Abstract
In general, the primary amino acid sequence of a polypeptide chain is thought to encode all the information necessary to determine the final folded structure of a protein. However, the contributions made by individual amino acid residues to the overall structure, dynamics and stability of the folded protein as well as the role(s) of individual residues in the kinetic pathways between the unfolded and folded states remains less clear. In recent years, there has been a substantial amount of progress in addressing these questions (Alber, 1989; Goldenberg et al., 1989; Lim and Sauer, 1989; Bowie et al., 1990; Dill, 1990; Kim and Baldwin, 1990; Pace et al., 1990; Matthews, 1991). The lysozyme produced by bacteriophage T4 offers an excellent experimental system to address these important questions. In addition, the collaborative research efforts of the Matthews (crystallography, structural bases of protein stability), Schellman (thermodynamics), Hudson (nanosecond dynamics) and our laboratories at the University of Oregon offer a nearly unique environment for the investigation of these issues.
Preview
Unable to display preview. Download preview PDF.
References
Alber, T. (1989). Mutational effects on protein stability. Ann. Rev. Biochem., 58, 765–798
Alber, T., Dao-pin, S., Wilson, K., Wozniak, J. A., Cook, S. P. and Matthews, B. W. (1987). Contributions of hydrogen bonds of Thr 157 to the thermodynamic stability of phage T4 lysozyme. Nature, 330, 41–46
Anderson, D. E., Becktel, W. J. and Dahlquist, F. W. (1990). pH-induced denaturation of proteins: A single salt bridge contributes 3–5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry, 29, 2403–2408
Bax, A., Griffey, R. H. and Hawkins, B. L. (1983). Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR. J. Magn. Reson., 55, 301–315
Bax, A., Sparks, S. W. and Torchia, D. A. (1988). Long range heteronuclear correlation. A powerful tool for the NMR analysis of medium-size proteins. J. Am. Chem. Soc., 110, 7926–7927
Bax, A. and Summers, M. F. (1986). Proton and carbon-13 assignments from sensitivity-enhanced detection of heteronuclear multiple-bond connectivity by 2D multiple quantum NMR. J. Am. Chem. Soc., 108, 2093–2094
Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A. and Sauer, R. T. (1990). Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science, 247, 1306–1310
Briggs, M. S. and Roder, H. (1992). Early hydrogen bonding events in the folding reaction of ubiquitin. Proc. Natl Acad. Sci. USA, 89, 2017–2021
Brown, L. R., DeMaro, A., Richarz, R., Wagner, G. and Wüthrich, K. (1978). The influence of a single salt bridge on static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor. Proton and carbon-13 nuclear magnetic resonance studies of the native and transaminated inhibitor. Eur. J. Biochem., 88, 87–95
Bycroft, M., Matouschek, A., Kellis, J. T., Jr., Serrano, L. and Fersht, A. R (1990). Detection and characterization of a folding intermediate in barnase by NMR. Nature, 346, 488–490
Cybulski, S. M. and Scheiner, S. (1989). Hydrogen bonding and proton transfers involving the carboxylate group. J. Am. Chem. Soc., 111, 23–31
Dao-pin, S., Anderson, D. E., Baase, W. A., Dahlquist, F. W. and Matthews, B. W. (1991a). Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme. Biochemistry, 30, 11521–11529
Dao-pin, S., Sauer, U., Nicholson, H. and Matthews, B. W. (1991b). Contributions of engineered surface salt bridges to the stability of T4 lysozyme determined by directed mutagenesis. Biochemistry, 30, 7142–7153
Dao-pin, S., Söderlind, E., Baase, W. A., Wozniak, J. A., Sauer, U. and Matthews, B. W. (1991c). Cumulative site-directed charge-change replacements in bacteriophage T4 lysozyme suggest that long-range electrostatic interactions contribute little to protein stability. J. Mol. Biol., 221, 873–887
Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133–7155
