Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins.

Publisher Summary This chapter describes advances in the use of coupling constants and chemical shifts in structural studies of peptides and proteins. Coupling constant information can be incorporated into the input data for structure calculations, giving direct information on dihedral angles and stereospecific assignments of prochiral groups such as β-methylene protons and the methyl groups of leucine and valine. Because of the complexity of the interactions that influence the chemical shift of each nucleus, this type of information is more useful at the structure refinement stage. However, the determination of protein and peptide structure using information from nuclear magnetic resonance (NMR) experiments in solution is now a well-established method, and it is frequently used as an adjunct to X-ray crystal structure determination, as well as in cases where crystals are unavailable. With increasing size of the proteins for which three-dimensional (3D) structure determination by NMR is attempted, there will be an increasing reliance on 3D and higher dimensional spectroscopy utilizing transfer pathways selective for particular coupling constants. The method of J doubling is suggested to increase accuracy of coupling constant measurements in large molecules.

[1]  R. Zürcher.  Chapter 5 The cause and calculation of proton chemical shifts in non-conjugated organic compounds , 1967 .

[2]  C. Dobson,et al.  Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants. , 1991, Biochemistry.

[3]  J. Feeney,et al.  Long range 13C1H spin-spin coupling constants in amino acids. Conformational applications , 1975 .

[4]  P. Schmieder,et al.  Determination of the ϕ angle in a peptide backbone by NMR spectroscopy with a combination of homonuclear and heteronuclear coupling constants , 1992, Biopolymers.

[5]  J. Markley,et al.  Calculation of nuclear spin-spin coupling constants with ab initio molecular orbital wave functions , 1993 .

[6]  A. Warshel,et al.  Electrostatic energy and macromolecular function. , 1991, Annual review of biophysics and biophysical chemistry.

[7]  Ad Bax,et al.  The use of 1JCαHα coupling constants as a probe for protein backbone conformation , 1993 .

[8]  Kurt Wüthrich,et al.  Analysis of the 1H‐NMR spectra of ferrichrome peptides. I. The non‐amide protons , 1978 .

[9]  G. Montelione,et al.  Accurate measurements of long-range heteronuclear coupling constants from homonuclear 2D NMR spectra of isotope-enriched proteins , 1989 .

[10]  F. Blanco,et al.  Periodic properties of proton conformational shifts in isolated protein helices. An experimental study. , 1992, European journal of biochemistry.

[11]  A. Bax,et al.  Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts , 1991 .

[12]  R. Abraham.  The proton magnetic resonance spectra of porphyrins , 1961 .

[13]  P L Weber,et al.  Determining stereo-specific 1H nuclear magnetic resonance assignments from distance geometry calculations. , 1988, Journal of molecular biology.

[14]  A. Bax,et al.  An alternative 3D NMR technique for correlating backbone 15N with side chain Hβ resonances in larger proteins , 1991 .

[15]  P. Schmieder,et al.  A new 1H15N13C triple-resonance experiment for sequential assignments and measuring homonuclear HαHN vicinal coupling constants in polypeptides , 1991 .

[16]  D. Case,et al.  A new analysis of proton chemical shifts in proteins , 1991 .

[17]  S. Fesik,et al.  A method for measuring 1H-1H coupling constants in 13C-labeled molecules , 1991 .

[18]  C. Griesinger,et al.  Determination of proton-proton coupling constants in 13C-labeled molecules , 1992 .

[19]  K Wüthrich,et al.  Systematic application of high-resolution, phase-sensitive two-dimensional 1H-NMR techniques for the identification of the amino-acid-proton spin systems in proteins. Rabbit metallothionein-2. , 1985, European journal of biochemistry.

[20]  R. Dwek,et al.  Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution. , 1980, Biochemistry.

[21]  D. Neri,et al.  New nuclear magnetic resonance experiment for measurements of the vicinal coupling constants 3JHN.alpha. in proteins , 1990 .

