Abstract
This is a summary of the background, and some of the experimental research in my laboratory, on the physical chemical properties of proteins. The experimental studies were carried out to obtain information about the three-dimensional structure and folding/unfolding pathways of bovine pancreatic ribonuclease A and three of its structural homologs, ribonuclease B, frog onconase, and bovine angiogenin.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Acharya KR, Shapiro R, Riordan JF, Vallee BL (1995) Crystal structure of bovine angiogenin at 1.5-A resolution. Proc Nat Acad Sci USA 92:2949–2953
Altmann KH, Scheraga HA (1990) Local structure in ribonuclease A. Effect of amino acid substitutions on the preferential formation of the native disulfide loop in synthetic peptides corresponding to residues Cys58–Cys72 of bovine pancreatic ribonuclease A. J Am Chem Soc 112:4926–4931
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230
Bhat R, Wedemeyer WJ, Scheraga HA (2003) Proline isomerization in bovine pancreatic ribonuclease A. 2. Folding conditions. Biochemistry 42:5722–5728
Brandts JF, Halvorson HR, Brennan M (1975) Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14:4953–4963
Bruice TW, Kenyon GL (1982) Novel alkyl alkanethiolsulfonate sulfhydryl reagents. Modification of derivatives of L-cysteine. J Protein Chem 1:47–58
Burgess AW, Scheraga HA (1975) A hypothesis for the pathway of the thermally–induced unfolding of bovine pancreatic ribonuclease. J Theor Biol 53:403–420
Burgess AW, Weinstein LI, Gabel D, Scheraga HA (1975) Immobilized carboxypeptidase A as a probe for studying the thermally induced unfolding of bovine pancreatic ribonuclease. Biochemistry 14:197–200
Canfield RE (1963) The amino acid sequence of egg white lysozyme. J Biol Chem 238:2698–2707
Carty RP, Pincus MR, Scheraga HA (2002) Interactions that favor the native over the non-native disulfide bond among residues 58–72 in the oxidative folding of bovine pancreatic ribonuclease A. Biochemistry 41:14815–14819
Cleland WW (1964) Dithiothreitol, a new protective reagent for SH groups. Biochemistry 3:480–482
Creighton TE (1977) Kinetics of refolding of reduced ribonuclease. J Mol Biol 113:329–341
Creighton TE (1979) Intermediates in the refolding of reduced ribonuclease A. J Mol Biol 129:411–431
Creighton TE (1986) Disulfide bonds as probes of protein folding pathways. Methods Enzymol 131:83–1061
Creighton TE, Hillson DA, Freedman RB (1980) Catalysis by protein-disulphide isomerase of the unfolding and refolding of proteins with disulphide bonds. J Mol Biol 142:43–62
Dodge RW, Scheraga HA (1996) Folding and unfolding kinetics of the proline-to-alanine mutants of bovine pancreatic ribonuclease A. Biochemistry 35:1548–1559
Dodge RW, Laity JH, Rothwarf DM, Shimotakahara S, Scheraga HA (1994) Folding pathway of guanidine-denatured disulfide-intact wildtype and mutant bovine pancreatic ribonuclease A. J Protein Chem 13:409–421
Donovan JW, Laskowski M Jr, Scheraga HA (1958) Influence of ionization of carboxyl groups on the ultraviolet absorption spectrum of lysozyme. Biochim Biophys Acta 29:455–456
Dyson HJ, Rance N, Houghton RA, Lerner RA, Wright PE (1988) Folding of immunogenic fragments of proteins in water solution. 1. Sequence requirements for the formation of a reverse turn. J Mol Biol 201:161–200
Fu D, Chen L, O’Neill RA (1994) A detailed structural characterization of ribonuclease B oligosaccharides by 1H NMR spectroscopy and mass spectrometry. Carbohydr Res 261:173–186
Gahl RF, Scheraga HA (2009) Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues. Biochemistry 48:2740–2751
Gahl RF, Narayan M, Xu G, Scheraga HA (2008) Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues. Protein Eng Des Sel 21:223–231
Garel JR, Nall BT, Baldwin RL (1976) Guandine-unfolded state of ribonuclease A contains both fast- and slow-folding species. Proc Natl Acad Sci USA 73:1853–1857
Gindulyte A, Bashan A, Agmon I, Massa L, Yonath A, Karle J (2006) The transition state for formation of the peptide bond in ribosome. Proc Natl Acad Sci USA 130:13327–13332
