragment 255-316 of thermolysin: a dimer formed by subunits having the native structure. Biochemistry.; 33: 14834-47.
• Ringe D, Petsko GA. (1985) Mapping protein dynamics by X-ray diffraction. Prog Biophys Mol Biol.; 45: 197-235.
• Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. (2001) Sequence complexity of disordered proteins. Proteins.; 42: 38-48.
• Rose GD. (1979) Hierarchic organization of domains in globular proteins. J Mol Biol.; 134: 447-70.
• Sacchettini JC, Kelly JW. (2002) Therapeutic strategies for human amyloid diseases. Nat Rev Drug Discov.; 1: 267-75.
• Sasahara K, Demura M, Nitta K. (2000) Partially unfolded equilibrium state of hen lysozyme studied by circular dichroism spectroscopy. Biochemistry.; 39: 6475-82.
• Schechter I, Berger A. (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun.; 27: 157-62.
• Schulman BA, Redfield C, Peng ZY, Dobson CM, Kim PS. (1995) Different subdomains are most protected from hydrogen exchange in molten globule and native states of human alpha-lactalbumin. J Mol Biol.; 253: 651-7.
• Schulman BA, Kim PS, Dobson CM, Redfield C. (1997) A residue-specific NMR view of the non-cooperative unfolding of a molten globule. Nat Struct Biol.; 4: 630-4.
• Selkoe DJ. (2003) Folding proteins in fatal ways. Nature.; 426: 900-4.
• Siddiqui AS, Barton GJ. (1995) Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions. Protein Sci.; 4: 872-84.
• Spolaore B, Bermejo R, Zambonin M, Fontana A. (2001) Protein interactions leading to conformational changes monitored by limited proteolysis: Apo form and fragments of horse cytochrome c. Biochemistry.; 40: 9460-8.
• Spolaore B, Polverino de Laureto P, Zambonin M, Fontana A. (2004) Limited proteolysis of human growth hormone at low pH: Isolation, characterization and complementation of the two biologically relevant fragments 1-44 and 45-191. Biochemistry.; 43: 6576-86.
• Stefani M, Dobson CM. (2003) Protein aggregation and aggregate toxicity: New insights into protein folding, misfolding diseases and biological evolution. J Mol Med.; 81: 678-99.
• Stella L, Di Iorio EE, Nicotra M, Ricci G. (1999) Molecular dynamics simulations of human glutathione transferase P1-1: Conformational fluctuations of the apo structure. Proteins Struct Funct Genet.; 37: 10-9.
• Sternberg MJE, Grace DEP, Phillips DC. (1979) Dynamic information from protein crystallography: An analysis of temperature factors from refinement of the hen egg-white lysozyme. J Mol Biol.; 130: 231-53.
• Sunde M, Blake C. (1997) The structure of amyloid fibrils by electron microscopy and X-ray diffration. Adv Protein Chem.; 50: 123-59.
• Svensson M, Sabharwal H, Hakansson A, Mossberg AK, Lipniunas P, Leffler H, Svanborg C, Linse S. (1999) Molecular characterization of alpha-lactalbumin folding variants that induce apoptosis in tumor cells. J Biol Chem.; 274: 6388-96.
• Svensson M, Hakansson A, Mossberg AK, Linse S, Svanborg C. (2000) Conversion of alpha-lactalbumin to a protein inducing apoptosis. Proc Natl Acad Sci USA.; 97: 4221-6.
• Taniuchi H, Parr GR, Juillerat MA. (1986) Complementation in folding and fragment exchange. Methods Enzymol.; 131: 185-217.
• Tirado-Rives J, Jorgensen WL. (1993) Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry.; 32: 4175-84.
• Tsai CJ, Xu D, Nussinov A. (1998) Protein folding via binding and viceversa. Fold Des.; 3: R71-80.
• Uversky VN. (2002) Natively unfolded proteins: A point where biology waits for physics. Protein Sci.; 11: 739-56.
• Uversky VN, Gillespie JR, Fink AL. (2000) Why are "natively unfolded" proteins unstructured under physiological conditions? Proteins.; 41: 415-27.
• Vindigni A, De Filippis V, Zanotti G, Visco C, Orsini G, Fontana A. (1994) Probing the structure of hirudin from Hirudinaria manillensis by limited proteolysis: Isolation, characterization and thrombin-inhibitory properties of N- terminal fragments. Eur J Biochem.; 226: 323-33.
• Vita C, Fontana A. (1982) Domain characteristics of the carboxyl-terminal fragment 206-316 of thermolysin: unfolding thermodynamics. Biochemistry.; 21: 5196-202.
• Vita C, Dalzoppo D, Fontana A. (1984) Independent folding of the carboxyl-terminal fragment 228-316 of thermolysin. Biochemistry.; 23: 5512-9.
• Wetlaufer DB. (1973) Nucleation, rapid folding and globular intrachain regions in proteins. Proc Natl Acad Sci USA.; 70: 697-701.
• Wetlaufer DB. (1981) Folding of protein fragments. AdvProtein Chem.; 34: 61-92.
• Wijesinha-Bettoni R, Dobson CM, Redfield C. (2001) Comparison of the structural and dynamical properties of holo and apo bovine alpha-lactalbumin by NMR spectroscopy. J Mol Biol.; 307: 885-98.
• Wright PE, Dyson HJ. (1999) Intrinsically unstructured proteins: Reassessing the protein structure-function paradigm. J Mol Biol.; 293: 321-31.
• Wu LC, Grandori R, Carey J. (1994) Autonomous subdomains in protein folding. Protein Sci.; 3: 369-71.
• Wu LC, Peng ZY, Kim PS. (1995) Bipartite structure of the alpha-lactalbumin molten globule. Nat Struct Biol.; 2: 281-6.
• Yutani K, Ogasahara K, Kuwajima K. (1992) Absence of the thermal transition in apo-alpha-lactalbumin in the molten globule state: A study by differential scanning microcalorimetry. J Mol Biol.; 228: 347-50.
• Zehfus MH. (1987) Continuous compact protein domains. Proteins Struct Funct Genet.; 2: 90-110.