[22]  R. Kaptein,et al.  Stereospecific assignments of 1H‐nmr methyl lines and conformation of valyl residues in the lac repressor headpiece , 1985 .

[23]  R. Brunne,et al.  Structure refinement using time-averaged J-coupling constant restraints , 1993, Journal of biomolecular NMR.

[24]  Bolong Cao,et al.  Peptide/protein structure analysis using the chemical shift index method: Upfield α-CH values reveal dynamic helices and αL sites , 1992 .

[25]  Analysis of .chi.1 rotamer populations from NMR data by the CUPID method , 1992 .

[26]  G. Montelione,et al.  A general approach for determining scalar coupling constants in polypeptides and proteins , 1992, Biopolymers.

[27]  M. Williamson,et al.  Determination of the magnetic anisotropy of the oxygen atom and 1H chemical-shift calculation of proteins , 1992 .

[28]  M. Jiménez,et al.  Conformational properties of the isolated 1–23 fragment of human hemoglobin α-chain , 1988 .

[29]  L. Mueller.  P.E.COSY, a simple alternative to E.COSY , 1987 .

[30]  P E Wright,et al.  Defining solution conformations of small linear peptides. , 1991, Annual review of biophysics and biophysical chemistry.

[31]  A. D. Buckingham,et al.  CHEMICAL SHIFTS IN THE NUCLEAR MAGNETIC RESONANCE SPECTRA OF MOLECULES CONTAINING POLAR GROUPS , 1960 .

[32]  R. Harris.  Nuclear magnetic resonance spectroscopy : a physicochemical view , 1985 .

[33]  F M Poulsen,et al.  Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of phi-angles. , 1991, Journal of molecular biology.

[34]  Timothy F. Havel,et al.  Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. , 1987, Journal of molecular biology.

[35]  R. J. Abraham.  A ring current model for the heme ring , 1981 .

[36]  A. Bax,et al.  Measurement of two-bond JCOHα coupling constants in proteins uniformly enriched with13C , 1992 .

[37]  S. Kuroki,et al.  Hydrogen-bonding effect on carbon-13 NMR chemical shifts of L-alanine residue carbonyl carbons of peptides in the solid state , 1992 .

[38]  K. Sharp,et al.  Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.

[39]  A. Gronenborn,et al.  Assignment of the side-chain proton and carbon-13 resonances of interleukin-1.beta. using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy , 1990 .

[40]  D. B. Chesnut.  Some Recent ab initio Calculations of the NMR Chemical Shift , 1991 .

[41]  I. Ando,et al.  Intermolecular hydrogen-bonding effect on carbon-13 NMR chemical shifts of glycine residue carbonyl carbons of peptides in the solid state , 1988 .

[42]  D. Case,et al.  High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin. , 1991, Journal of molecular biology.

[43]  K Wüthrich,et al.  Determination of the complete three-dimensional structure of the alpha-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry. , 1988, Journal of molecular biology.

[44]  L. Kay,et al.  Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. , 1991, Biochemistry.

[45]  P E Wright,et al.  Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. , 1993, Biochemistry.

[46]  C. Griesinger,et al.  Determination of Hα,Hβ and Hβ,C′ coupling constants in13C-labeled proteins , 1992 .

[47]  F. Richards,et al.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. , 1992, Biochemistry.

[48]  F. Bovey,et al.  Calculation of Nuclear Magnetic Resonance Spectra of Aromatic Hydrocarbons , 1958 .

[49]  G. Marius Clore,et al.  Stereospecific assignment of β-methylene protons in larger proteins using 3D15N-separated Hartmann-Hahn and13C-separated rotating frame Overhauser spectroscopy , 1991, Journal of biomolecular NMR.

[50]  D. B. Chesnut,et al.  Ab initio determination of chemical shielding in a model dipeptide , 1991 .

[51]  J. Rizo,et al.  Conformational behavior of Escherichia coli OmpA signal peptides in membrane mimetic environments. , 1993, Biochemistry.