Grafl R, Lang K, Vogal H, Schmid FX (1987) The mechanism of folding of pancreatic ribonucleases is independent of the presence of covalently linked carbohydrate. J Biol Chem 262:10624–10629
Griffith JH, Scheraga HA (2004) Statistical thermodynamics of aqueous solutions. I. Water structure, solutions with non-polar solutes, and hydrophobic interactions. J Mol Struct 682:97–113
Haas E, McWherter CA, Scheraga HA (1988) Conformational unfolding in the N–terminal region of ribonuclease A detected by nonradiative energy transfer. Distribution of interresidue distances in the native, denatured and reduced-denatured states. Biopolymers 27:1–21
Harrington WF, Schellman JA (1956) Evidence for the instability of hydrogen-bonded peptide structures in water, based on studies of ribonuclease and oxidized ribonuclease. C R Trav Lab Carlsberg Chim 30:21–43
Heinrikson L (1966) On the alkylation of amino acid residues at the active site of ribonuclease. J Biol Chem 241:1393–1405
Hermans J Jr, Scheraga HA (1961a) Structural studies of ribonuclease. V. Reversible change of configuration. J Am Chem Soc 83:3283–3292
Hermans J Jr, Scheraga HA (1961b) Structural studies of ribonuclease. VI. Abnormal ionizable groups. J Am Chem Soc 83:3293–3300
Hirs CHW, Moore S, Stein WH (1960) The sequence of the amino acid residues in performic acid-oxidized ribonuclease. J Biol Chem 235:633–647
Houry WA, Scheraga HA (1996a) The nature of the unfolded state of ribonuclease A: effect of cis-trans X-Pro peptide bond isomerization. Biochemistry 35:11719–11733
Houry WA, Scheraga HA (1996b) Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange. Biochemistry 35:11734–11746
Houry WA, Rothwarf DM, Scheraga HA (1994) A very fast phase in the refolding of disulfide-intact ribonuclease A: implications for the refolding and unfolding pathways. Biochemistry 33:2516–2530
Houry WA, Rothwarf DM, Scheraga HA (1995) The nature of the initial step in the conformational folding of disulfide-intact ribonuclease A. Nat Struct Biol 2:495–503
Iwaoka M, Juminaga D, Scheraga HA (1998) Regeneration of three-disulfide mutants of bovine pancreatic ribonuclease A missing the 65–72 disulfide bond: characterization of a minor folding pathway of ribonuclease A and kinetic roles of Cys65 and Cys72. Biochemistry 37:4490–4501
Jang SH, Kang DK, Chang SI, Scheraga HA, Shin HC (2004) High level production of bovine angiogenin in E. coli by an efficient refolding procedure. Biotechnol Lett 26:1501–1504
Jang SH, Song HD, Kang DK, Chang SI, Kim MK, Cho KW, Scheraga HA, Shin HC (2009) Role of the surface loop on the structure and biological activity of angiogenin. BMB Rep 42:829–833
Juminaga D, Wedemeyer WJ, Garduño-Júarez R, McDonald MA, Scheraga HA (1997) Tyrosyl interactions in the folding and unfolding of bovine pancreatic ribonuclease A: a study of tyrosine-to-phenylalanine mutants. Biochemistry 36:10131–10145
Juminaga D, Wedemeyer WJ, Scheraga HA (1998) Proline isomerization in bovine pancreatic ribonuclease A. I. Unfolding conditions. Biochemistry 37:11614–11620
Kim PS, Baldwin RL (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 51:459–489
Konishi Y, Scheraga HA (1980a) Regeneration of ribonuclease A from the reduced protein. 1. Conformational analysis of the intermediates by measurements of enzymatic activity, optical density and optical rotation. Biochemistry 19:1308–1316
Konishi Y, Scheraga HA (1980b) Regeneration of ribonuclease A from the reduced protein. 2. Conformational analysis of the intermediates by nuclear magnetic resonance spectroscopy. Biochemistry 19:1316–1322
Konishi Y, Ooi T, Scheraga HA (1981) Regeneration of ribonuclease A from the reduced protein. Isolation and identification of intermediates, and equilibrium treatment. Biochemistry 20:3945–3955
Konishi Y, Ooi T, Scheraga HA (1982a) Regeneration of ribonuclease A from the reduced protein. Rate-limiting steps. Biochemistry 21:4734–4740
Konishi Y, Ooi T, Scheraga HA (1982b) Regeneration of ribonuclease A from the reduced protein. Energetic analysis. Biochemistry 21:4741–4748
