Hostname: page-component-586b7cd67f-vdxz6 Total loading time: 0 Render date: 2024-11-25T06:19:19.110Z Has data issue: false hasContentIssue false
  • English
  • Français

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes

Published online by Cambridge University Press:  17 March 2009

Gerhard Wagner
Gerhard Wagner
Affiliation:
Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule ETH-Hönggerberg, CH-8093 Zürich, Switzerland
Get access Rights & Permissions [Opens in a new window]

Extract

The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 16 , Issue 1 , February 1983 , pp. 1 - 57
Copyright
Copyright © Cambridge University Press 1983

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Artymiuk, P. J., Blake, C. C. F., Grace, D. E. P., Oatley, S. J., Phillips, D. C. & Sternberg, M. J. E. (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, Lond., 280, 563–568.CrossRefGoogle ScholarPubMed
Austin, R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I. C. (1975). Dynamics of ligand binding to myoglobin. Biochemistry, Philad. 14, 5355–5373.CrossRefGoogle ScholarPubMed
Beece, D., Eisenstein, L., Frauenfelder, H., Good, D., Marden, M. C., Reinisch, L., Reynolds, A. H., Sorensen, L. B. & Yue, K. T. (1981). Solvent viscosity and protein dynamics. Biochemistry, Philad. 19, 5147–5157.CrossRefGoogle Scholar
Brown, L. R., DeMarco, A., Richarz, R., Wagner, G. & Wüthrich, K. (1978). The influence of a single salt bridge on the static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor: 1H and 13C NMR studies of the native and the transaminated inhibitor. Eur. J. Biochem. 88, 87–95.CrossRefGoogle Scholar
Campbell, I. D., Dobson, C. M., Moore, G. R., Perkins, S. J. & Williams, R. J. P. (1976). Temperature dependent molecular motions of a tyrosine residue of ferrocytochrome c. FEES Lett. 70, 96–100.CrossRefGoogle ScholarPubMed
Careri, G., Fasella, P. & Gratton, E. (1975). Statistical time events in enzymes: a physical assessment. CRC Crit. Rev. Biochem. 3, 141–164.CrossRefGoogle ScholarPubMed
Carter, J. V., Knox, D. G. & Rosenberg, A. (1978). Pressure effects on folded proteins in solution. J. biol. Chem. 253, 1947–1953.CrossRefGoogle ScholarPubMed
Chothia, C. & Janin, J. (1975). Principles of protein-protein recognition. Nature, Lond. 256, 705–708.CrossRefGoogle ScholarPubMed
Cooper, A. (1976). Thermodynamic fluctuations in protein molecules. Proc. natn. Acad. Sci. U.S.A. 73, 2740–2741.CrossRefGoogle ScholarPubMed
Creighton, T. E. (1978). Experimental studies of protein folding and unfolding. Prog. Biophys. Molec. Biol. 33, 231–297.CrossRefGoogle ScholarPubMed
Deisenhofer, J. & Steigemann, W. (1975). Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1–5 Å resolution. Acta crystallogr. B 31, 238–250.CrossRefGoogle Scholar
Dubs, A., Wagner, G. & Wüthrich, K. (1979). Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor. Biochim. biophys. Acta. 577, 177–194.CrossRefGoogle ScholarPubMed
Eigen, M. (1964). Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Angew. Chem. 3, 1–19.CrossRefGoogle Scholar
Englander, S. W. & Poulsen, A. (1969). Hydrogen-tritium exchange of the random chain polypeptide. Biopolymers 7, 379–393.CrossRefGoogle Scholar
Englander, S. W., Downer, S. W. & Teitelbaum, H. (1972). Hydrogen exchange. A. Rev. Biochem. 41, 903–924.CrossRefGoogle ScholarPubMed
Eyring, H. (1935). The activated complex in chemical reactions. J. chem. Phys. 3, 107–115.Google Scholar
Frauenfelder, H., Petsko, G. A. & Tsernoglou, D. (1979).Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, Lond. 280, 558–563.CrossRefGoogle ScholarPubMed
Grote, R. F. & Hynes, J. T. (1980). The stable state picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models. J. chem. Phys. 73, 2715–2732.CrossRefGoogle Scholar
Gurd, F. R. N. & Rothgeb, T. M. (1979). Motions in proteins. Adv. Protein Chem. 33, 73–165.CrossRefGoogle ScholarPubMed
