Skip to main content
×
Home
    • Aa
    • Aa

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

  • Gerhard Wagner (a1)
Abstract

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.

Copyright
References
Hide All
P. J. Artymiuk , C. C. F. Blake , D. E. P. Grace , S. J. Oatley , D. C. Phillips & M. J. E. Sternberg (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, Lond., 280, 563568.

R. H. Austin , K. W. Beeson , L. Eisenstein , H. Frauenfelder & I. C. Gunsalus (1975). Dynamics of ligand binding to myoglobin. Biochemistry, Philad. 14, 53555373.

D. Beece , L. Eisenstein , H. Frauenfelder , D. Good , M. C. Marden , L. Reinisch , A. H. Reynolds , L. B. Sorensen & K. T. Yue (1981). Solvent viscosity and protein dynamics. Biochemistry, Philad. 19, 51475157.

L. R. Brown , A. DeMarco , R. Richarz , G. Wagner & K. Wüthrich (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, 8795.

I. D. Campbell , C. M. Dobson , G. R. Moore , S. J. Perkins & R. J. P. Williams (1976). Temperature dependent molecular motions of a tyrosine residue of ferrocytochrome c. FEES Lett. 70, 96100.

G. Careri , P. Fasella & E. Gratton (1975). Statistical time events in enzymes: a physical assessment. CRC Crit. Rev. Biochem. 3, 141164.

C. Chothia & J. Janin (1975). Principles of protein-protein recognition. Nature, Lond. 256, 705708.

A. Cooper (1976). Thermodynamic fluctuations in protein molecules. Proc. natn. Acad. Sci. U.S.A. 73, 27402741.

T. E. Creighton (1978). Experimental studies of protein folding and unfolding. Prog. Biophys. Molec. Biol. 33, 231297.

J. Deisenhofer & W. Steigemann (1975). Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1–5 Å resolution. Acta crystallogr. B 31, 238250.

A. Dubs , G. Wagner & K. Wüthrich (1979). Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor. Biochim. biophys. Acta. 577, 177194.

M. Eigen (1964). Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Angew. Chem. 3, 119.

S. W. Englander & A. Poulsen (1969). Hydrogen-tritium exchange of the random chain polypeptide. Biopolymers 7, 379393.

S. W. Englander , S. W. Downer & H. Teitelbaum (1972). Hydrogen exchange. A. Rev. Biochem. 41, 903924.

H. Frauenfelder , G. A. Petsko & D. Tsernoglou (1979).Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, Lond. 280, 558563.

R. F. Grote & J. T. Hynes (1980). The stable state picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models. J. chem. Phys. 73, 27152732.

F. R. N. Gurd & T. M. Rothgeb (1979). Motions in proteins. Adv. Protein Chem. 33, 73165.

R. Hetzel , K. Wüthrich , J. Deisenhofer & R. Huber (1976). Dynamics of the basic pancreatic trypsin inhibitor (BPTI). II. Semi-empirical energy calculations. Biophys. Struct. & Mechanism 2, 159180.

B. D. Hilton & C. K. Woodward (1979). On the mechanism of isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biochemistry, Philad. 18, 58345841.

B. D. Hilton , K. Trudeau & C. K. Woodward (1981). Hydrogen exchange rates in pancreatic trypsin inhibitor are not correlated to thermal stability in urea. Biochemistry, Philad. 20, 46974703.

R. L. Huber (1979). Conformational flexibility and its functional significance in some protein molecules. Trends Biochem. Sci. 4, 271276.

A. Hvidt & S. O. Nielsen (1966). Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287386.

M. Jullien & R. L. Baldwin (1981). The role of proline residues in the folding kinetics of the bovine pancreatic trypsin inhibitor derivative RCAM (14–38). J. molec. Biol. 145, 265280.

M. Karplus & J. A. Mccammon (1981 a). The internal dynamics of globular proteins. C.R.C. Crit. Rev. Biochem. 9, 293349.

M. Karplus & J. A. Mccammon (1981 b). Pressure dependence of aromatic ring rotations in proteins: a collisional interpretation. FEBS Lett. 131, 3436.

A. A. Kossiakoff (1982). Protein dynamics investigated by the neutron diffraction hydrogen exchange technique. Nature, Lond. 296, 713721.

H. A. Kramers (1940). Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 285304.

R. Kubo (1966). The fluctuation-dissipation theorem. Rep. Prog. Phys. 29, 255284.

B. Lee & F. M. Richards (1971). The interpretation of protein structures: Estimation of static accessibility. J. molec. Biol. 55, 379400.

M. Levitt (1981). Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein. Nature, Land. 294, 379380.

G. Lipari & A. Szabo (1982). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104, 45594570.

T. D. Marinetti , G. H. Snyder & B. D. Sykes (1976). Nuclear magnetic resonance determination of intramolecular distances in bovine pancreatic trypsin inhibitor using nitrotyrosine chelation of lanthanides. Biochemistry, Philad.15, 46004608.