Konishi Y, Ooi T, Scheraga HA (1982c) Regeneration of RNase A from the reduced protein: models of regeneration pathways. Proc Natl Acad Sci USA 79:5734–5738
Kresheck GC, Scheraga HA (1966) Structural studies of ribonuclease. XXV. Enthalpy changes accompanying acid denaturation. J Am Chem Soc 88:4588–4591
Laity JH, Lester CC, Shimotakahara S, Zimmerman DE, Montelione GT, Scheraga HA (1997) Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A. Biochemistry 36:12683–12699
Laskowski M Jr, Scheraga HA (1954) Thermodynamic considerations of protein reactions. I. Modified reactivity of polar groups. J Am Chem Soc 76:6305–6319
Laskowski M Jr, Scheraga HA (1956) Thermodynamic considerations of protein reactions. II. Modified reactivity of primary valence bonds. J Am Chem Soc 78:5793–5798
Laskowski M Jr, Widom JM, McFadden ML, Scheraga HA (1956) Differential ultraviolet spectra of insulin. Biochim Biophys Acta 19:581–582
Leland PA, Raines RT (2001) Cancer chemotherapy – ribonucleases to the rescue. Chem Biol 8:405–413
Lester CC, Xu X, Laity JH, Shimotakahara S, Scheraga HA (1997) Regeneration studies of an analog of ribonuclease A missing disulfide bonds 65–72 and 40–95. Biochemistry 36:13068–13076
Li LK, Riehm JP, Scheraga HA (1966) Structural studies of ribonuclease. XXIII. Pairing of the tyrosyl and carboxyl groups. Biochemistry 5:2043–2048
Li YJ, Rothwarf DM, Scheraga HA (1995) Mechanism of reductive protein unfolding. Nat Struct Biol 2:489–494
Lin LN, Brandts JF (1983) Mechanism for the unfolding and refolding of ribonuclease A. Kinetic studies utilizing spectroscopic methods. Biochemistry 22:564–573
Matheson RR Jr, Scheraga HA (1979) Steps in the pathway of the thermal unfolding of ribonuclease A. A nonspecific surface-labeling study. Biochemistry 12:2437–2445
Matheson RR Jr, Dugas H, Scheraga HA (1977a) Electron paramagnetic resonance spectroscopy as a monitor of the pathway of the thermal unfolding of ribonuclease A. Biochem Biophys Res Commun 74:869–876
Matheson RR Jr, Van Wart HE, Burgess AW, Weinstein LI, Scheraga HA (1977b) Study of protein topography with flash–photolytically–generated non-specific surface–labeling reagents: surface labeling of ribonuclease A. Biochemistry 16:396–403
McWherter CA, Haas E, Leed AR, Scheraga HA (1986) Conformational unfolding in the N–terminal region of ribonuclease A detected by nonradiative energy transfer. Biochemistry 25:1951–1963
Milburn PJ, Scheraga HA (1988) Local interactions favor the native 8-residue disulfide loop in the oxidation of a fragment corresponding to the sequence Ser-50-Met-79 derived from bovine pancreatic ribonuclease A. J Protein Chem 7:377–398
Montelione GT, Scheraga HA (1989) Formation of local structures in protein folding. Acc Chem Res 22:70–76
Mosimann SC, Ardelt W, James NM (1994) Refined 1.7 Å X-ray crystallographic structure of P-30 protein, an amphibian ribonuclease with anti-tumor activity. J Mol Biol 236:1141–1153
Narayan M, Xu G, Ripoll DR, Zhai H, Breuker K, Wanjalla C, Leung HJ, Navon A, Welker E, McLafferty FW, Scheraga HA (2004) Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. J Mol Biol 338:795–809
Navon A, Ittah V, Laity JH, Scheraga HA, Haas E, Gussakovsky EE (2001a) Local and long-range interactions in the thermal unfolding transition of bovine pancreatic ribonuclease A. Biochemistry 40:93–104
Navon A, Ittah V, Landsman P, Scheraga HA, Haas E (2001b) Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry 40:105–118
Navon A, Ittah V, Scheraga HA, Haas E (2002) Formation of the hydrophobic core of ribonuclease A through sequential coordinated conformational transitions. Biochemistry 41:14225–14231
Némethy G, Scheraga HA (1962) The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J Phys Chem 66:1773–1789
Némethy G, Scheraga HA (1965) Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers 3:155–184
Ooi T, Scheraga HA (1964a) Structural studies of ribonuclease. XII. Enzymic hydrolysis of active tryptic modifications of ribonuclease. Biochemistry 3:641–647