Hetzel, R., Wüthrich, K., Deisenhofer, J. & Huber, R.(1976). Dynamics of the basic pancreatic trypsin inhibitor (BPTI). II. Semi-empirical energy calculations. Biophys. Struct. & Mechanism 2, 159–180.CrossRefGoogle ScholarPubMed
Hilton, B. D. & Woodward, C. K. (1979). On the mechanism of isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biochemistry, Philad. 18, 5834–5841.CrossRefGoogle ScholarPubMed
Hilton, B. D., Trudeau, K. & Woodward, C. K. (1981). Hydrogen exchange rates in pancreatic trypsin inhibitor are not correlated to thermal stability in urea. Biochemistry, Philad. 20, 4697–4703.CrossRefGoogle Scholar
Huber, R. L. (1979). Conformational flexibility and its functional significance in some protein molecules. Trends Biochem. Sci. 4, 271–276.CrossRefGoogle Scholar
Hvidt, A. & Nielsen, S. O. (1966). Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287–386.CrossRefGoogle ScholarPubMed
Jullien, M. & Baldwin, R. L. (1981). The role of proline residues in the folding kinetics of the bovine pancreatic trypsin inhibitor derivative RCAM (14–38). J. molec. Biol. 145, 265–280.CrossRefGoogle ScholarPubMed
Karplus, M. & Mccammon, J. A. (1980). Dynamics of tyrosine ring rotations in a globular protein. Biopolymers 19, 1375–1405.Google Scholar
Karplus, M. & Mccammon, J. A. (1981 a). The internal dynamics of globular proteins. C.R.C. Crit. Rev. Biochem. 9, 293–349.CrossRefGoogle ScholarPubMed
Karplus, M. & Mccammon, J. A. (1981 b). Pressure dependence of aromatic ring rotations in proteins: a collisional interpretation. FEBS Lett. 131, 34–36.CrossRefGoogle Scholar
Kossiakoff, A. A. (1982). Protein dynamics investigated by the neutron diffraction hydrogen exchange technique. Nature, Lond. 296, 713–721.CrossRefGoogle ScholarPubMed
Kramers, H. A. (1940). Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 285–304.CrossRefGoogle Scholar
Kubo, R. (1966). The fluctuation-dissipation theorem. Rep. Prog. Phys. 29, 255–284.CrossRefGoogle Scholar
Landolt-Börnstein, (1969). Zahlemuerte und Funktionen, Transport-phänomene, vol. I. Berlin: Springer Verlag.Google Scholar
Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. J. molec. Biol. 55, 379–400.CrossRefGoogle ScholarPubMed
Levitt, M. (1981). Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein. Nature, Land. 294, 379–380.CrossRefGoogle ScholarPubMed
Levy, R. M., Karplus, M. & Mccammon, J. A. (1981). Increase of 13C NMR relaxation times in proteins due to picosecond motional averaging. J. Am. chem. Soc. 94, 2657–2660.Google Scholar
Lumry, R. & Rosenberg, A. (1975). The mobile defect hypothesis of protein function. Coll. Int. C.N.R.S. L'Eau. Syst. Biol. 246, 55–63.Google Scholar
Lipari, G. & Szabo, A. (1982). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 4559–4570.CrossRefGoogle Scholar
Marinetti, T. D., Snyder, G. H. & Sykes, B. D. (1976). Nuclear magnetic resonance determination of intramolecular distances in bovine pancreatic trypsin inhibitor using nitrotyrosine chelation of lanthanides. Biochemistry, Philad. 15, 4600–4608.CrossRefGoogle ScholarPubMed
Masson, A. & Wüthrich, K. (1973). Proton magnetic resonance investigation of the conformational properties of the basic pancreatic trypsin inhibitor. FEBS Lett. 31, 114–118.CrossRefGoogle ScholarPubMed
McCammon, J. A. & Karplus, M. (1979). Dynamics of activated processes in globular proteins. Proc. natn. Acad. Sci. U.S.A. 76, 3585–3589.CrossRefGoogle ScholarPubMed
McCammon, J. A. & Karplus, M. (1980). Dynamics of tyrosine ring rotations in a globular protein. Biopolymers 19, 1375–1405.CrossRefGoogle Scholar
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. chem. Phys. 21, 1087–1092.CrossRefGoogle Scholar
Molday, R. S., Englander, S. W. & Kallen, R. G. (1972). Primary structure effects on peptide group hydrogen exchange. Biochemistry, Philad. II, 150–158.CrossRefGoogle Scholar