A. Masson & K. Wüthrich (1973). Proton magnetic resonance investigation of the conformational properties of the basic pancreatic trypsin inhibitor. FEBS Lett. 31, 114118.

J. A. McCammon & M. Karplus (1979). Dynamics of activated processes in globular proteins. Proc. natn. Acad. Sci. U.S.A. 76, 35853589.

J. A. McCammon & M. Karplus (1980). Dynamics of tyrosine ring rotations in a globular protein. Biopolymers 19, 13751405.

N. Metropolis , A. W. Rosenbluth , M. N. Rosenbluth , A. H. Teller & E. Teller (1953). Equation of state calculations by fast computing machines. J. chem. Phys. 21, 10871092.

F. A. Momany , R. F. McGuire , A. W. Burges & H. A. Scheraga (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, 23612381.

F. M. Pohl (1976). Temperature-dependence of the kinetics of folding of chymotrypsinogen A. FEES Lett. 65, 293296.

P. L. Privalov (1979). Stability of proteins. Small globular proteins. Adv. Protein Chem. 33, 167241.

F. M. Richards (1977). Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioengng. 6, 151176.

F. M. Richards (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, 4763.

R. Richarz , P. Sehr , G. Wagner & K. Wüthrich (1979). Kinetics of the exchange of individual amide protons in the basic pancreatic trypsin inhibitor. J. molec. Biol. 130, 1930.

R. Richarz , K. Nagayama & K. Wüthrich (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, 51895196.

J. J. Rosa & F. M. Richards (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, 399416.

G. H. Snyder , R. Rowan , S. Karplus & B. D. Sykes (1975). Complete tyrosine assignments in the high field 1H nuclear magnetic resonance spectrum of the bovine pancreatic trypsin inhibitor. Biochemistry, Philad.14, 37653777.

J. L. Skinner & P. G. Wolynes (1978). Relaxation processes and chemical kinetics. J. chem. Phys. 69, 21432150.

J. P. Vincent , R. Chicheportiche & M. Lazdunski (1971). The conformational properties of the basic pancreatic trypsin inhibitor. Eur. J. Biochem. 23, 401411.

E. Tüchsen , A. Hvidt & M. Ottesen (1980). Enzymes immobilyzed as crystals. Hydrogen exchange of crystalline lysozyme. Biochimie 62, 563566.

G. Wagner (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, 280284.

G. Wagner (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, 614620.

G. Wagner & K. Wüthrich (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, 3137.

G. Wagner & K. Wüthrich (1979 b). Structural interpretation of the amide proton exchange in the basic pancreatic trypsin inhibitor and related proteins. J. molec. Biol. 134, 7594.

G. Wagner & K. Wüthrich (1982 a). Sequential resonance assignments in protein 1H NMR spectra: basic pancreatic trypsin inhibitor. J. molec. Biol. 155, 347366.

G. Wagner & K. Wüthrich (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, 343361.

G. Wagner , A. DeMarco & K. Wüthrich (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, 139158.

G. Wagner , K. Wüthrich & H. Tschesche (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, 6776.

G. Wagner , K. Wüthrich & H. Tschesche (1978 b). A 1H NMR study of the solution conformation of the isoinhibitor K from Helix pomatia. Eur. J. Biochem. 89, 367377.

G. Wagner , H. Tschesche & K. Wüthrich (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, 239248.

G. Wagner , A. J. Kalb & K. Wüthrich (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, 249253.

A. Wlodawer & L. Sjölin (1982). Hydrogen exchange in RNase A: Neutron diffraction study. Proc. natn. Acad. Sci. U.S.A. 79, 14181422.

C. K. Woodward & B. D. Hilton (1980). Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. Biophys. J. 32, 561575.

K. Wüthrich & G. Wagner (1975). NMR investigations of the dynamics of the aromatic amino acid residues in the basic pancreatic trypsin inhibitor. FEBS Lett. 50, 265268.

K. Wüthrich & G. Wagner (1979 a). Internal motions in globular proteins. Trends Biochem. Sci. 3, 227230.

K. Wüthrich & G. Wagner (1979 b). Nuclear magnetic resonance of labile protons in the basic pancreatic trypsin inhibitor. J. molec. Biol. 130, 118.

K. Wüthrich , A. Eugster & G. Wagner (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, 601604.

K. Wüthrich , G. Wagner , R. Richarz & W. Braun (1980 b). Correlation between internal mobility and stability of globular proteins. Biophys. J. 32, 549560.

Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 7 *
Loading metrics...

Abstract views

Total abstract views: 80 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 18th October 2017. This data will be updated every 24 hours.