Ooi T, Scheraga HA (1964b) Structural studies of ribonuclease. XIII. Physicochemical properties of tryptic modifications of ribonuclease. Biochemistry 3:648–652
Ooi T, Rupley JA, Scheraga HA (1963) Structural studies of ribonuclease. VIII. Tryptic hydrolysis of ribonuclease A at elevated temperature. Biochemistry 2:432–437
Pearson MA, Karplus PA, Dodge RW, Laity JH, Scheraga HA (1998) Crystal structures of two mutants that have implications for the folding of bovine pancreatic ribonuclease A. Protein Sci 7:1255–1258
Pradeep L, Shin HC, Scheraga HA (2006) Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family. FEBS Lett 580:5029–5032
Pradeep L, Kurinov I, Ealick SE, Scheraga HA (2007) Implementation of a k/k0 method to identify long-range structure in transition states during conformational folding/unfolding of proteins. Structure 15:1178–1189
Raleigh DP, Evans PA, Pitkeathly M, Dobson CM (1992) A peptide model for proline isomerism in the unfolded state of staphylococcal nuclease. J Mol Biol 228:338–342
Rothwarf DM, Scheraga HA (1991) Regeneration and reduction of native bovine pancreatic ribonuclease A with oxidized and reduced dithiothreitol. J Am Chem Soc 113:6293–6294
Rothwarf DM, Scheraga HA (1992) Equilibrium and kinetic constants for the thiol-disulfide interchange reaction between glutathione and dithiothreitol. Proc Natl Acad Sci USA 89:7944–7948
Rothwarf DM, Scheraga HA (1993a) Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution. Biochemistry 32:2671–2679
Rothwarf DM, Scheraga HA (1993b) Regeneration of bovine pancreatic ribonuclease A. 2. Kinetics of regeneration. Biochemistry 32:2680–2689
Rothwarf DM, Scheraga HA (1993c) Regeneration of bovine pancreatic ribonuclease A. 3. Dependence on the nature of the redox reagent. Biochemistry 32:2690–2697, Erratum: ibid., 32:7064 (1993)
Rothwarf DM, Scheraga HA (1993d) Regeneration of bovine pancreatic ribonuclease A. 4. Temperature dependence of the regeneration rate. Biochemistry 32:2698–2703
Rothwarf DM, Li YJ, Scheraga HA (1998a) Regeneration of bovine pancreatic ribonuclease A. Identification of two nativelike three-disulfide intermediates involved in separate pathways. Biochemistry 37:3760–3766
Rothwarf DM, Li YJ, Scheraga HA (1998b) Regeneration of bovine pancreatic ribonuclease A. Detailed kinetic analysis of two independent folding pathways. Biochemistry 37:3767–3776
Rudd PM, Joao HC, Coghill E, Fiten P, Saunders MR, Opdenakker G, Dwek RA (1994) Glycoforms modify the dynamic stability and functional activity of an enzyme. Biochemistry 33:17–22
Rupley JA, Scheraga HA (1960) Digestion of ribonuclease A with chymotrypsin and trypsin at high temperatures. Biochim Biophys Acta 44:191–193
Rupley JA, Scheraga HA (1963) Structural studies of ribonuclease. VII. Chymotryptic hydrolysis of ribonuclease A at elevated temperatures. Biochemistry 2:421–431
Ryle AP, Sanger F, Smith LF, Kitai R (1955) The disulphide bonds of insulin. Biochem J 60:541–556
Sanger F (1952) The arrangement of amino acids in proteins. Adv Protein Chem 7:1–66
Scheraga HA (1957) Tyrosyl–carboxylate ion hydrogen bonding in ribonuclease. Biochim Biophys Acta 23:196–197
Scheraga HA (1967) Structural studies of pancreatic ribonuclease. Fed Proc 26:1380–1387
Scheraga HA (1968) Calculations of conformations of polypeptides. Adv Phys Org Chem 6:103–184
Scheraga HA (2008) From helix-coil transitions to protein folding. Biopolymers 89:479–485 (2008)
Scheraga HA (2011) Respice, adspice, and prospice. Annu Rev Biophys 40:1–39
Scheraga HA, Konishi Y, Ooi T (1984) Multiple pathways for regenerating ribonuclease A. Adv Biophys 18:21–41
Scheraga HA, Konishi Y, Rothwarf DM, Mui PW (1987) Toward an understanding of the folding of ribonuclease A. Proc Natl Acad Sci USA 84:5740–5744
Scheraga HA, Pillardy J, Liwo A, Lee J, Czaplewski C, Ripoll DR, Wedemeyer WJ, Arnautova YA (2002) Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J Comput Chem 23:28–34
Scheraga HA, Liwo A, Ołdziej S, Czaplewski C, Pillardy J, Ripoll DR, Vila JA, Kazmierkiewicz R, Saunders JA, Arnautova YA, Jagielski A, Chinchio M, Nanias M (2004) The protein folding problem: global optimization of force fields. Front Biosci 9:3296–3323