Momany, F. A., McGuire, R. F., Burges, A. W. & Scheraga, H. A. (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, non bonded interactions and intrinsic torsional potential for naturally occuring amino acids. J. phys. Chem. 79, 2361–2381.CrossRefGoogle Scholar
Nagayama, K. & Wüthrich, K. (1981). Systematic application of two-dimensional 1H nuclear-magnetic-resonance techniques for studies of proteins, i. combined use of spin-echo-correlated spectroscopy and J-resolved spectroscopy for the identification of complete spin systems of non-labile protons in amino-acid residues. Eur. J. Biochem. 114, 369–374.CrossRefGoogle ScholarPubMed
Pelzer, H. & Wigner, E. (1932). Ueber die Geschwindigkeitskonstante von Austauschreaktionen. Z. phys. Chem. B 15, 445–471.CrossRefGoogle Scholar
Pohl, F. M. (1976). Temperature-dependence of the kinetics of folding of chymotrypsinogen A. FEES Lett. 65, 293–296.CrossRefGoogle ScholarPubMed
Privalov, P. L. (1979). Stability of proteins. Small globular proteins. Adv. Protein Chem. 33, 167–241.CrossRefGoogle ScholarPubMed
Richards, F. M. (1977). Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioengng. 6, 151–176.CrossRefGoogle ScholarPubMed
Richards, F. M. (1979). Packing defects, cavities, volume fluctuations, and access to the interior of proteins. Including some general comments on surface area and protein structure. Carlsberg Res. Commun. 44, 47–63.CrossRefGoogle Scholar
Richarz, R., Sehr, P., Wagner, G. & Wüthrich, K. (1979). Kinetics of the exchange of individual amide protons in the basic pancreatic trypsin inhibitor. J. molec. Biol. 130, 19–30.CrossRefGoogle ScholarPubMed
Richarz, R., Nagayama, K. & Wüthrich, K. (1980). Carbon-13 nuclear magnetic resonance relaxation studies of internal mobility of the polypeptide chain in basic pancreatic trypsin inhibitor and a selectively reduced analogue. Biochemistry, Philad. 19, 5189–5196.CrossRefGoogle Scholar
Roder, H. (1981). Interne Mobilität in Proteinen unter nativen und denaturierenden Bedingungen: Untersuchung von Trypsin-Inhibitoren mil spektroskopischen Methoden. Ph.D. Thesis Nr. 6932, ETH Zürich.Google Scholar
Rosa, J. J. & Richards, F. M. (1979). An experimental procedure of increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: applications to ribonuclease S peptide. J. molec. Biol. 133, 399–416.CrossRefGoogle ScholarPubMed
Snyder, G. H., Rowan, R., Karplus, S. & Sykes, B. D. (1975). Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor. Biochemistry, Philad. 14, 3765–3777.CrossRefGoogle ScholarPubMed
Skinner, J. L. & Wolynes, P. G. (1978). Relaxation processes and chemical kinetics. J. chem. Phys. 69, 2143–2150.CrossRefGoogle Scholar
Vincent, J. P., Chicheportiche, R. & Lazdunski, M. (1971). The conformational properties of the basic pancreatic trypsin inhibitor. Eur. J. Biochem. 23, 401–411.CrossRefGoogle ScholarPubMed
Tüchsen, E., Hvidt, A. & Ottesen, M. (1980). Enzymes immobilyzed as crystals. Hydrogen exchange of crystalline lysozyme. Biochimie 62, 563–566.CrossRefGoogle Scholar
Von Hippel, P. H. & Wong, K.-Y. (1965). On the conformational mobility of globular proteins. J. biol. Chem. 240, 3909–3923.CrossRefGoogle Scholar
Wagner, G. (1980 a). Activation volumes for the rotational motion of interior aromatic rings in globular proteins determined by high resolution 'H NMR at variable pressure. FEBS Lett. 112, 280–284.CrossRefGoogle Scholar
Wagner, G. (1980 b). Anovel application of Nuclear Overhauser Enhancement (NOE) in proteins: analysis of correlated events in the exchange of internal labile protons. Biochem. biophys. Res. Commun. 97, 614–620.CrossRefGoogle Scholar
Wagner, G. (1982). Internal mobility in globular proteins. Comments Mol. Cell. Biophys. I, 261–280.Google Scholar
Wagner, G. & Wüthrich, K. (1979 a). Correlation between the amide proton exchange rates and the denaturation temperature in globular proteins related to the basic pancreatic trypsin inhibitor. J. molec. Biol. 130, 31–37.CrossRefGoogle Scholar