[52]  Tigelaar Hl,et al.  Molecular Zeeman effect in formamide and the -proton chemical shift in poly(L-alanine). , 1972 .

[53]  H. Schwalbe,et al.  Stereospecific assignment of leucine methyl groups with carbon-13 in natural abundance or with random 13C labeling , 1992 .

[54]  L. Kay,et al.  New methods for the measurement of NHCαH coupling constants in 15N-labeled proteins , 1990 .

[55]  P. Hansen.  Assignment of the natural abundance 13C spectrum of proteins using 13C 1H-detected heteronuclear multiple-bond correlation NMR spectroscopy: structural information and stereospecific assignments from two- and three-bond carbon-hydrogen coupling constants. , 1991, Biochemistry.

[56]  K. Wüthrich,et al.  Structural interpretation of vicinal proton-proton coupling constants 3JH alpha H beta in the basic pancreatic trypsin inhibitor measured by two-dimensional J-resolved NMR spectroscopy. , 2005, European journal of biochemistry.

[57]  E. Oldfield,et al.  A Molecular Model for the Major Conformational Substates in Heme Proteins , 1991 .

[58]  R. Hodges,et al.  Relationship between amide proton chemical shifts and hydrogen bonding in amphipathic .alpha.-helical peptides , 1992 .

[59]  M. Williamson,et al.  Secondary‐structure dependent chemical shifts in proteins , 1990, Biopolymers.

[60]  C. Griesinger,et al.  Peptide conformations. 42. Conformation of side chains in peptides using heteronuclear coupling constants obtained by two-dimensional NMR spectroscopy , 1987 .

[61]  N. Clayden,et al.  Peptide group shifts , 1982 .

[62]  D. Lilley,et al.  Carbon-13-NMR of peptides and proteins , 1978 .

[63]  R. Mallion,et al.  Ring current theories in nuclear magnetic resonance , 1979 .

[64]  C. Dobson,et al.  1H-NMR analysis of turkey egg-white lysozyme and comparison with hen egg-white lysozyme. , 1993, European journal of biochemistry.

[65]  P. Schmieder,et al.  Determination of heteronuclear long-range couplings to heteronuclei in natural abundance by two- and three-dimensional NMR spectroscopy , 1991, Journal of biomolecular NMR.

[66]  D. Cowburn,et al.  Nitrogen-15 chemical shifts of backbone amides in bovine pancreatic trypsin inhibitor and apamin [Erratum to document cited in CA111(17):149076x] , 1990 .

[67]  S. Grdadolnik,et al.  Use of one-bond C.alpha.-H.alpha. coupling constants as restraints in MD simulations , 1992 .

[68]  R. R. Ernst,et al.  Two-dimensional correlation of connected NMR transitions , 1985 .

[69]  D. Cowburn,et al.  15N Chemical Shifts of Backbone Amides in Bovine Pancreatic Trypsin Inhibitor and Apamin , 1989 .

[70]  T. Asakura,et al.  1H‐ and 13C‐NMR studies of N‐acetyl‐L‐alanine methylester and N‐acetyl‐L‐alanine methylamide. I. Self‐association , 1979 .

[71]  W. M. Westler,et al.  The "CUPID" method for calculating the continuous probability distribution of rotamers from NMR data , 1992 .

[72]  O. Jardetzky,et al.  α-Proton chemical shifts and secondary structure in proteins , 1989 .

[73]  A. Bax,et al.  Measurement of15N-13C J couplings in staphylococcal nuclease , 1991, Journal of biomolecular NMR.

[74]  K. Wüthrich,et al.  Carbon‐13 NMR chemical shifts of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐ X‐L‐ Ala‐OH , 1978 .

[75]  M. Williamson,et al.  Calculation of chemical shifts of protons on alpha carbons in proteins , 1991 .

[76]  Peter Pulay,et al.  Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations , 1990 .

