Structure and dynamics of the neutrophil defensins NP‐2, NP‐5, and HNP‐1: NMR studies of amide hydrogen exchange kinetics

The exchange kinetics for the slowly exchanging amide hydrogens in three defensins, rabbit NP‐2, rabbit NP‐5, and human HNP‐1, have been measured over a range of pH at 25°C using 1D and 2D NMR methods. These NHs have exchange rates 102 to 105 times slower than rates from unstructured model peptides. The observed distribution of exchange rates under these conditions can be rationalized by intramolecular hydrogen bonding of the individual NHs, solvent accessibility of the NHs, and local fluctuations in structure. The temperature dependencies of NH chemical shifts (NH temperature coefficients) were measured for the defensins and these values are consistent with the defensin structure. A comparison is made between NH exchange kinetics, NH solvent accessibility, and NH temperature coefficients of the defensins and other globular proteins. Titration of the histidine side chain in NP‐2 was examined and the results are mapped to the three‐dimensional structure. © 1994 Wiley‐Liss, Inc.

[1]  K. Constantine,et al.  Characterization of the backbone dynamics of an anti‐digoxin antibody VL domain by inverse detected 1H–15N NMR: Comparisons with X‐ray data for the Fab , 1993, Proteins.

[2]  L Mayne,et al.  Primary structure effects on peptide group hydrogen exchange. , 1972, Proteins.

[3]  Douglas E. Jones,et al.  Paneth cells of the human small intestine express an antimicrobial peptide gene. , 1992, The Journal of biological chemistry.

[4]  S. Miller,et al.  Enteric defensins: antibiotic peptide components of intestinal host defense , 1992, The Journal of cell biology.

[5]  D. Eisenberg,et al.  Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization. , 1991, Science.

[6]  M. Ultsch,et al.  Neutron structure of subtilisin BPN': effects of chemical environment on hydrogen-bonding geometries and the pattern of hydrogen-deuterium exchange in secondary structure elements. , 1991, Biochemistry.

[7]  T. Ganz,et al.  Defensins: Endogenous antibiotic peptides of animal cells , 1991, Cell.

[8]  S W Englander,et al.  Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. , 1990, Biochemistry.

[9]  H. Roder,et al.  An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. , 1990, Science.

[10]  S. Linse,et al.  Ca2+ binding to calbindin D9k strongly affects backbone dynamics: measurements of exchange rates of individual amide protons using 1H NMR. , 1990, Biochemistry.

[11]  C. Perrin,et al.  Exchange of amide protons. Effect of intramolecular hydrogen bonding , 1990 .

[12]  J. Fallon,et al.  Developmental regulation of cryptdin, a corticostatin/defensin precursor mRNA in mouse small intestinal crypt epithelium , 1989, The Journal of cell biology.

[13]  A. Pardi,et al.  Solution structures of the rabbit neutrophil defensin NP-5. , 1988, Journal of molecular biology.

[14]  C. Dobson,et al.  Sequential 1H NMR assignments and secondary structure of hen egg white lysozyme in solution. , 1988, Biochemistry.

[15]  A. Rashin.  Correlation between calculated local stability and hydrogen exchange rates in proteins. , 1987, Journal of molecular biology.

[16]  A. Pardi,et al.  Two-dimensional NMR studies of the antimicrobial peptide NP-5. , 1987, Biochemistry.

[17]  B. Sykes,et al.  Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using 13C NMR hydrogen/deuterium isotope shifts. , 1987, Biochemistry.

[18]  A. Wand,et al.  Two-dimensional 1H NMR studies of cytochrome c: hydrogen exchange in the N-terminal helix. , 1986, Biochemistry.

[19]  F. Bermejo,et al.  A study of the NH NMR signals of Gly-Gly-X-Ala tetrapeptides in H2O at low temperature. , 1986 .

[20]  Kurt Wüthrich,et al.  Origin of τ2 and τ2 ridges in 2D NMR spectra and procedures for suppression , 1986 .

[21]  R I Lehrer,et al.  Primary structures of three human neutrophil defensins. , 1985, The Journal of clinical investigation.

[22]  M. Selsted,et al.  Purification and antibacterial activity of antimicrobial peptides of rabbit granulocytes , 1984, Infection and immunity.

[23]  N. Kallenbach,et al.  Hydrogen exchange and structural dynamics of proteins and nucleic acids , 1983, Quarterly Reviews of Biophysics.

[24]  G. Wagner.  Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes , 1983, Quarterly Reviews of Biophysics.

[25]  A. Rosenberg,et al.  Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. , 2006, Methods of biochemical analysis.

[26]  A. Percy,et al.  Thermodynamics of structural fluctuations in lysozyme as revealed by hydrogen exchange kinetics. , 1982, Biochemistry.

[27]  D. States,et al.  A two-dimensional nuclear overhauser experiment with pure absorption phase in four quadrants☆ , 1982 .

[28]  P. S. Kim,et al.  Influence of charge on the rate of amide proton exchange. , 1982, Biochemistry.

[29]  R. Dickerson,et al.  Conformation change of cytochrome c. II. Ferricytochrome c refinement at 1.8 A and comparison with the ferrocytochrome structure. , 1981, Journal of molecular biology.

[30]  C. Woodward,et al.  Hydrogen isotope exchange kinetics of single protons in bovine pancreatic trypsin inhibitor. , 1980, Biophysical journal.

[31]  Richard R. Ernst,et al.  Elucidation of cross relaxation in liquids by two-dimensional N.M.R. spectroscopy , 1980 .

[32]  Kurt Wüthrich,et al.  Experimental techniques of two-dimensional correlated spectroscopy , 1980 .

[33]  K Wüthrich,et al.  A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. , 1980, Biochemical and biophysical research communications.

[34]  J. J. Rosa,et al.  An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide. , 1979, Journal of molecular biology.

[35]  K. Wüthrich,et al.  Nuclear magnetic resonance of labile protons in the basic pancreatic trypsin inhibitor. , 1979, Journal of molecular biology.

[36]  K. Wüthrich,et al.  Kinetics of the exchange of individual amide protons in the basic pancreatic trypsin inhibitor. , 1979, Journal of molecular biology.

[37]  G. S. Manning.  The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.

[38]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[39]  R. R. Ernst,et al.  Two‐dimensional spectroscopy. Application to nuclear magnetic resonance , 1976 .

[40]  J. Markley.  Observation of histidine residues in proteins by nuclear magnetic resonance spectroscopy , 1975 .

[41]  R Diamond,et al.  Real-space refinement of the structure of hen egg-white lysozyme. , 1977, Journal of molecular biology.

[42]  Yawen Bai,et al.  Primary structure effects on peptide group hydrogen exchange , 1993, Biochemistry.

[43]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[44]  P. K. Glasoe,et al.  USE OF GLASS ELECTRODES TO MEASURE ACIDITIES IN DEUTERIUM OXIDE1,2 , 1960 .