Dixon, M. M., Nicholson, H., Shewchuck, L., Baase, W. A. and Matthews, B. W. (1992). The structure of a ‘hinge-bending’ T4 lysozyme mutation, Ile 3, Pro. J. Mol. Biol. (in press)
Dolgikh, D. A., Kolomiets, A. P., Bolotina, I. A. and Ptitsyn, O. B. (1984). ‘Molten-globule’ state accumulates in carbonic anhydrase folding. FEBS Lett., 165, 88–92
Eriksson, A. E., Baase, W. A., Wozniak, J. A. and Matthews, B. W. (1992a). A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature, 355, 371–373
Eriksson, A. E., Baase, W. A., Zhang, X.-J., Heinz, S. W., Blaber, M., Baldwin, E. P. and Matthews, B. W. (1992). Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science, 255, 178–183
Faber, H. R. and Matthews, B. W. (1990). A mutant T4 lysozyme displays five different crystal conformations. Nature, 348, 263–266
Gil’manshin, R. I. and Ptitsyn, O. B. (1987). An early intermediate of refolding α-lactalbumin forms within 20 ms. FEBS Lett., 223, 327–329
Goldenberg, D. P., Frieden, R. W., Haack, J. A. and Morrison, T. B. (1989). Mutational analysis of a protein-folding pathway. Nature, 338, 127–132
Goto, Y., Calciano, L. J. and Fink, A. L. (1990). Acid-induced folding of proteins. Proc. Natl Acad. Sci. USA, 87, 573–577
Griffey, R. H., Redfield, A. G., McIntosh, L. P., Oas, T. G. and Dahlquist, F. W. (1986). Assignment of proton amide resonances of T4 lysozyme using 13C and 15N multiple isotopic labelling. J. Am. Chem. Soc., 108, 6816–6817
Heinz, D. W., Baase, W. A. and Matthews, B. W. (1992). Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. Proc. Natl Acad. Sci. USA, 89, 3751–3755
Hughson, F. M., Wright, P. E. and Baldwin, R. L. (1990). Structural characterization of a partly folded apomyoglobin intermediate. Science, 249, 1544–1548
Ikeguchi, M., Kuwajima, K., Mitani, M. and Sugai, S. (1986). Evidence for identity between the equilibrium unfolding intermediate and a transient folding: a comparative study of the folding reactions of α-lactalbumin and lysozyme. Biochemistry, 25, 6965–6972
Karpusas, M., Baase, W. A., Matsumura, M. and Matthews, B. W. (1989). Hydrophobic packing in T4 lysozyme probed by cavity-filled mutants. Proc. Natl Acad. Sci. USA, 86, 8237–8241
Kim, P. S. and Baldwin, R. L. (1990). Intermediates in the folding reactions of small proteins. Ann. Rev. Biochem., 59, 459–489
Kuwajima, K., Hiraoka, Y., Ikeguchi, M. and Sugai, S. (1985). Comparison of the transient folding intermediates in lysozyme and α-lactalbumin. Biochemistry, 24, 874–881
Kuwajima, K., Yamaya, H., Miwa, S., Sugai, S. and Nagamura, T. (1987). Rapid formation of secondary structure framework in protein folding studied by stopped-flow circular dichroism. FEBS Lett., 221, 115–118
Langsetmo, K., Fuchs, J. A. and Woodward, C. (1991). The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pK a of 7.5. Its titration produces a related shift in global stability. Biochemistry, 30, 7603–7609
Lee, B. and Richards, F. M. (1971). Interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379–400
Lim, W. A. and Sauer, R. T. (1989). Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature, 339, 31–36
Lu, J. and Dahlquist, F. W. (1992). Detection and characterization of an early folding intermediate of T4 lysozyme using pulsed hydrogen exchange and two-dimensional NMR. Biochemistry, 31, 4749–4756
McCoy, L. F. J., Rowe, E. S. and Wong, K. P. (1980). Multiparameter kinetic study on the unfolding and refolding of bovine carbonic anhydrase B. Biochemistry, 19, 4738–4743
McIntosh, L. P., Wand, A. J., Lowry, D. F., Redfield, A. G. and Dahlquist, F. W. (1990). Assignment of backbone 1H and 15N-NMR resonances of bacteriophage T4 lysozyme. Biochemistry, 29, 6341–6362
Malcomb, B. A., Rosenberg, S., Corey, M. J., Allen, J. S., deBaetselier, A. and Kirsh, J. F. (1989). Site-directed mutagenesis of the catalytic residues Asp-52 and Glu-35 of chicken egg white lysozyme. Proc. Natl Acad. Sci. USA, 86, 133–137
Matsumura, M. Becktel, W. J., Levitt, M. and Matthews, B. W. (1989). Stabilization of phage T4 lysozyme by engineered disulfide bonds. Proc. Natl Acad. Sci. USA, 86, 6562–6566