[77]  G. Montelione,et al.  Accurate measurements of proton scalar coupling constants using carbon-13 isotropic mixing spectroscopy , 1992 .

[78]  K. Kopple,et al.  A dihedral angle‐vicinal proton coupling constant correlation for the α–β bond of amino acid residues , 1973 .

[79]  F. Poulsen,et al.  Positive φ-angles in proteins by nuclear magnetic resonance spectroscopy , 1992 .

[80]  B. Pullman,et al.  Quantum mechanical calculations of NMR chemical shifts in nucleic acids , 1987, Quarterly Reviews of Biophysics.

[81]  H. Dyson,et al.  Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal. , 1993, Biochemistry.

[82]  E. Oldfield,et al.  Chemical shifts in proteins : an ab initio study of carbon-13 nuclear magnetic resonance chemical shielding in glycine, alanine, and valine residues , 1993 .

[83]  H. Mcconnell,et al.  Theory of Nuclear Magnetic Shielding in Molecules. I. Long‐Range Dipolar Shielding of Protons , 1957 .

[84]  W. M. Westler,et al.  A relational database for sequence-specific protein NMR data , 1991, Journal of biomolecular NMR.

[85]  G. Wider,et al.  A heteronuclear three-dimensional NMR experiment for measurements of small heteronuclear coupling constants in biological macromolecules , 1989 .

[86]  M. Akke,et al.  15N NMR assignments and chemical shift analysis of uniformly labeled15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states , 1992, FEBS letters.

[87]  P. Wright,et al.  NMR evidence for multiple conformations in a highly helical model peptide. , 1993, Biochemistry.

[88]  B. Stockman,et al.  Proton, carbon, and nitrogen chemical shifts accurately delineate differences and similarities in secondary structure between the homologous proteins IRAP and IL-1β , 1992, Journal of biomolecular NMR.

[89]  M. Barfield,et al.  Ab initio IGLO studies of the conformational dependencies of .alpha.-, .beta.-, and .gamma.-substituent effects in the carbon-13 NMR spectra of aliphatic and alicyclic hydrocarbons , 1990 .

[90]  G. Bodenhausen,et al.  Two-dimensional correlation of directly and remotely connected transitions by z-filtered COSY , 1986 .

[91]  A. Bax,et al.  1H and13C Assignments from Sensitivity-Enhanced Detection of Heteronuclear Multiple-Bond Connectivity by 2D Multiple Quantum NMR , 1986 .

[92]  G. Montelione,et al.  Accurate measurements of homonuclear HN-H.alpha. coupling constants in polypeptides using heteronuclear 2D NMR experiments , 1989 .

[93]  Ulrich Fleischer,et al.  The IGLO-Method: Ab-initio Calculation and Interpretation of NMR Chemical Shifts and Magnetic Susceptibilities , 1990 .

[94]  M. Karplus,et al.  Fluctuations and averaging of proton chemical shifts in the bovine pancreatic trypsin inhibitor. , 1982, Biochemistry.

[95]  P. Wright,et al.  Relationship between1H and13C NMR chemical shifts and the secondary and tertiary structure of a zinc finger peptide , 1992, Journal of biomolecular NMR.

[96]  M. Zerner,et al.  Calculation of 13C‐NMR chemical shift using the intermediate neglect of differential overlap model , 1992 .

[97]  Robert J.P. Williams,et al.  Structural information from NMR secondary chemical shifts of peptide α C−H protons in proteins , 1983 .

[98]  H. Dyson,et al.  Effect of disulfide bridge formation on the NMR spectrum of a protein: Studies on oxidized and reduced Escherichia coli thioredoxin , 1994, Journal of biomolecular NMR.

[99]  A. Hinck,et al.  Solution studies of staphylococcal nuclease H124L. 2. 1H, 13C, and 15N chemical shift assignments for the unligated enzyme and analysis of chemical shift changes that accompany formation of the nuclease-thymidine 3',5'-bisphosphate-calcium ternary complex. , 1992, Biochemistry.