Schmid FX (1986) Fast-folding and slow-folding forms of unfolded proteins. Meth Enzymol 131:70–82
Scott RA, Scheraga HA (1963) Structural studies of ribonuclease. XI. Kinetics of denaturation. J Am Chem Soc 85:3866–3873
Sendak RA, Rothwarf DM, Wedemeyer WJ, Houry WA, Scheraga HA (1996) Kinetic and thermodynamic studies of the folding/unfolding of a tryptophan-containing mutant of ribonuclease A. Biochemistry 35:12978–12992
Shimotakahara S, Rios CB, Laity JH, Zimmerman DE, Scheraga HA, Montelione GT (1997) NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms. Biochemistry 36:6915–6929
Shugar D (1952) The ultraviolet absorption spectrum of ribonuclease. Biochem J 52:142–149
Talluri S, Falcomer CM, Scheraga HA (1993) Energetic and structural basis for the preferential formation of the native disulfide loop involving Cys-65 and Cys-72 in synthetic peptide fragments derived from the sequence of ribonuclease A. J Am Chem Soc 115:3041–3047
Talluri S, Rothwarf DM, Scheraga HA (1994) Structural characterization of a three-disulfide intermediate of ribonuclease A involved in both the folding and unfolding pathways. Biochemistry 33:10437–10449
Tanford C, Hauenstein JD, Rands DG (1955) Phenolic hydroxyl ionization in proteins. II. Ribonuclease. J Am Chem Soc 77:6409–6413
Volles MJ, Xu X, Scheraga HA (1999) Distribution of disulfide bonds in the two-disulfide intermediates in the regeneration of bovine pancreatic ribonuclease A. Biochemistry 38:7284–7293
Wearne SJ, Creighton TE (1988) Further experimental studies of the disulfide folding transition of ribonuclease A. Proteins Struct Funct Genet 4:251–261
Wedemeyer WJ, Welker E, Scheraga HA (2002) Proline cis-trans isomerization and protein folding. Biochemistry 41:14637–14644
Welker E, Narayan M, Volles MJ, Scheraga HA (1999) Two new structured intermediates in the oxidative folding of RNase A. FEBS Lett 460:477–479
Welker E, Maki K, Ramachandra Shastry MC, Juminaga D, Bhat R, Scheraga HA, Roder H (2004) Ultra-rapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proc Natl Acad Sci USA 101:17681–17686
Welker E, Hathaway L, Xu G, Narayan M, Pradeep L, Shin HC, Scheraga HA (2007) Oxidative folding and N-terminal cyclization of onconase. Biochemistry 46:5485–5493
Williams RL, Greene SM, McPherson A (1987) The crystal structure of ribonuclease B at 2.5 Å resolution. J Biol Chem 262:16020–16031
Wlodawer A, Sjölin L (1983) Structure of ribonuclease A. Results of joint neutron and x-ray refinement at 2.0-Å resolution. Biochemistry 22:2720–2728
Xiong Y, Juminaga D, Swapna GVT, Wedemeyer WJ, Scheraga HA, Montelione GT (2000) Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease A. Protein Sci 9:421–426
Xu X, Scheraga HA (1998) Kinetic folding pathway of a three-disulfide mutant of bovine pancreatic ribonuclease A missing the [40–95] disulfide bond. Biochemistry 37:7561–7571
Xu X, Rothwarf DM, Scheraga HA (1996) Nonrandom distribution of the one-disulfide intermediates in the regeneration of ribonuclease A. Biochemistry 35:6406–6417
Xu G, Zhai H, Narayan M, McLafferty FW, Scheraga HA (2004a) Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry. Chem Biol 11:517–524
Xu G, Narayan M, Welker E, Scheraga HA (2004b) Characterization of the fast – forming intermediate, des [30–75], in the reductive unfolding of onconase. Biochemistry 43:3246–3254
Xu G, Narayan M, Scheraga HA (2005) The oxidative folding rate of bovine pancreatic ribonuclease is enhanced by a covalently attached oligosaccharide. Biochemistry 44:9817–9823
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Scheraga, H.A. (2011). Ribonucleases as Models for Understanding Protein Folding. In: Nicholson, A. (eds) Ribonucleases. Nucleic Acids and Molecular Biology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21078-5_15
Download citation
DOI: https://doi.org/10.1007/978-3-642-21078-5_15
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21077-8
Online ISBN: 978-3-642-21078-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)