Matsumura, M., Becktel, W. J. and Matthews, B. W. (1988). Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile3. Nature, 334, 406–410
Matsumura, M. and Matthews, B. W. (1989). Control of enzyme activity by an engineered disulfide bond. Science, 243, 792–794
Matthews, B. W. and Remington, S. J. (1974). The three-dimensional structure of the lysozyme from bacteriophage T4. Proc. Natl Acad. Sci. USA, 71, 4178–4182
Matthews, C. R. (1991). The mechanism of protein folding. Curr. Opinion Struct. Biol., 1, 28–35
Miranker, A., Radford, S. E., Karplus, M. and Dobson, C. M. (1991). Demonstration by NMR of folding domains in lysozyme. Nature, 349, 633–636
Molday, R. S., Englander, S. W. and Kallen, R. G. (1972). Primary structure effects on peptide group hydrogen exchange. Biochemistry, 11, 150–158
Muchmore, D. C., McIntosh, L. P., Russell, C. B., Anderson, E. E. and Dahlquist, F. W. (1990). Expression and 15N labelling of proteins for proton and nitrogen-15 NMR. Meth. Enzymol., 177, 44–73
Nicholson, H., Anderson, D. E., Dao-pin, S. and Matthews, B. W. (1991). Analysis of the interaction between charged side chains and the α-helix dipole using designed thermostable mutants of phage T4 lysozyme. Biochemistry, 30, 9816–9828
Nicholson, H., Becktel, W. J. and Matthews, B. W. (1988). Enhanced protein thermostability from designed mutations that interact with α-helix dipoles. Nature, 366, 651–656
Pace, C. N., Laurents, D. V. and Thomson, J. A. (1990). pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribo-nuclease T1. Biochemistry, 29, 2564–2572
Rennell, D., Bouvier, S. E., Hardy, L. W. and Poteete, A. (1991). Systematic mutation of bacteriophage T4 lysozyme. J. Mol Biol., 222, 67–87
Robertson, A. D. and Baldwin, R. L. (1991). Hydrogen exchange in thermally denatured ribonuclease. Biochemistry, 30, 9907–9914
Roder, H., Elove, G. A. and Englander, S. W. (1988). Structural characterization of folding intermediates in cytochrome c by hydrogen-exchange labelling and proton NMR. Nature, 335, 700–704
Semisotnov, G. V., Rodionova, N. A., Kutyshenko, V. P., Ebert, B., Blanck, J. and Ptitsyn, O. B. (1987). Sequential mechanism of refolding of carbonic anhydrase B. FEBS Lett., 224, 9–13
Sharp, K. A. and Honig, B. (1990). Electrostatic interactions in macromolecules: theory and applications. Ann. Rev. Biophys. Biophys. Chem., 19, 301–332
Stites, W. E., Gittis, A. G., Lattman, E. E. and Shortle, D. (1991). In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core. J. Mol. Biol., 221, 7–14
Udgaonkar, J. B. and Baldwin, R. L. (1988). NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature, 335, 694–699
Udgaonkar, J. B. and Baldwin, R. L. (1990). Early folding intermediate of ribonuclease A. Proc. Natl Acad. Sci. USA, 87, 8197–201
Varadarajan, R., Lambright, D. G. and Boxer, S. G. (1989). Electrostatic interactions in wild-type and mutant recombinant human myoglobins. Biochemistry, 28, 3771–3781
Weaver, L. H. and Matthews, B. W. (1987). Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution. J. Mol. Biol., 193, 189–199
Zuiderweg, E. R. P. (1990). A proton-detected heteronuclear chemical-shift correlation experiment with improved resolution and sensitivity. J. Magn. Reson., 86, 346–357
Editor information
Editors and Affiliations
Copyright information
© 1993 The contributors
About this chapter
Cite this chapter
Anderson, D.E., Lu, J., McIntosh, L., Dahlquist, F.W. (1993). The Folding, Stability and Dynamics of T4 Lysozyme: A Perspective Using Nuclear Magnetic Resonance. In: Clore, G.M., Gronenborn, A.M. (eds) NMR of Proteins. Topics in Molecular and Structural Biology. Palgrave, London. https://doi.org/10.1007/978-1-349-12749-8_9
Download citation
DOI: https://doi.org/10.1007/978-1-349-12749-8_9
Publisher Name: Palgrave, London
Print ISBN: 978-1-349-12751-1
Online ISBN: 978-1-349-12749-8
eBook Packages: EngineeringEngineering (R0)