Wagner, G. & Wüthrich, K. (1979 b). Structural interpretation of the amide proton exchange in the basic pancreatic trypsin inhibitor and related proteins. J. molec. Biol. 134, 75–94.CrossRefGoogle ScholarPubMed
Wagner, G. & Wüthrich, K. (1982 a). Sequential resonance assignments in protein 1H NMR spectra: basic pancreatic trypsin inhibitor. J. molec. Biol. 155, 347–366.CrossRefGoogle Scholar
Wagner, G. & Wüthrich, K. (1982 b). Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor (BPTI) in solution: studies with two-dimensional nuclear magnetic resonance. J. molec. Biol. 160, 343–361.CrossRefGoogle ScholarPubMed
Wagner, G., DeMarco, A. & Wüthrich, K. (1976). Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI). I. 1H NMR studies. Biophys. struct. & Mechanism 2, 139–158.CrossRefGoogle Scholar
Wagner, G., Wüthrich, K. & Tschesche, H. (1978 a). A 1H NMR study of the conformation and the molecular dynamics of the glyco-protein cow colostrum trypsin inhibitor. Eur. J. Biochem. 86, 67–76.CrossRefGoogle Scholar
Wagner, G., Wüthrich, K. & Tschesche, H. (1978 b). A 1H NMR study of the solution conformation of the isoinhibitor K from Helix pomatia. Eur. J. Biochem. 89, 367–377.CrossRefGoogle Scholar
Wagner, G., Tschesche, H. & Wüthrich, K. (1979 a). The influence of a localized chemical modification of the basic pancreatic trypsin inhibitor on static and dynamic aspects of the molecular conformation in solution. Eur. J. Biochem. 95, 239–248.CrossRefGoogle ScholarPubMed
Wagner, G., Kalb, A. J. & Wüthrich, K. (1979 b). Conformational studies by 1H NMR of the basic pancreatic trypsin inhibitor after reduction of the disulfide bond 14–38. Influence of charge protecting groups on the stability of the protein. Eur. J. Biochem. 95, 249–253.CrossRefGoogle Scholar
Wagner, G., Anil, Kumar & Wüthrich, K. (1981). Systematic application of two-dimensional 1H NMR techniques for studies, of proteins. 2. Combined use of correlated spectroscopy and nuclear Overhauser spectroscopy for sequential assignments of-backbone resonances and elucidation of polypeptide secondary structures. Eur. J. Biochem. 114, 375–384.CrossRefGoogle Scholar
Wlodawer, A. & Sjölin, L. (1982). Hydrogen exchange in RNase A: Neutron diffraction study. Proc. natn. Acad. Sci. U.S.A. 79, 1418–1422.CrossRefGoogle ScholarPubMed
Woodward, C. K. & Hilton, B. D. (1980). Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biophys. J. 32, 561–575.CrossRefGoogle ScholarPubMed
Woodward, C., Simon, I. & Tüchsen, E. (1982). Hydrogen exchange and the dynamic structure of proteins. Mol. & Cell. Biochem. (in press).CrossRefGoogle Scholar
Wüthrich, K. (1976). Nuclear Magnetic Resonance in Biological Research - Peptides and Proteins, Amsterdam: North-Holland.Google Scholar
Wüthrich, K. & Wagner, G. (1975). NMR investigations of the dynamics of the aromatic amino acid residues in the basic pancreatic trypsin inhibitor. FEBS Lett. 50, 265–268.CrossRefGoogle ScholarPubMed
Wüthrich, K. & Wagner, G. (1979 a). Internal motions in globular proteins. Trends Biochem. Sci. 3, 227–230.CrossRefGoogle Scholar
Wüthrich, K. & Wagner, G. (1979 b). Nuclear magnetic resonance of labile protons in the basic pancreatic trypsin inhibitor. J. molec. Biol. 130, 1–18.CrossRefGoogle ScholarPubMed
Wüthrich, K. & Wagner, G. (1982). NMR studies of concerted motions in the interior and on the surface of globular proteins. Proc. Ciba Fdn. Symp. on Internal Motions in Proteins, London (in the press).Google Scholar
Wüthrich, K., Eugster, A. & Wagner, G. (1980 a). p2H dependence of the exchange with the solvent of interior amide protons in basic pancreatic trypsin inhibitor modified by reduction of the disulfide bond 14–38. J. molec. Biol. 144, 601–604.CrossRefGoogle Scholar
Wüthrich, K., Wagner, G., Richarz, R. & Braun, W. (1980 b). Correlation between internal mobility and stability of globular proteins. Biophys. J. 32, 549–560.CrossRefGoogle ScholarPubMed