[100]  J. Prestegard,et al.  Measurement of vicinal couplings from cross peaks in COSY spectra , 1989 .

[101]  C. L. Norris,et al.  Localized magnetic susceptibility anisotropies , 1973 .

[102]  David A. Case,et al.  Analysis of proton chemical shifts in regular secondary structure of proteins , 1994, Journal of biomolecular NMR.

[103]  R. Freeman,et al.  Accurate measurement of coupling constants by J doubling , 1992 .

[104]  I. Kuntz,et al.  Amide chemical shifts in many helices in peptides and proteins are periodic , 1991 .

[105]  P. Wright,et al.  CALIBRATION OF RING-CURRENT MODELS FOR THE HEME RING , 1985 .

[106]  K. Wüthrich.  Protein structure determination in solution by nuclear magnetic resonance spectroscopy. , 1989, Science.

[107]  W. Flygare,et al.  Magnetic interactions in molecules and an analysis of molecular electronic charge distribution from magnetic parameters , 1974 .

[108]  S. Grzesiek,et al.  A 3D triple-resonance NMR technique for qualitative measurement of carbonyl-Hβ J couplings in isotopically enriched proteins , 1992 .

[109]  E. Oldfield,et al.  Chemical-shift ranges in proteins , 1992 .

[110]  M H Saier,et al.  Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglc. , 1993, Biochemistry.

[111]  M. Williamson,et al.  Empirical Comparisons of Models for Chemical-Shift Calculation in Proteins , 1993 .

[112]  M. Billeter,et al.  Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα, in a globular protein: Use of 3JHNα for identification of helical secondary structure , 1984 .

[113]  F. Blanco,et al.  NMR chemical shifts: a tool to characterize distortions of peptide and protein helices , 1992 .

[114]  V. Bystrov.  Spin—spin coupling and the conformational states of peptide systems , 1976 .

[115]  A. Pastore,et al.  The relationship between chemical shift and secondary structure in proteins , 1990 .

[116]  A. Bax,et al.  Measurement of long-range 13C-13C J couplings in a 20-kDa protein-peptide complex , 1992 .

[117]  Venkataraman Thanabal,et al.  Structure-induced carbon-13 chemical shifts : a sensitive measure of transient localized secondary structure in peptides , 1992 .

[118]  M. Williamson,et al.  A method for the calculation of protein α-CH chemical shifts , 1992 .

[119]  E. Tüchsen,et al.  Hydrogen bonding monitored by deuterium isotope effects on carbonyl 13C chemical shift in BPTI: intra-residue hydrogen bonds in antiparallel beta-sheet. , 1991, International journal of biological macromolecules.

[120]  E. Oldfield,et al.  Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. , 1993, Science.

[121]  M. Rico,et al.  Characterization of low populated peptide helical structures in solution by means of NMR proton conformational shifts. , 1990, Biochemical and biophysical research communications.

[122]  N. Gresh,et al.  Theoretical variation of the H alpha chemical shift in acetyl-glycyl-N-methylamide and oligoglycines with molecular conformation and environment. , 1990, Biochemical and biophysical research communications.

[123]  Kurt Wüthrich,et al.  Stereospecific assignment of the methyl 1H NMR lines of valine and leucine in polypeptides by nonrandom 13C labelling , 1989 .

[124]  K. Wüthrich,et al.  Measurement of small heteronuclear 1H15N coupling constants in 15N-labeled proteins by 3D HNNHAB-COSY , 1991 .

[125]  F. Richards,et al.  Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. , 1991, Journal of molecular biology.

[126]  G. A. Gray,et al.  13C nuclear magnetic resonance of organophosphorus compounds XI—aminophosphines , 1980 .

[127]  C. S. Yannoni,et al.  Molecular sequence effect on the carbon-13 carbonyl chemical shift shielding tensor , 1990 .