Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution.

[1]  J. Weissman,et al.  Mechanism of GroEL action: Productive release of polypeptide from a sequestered position under groes , 1995, Cell.

[2]  Buildup rates of the nuclear Overhauser effect measured by two-dimensional proton magnetic resonance spectroscopy: implications for studies of protein conformation , 1981 .

[3]  K Wüthrich,et al.  Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[4]  K. Wüthrich,et al.  Uniform and Residue-specific 15N-labeling of Proteins on a Highly Deuterated Background , 2004, Journal of biomolecular NMR.

[5]  B. Nageswara Rao,et al.  Influence of molecular geometry on uncertainty in distances determined from NOE , 1989 .

[6]  I. Solomon.  Relaxation Processes in a System of Two Spins , 1955 .

[7]  Jocelyne Fiaux,et al.  Solution NMR techniques for large molecular and supramolecular structures. , 2002, Journal of the American Chemical Society.

[8]  V. Saudek,et al.  Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions , 1992, Journal of biomolecular NMR.

[9]  G. Bodenhausen,et al.  Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy , 1980 .

[10]  K Wüthrich,et al.  Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Glucagon bound to perdeuterated dodecylphosphocholine micelles. , 1982, Journal of molecular biology.

[11]  L. Kay,et al.  Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g. , 2002, Journal of the American Chemical Society.

[12]  K Wüthrich,et al.  The program XEASY for computer-supported NMR spectral analysis of biological macromolecules , 1995, Journal of biomolecular NMR.

[13]  J. Wieruszeski,et al.  Use of a water flip-back pulse in the homonuclear NOESY experiment , 1995, Journal of biomolecular NMR.

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

[15]  G. Wider,et al.  Improved sensitivity and coherence selection for [15N,1H]-TROSY elements in triple resonance experiments , 1999, Journal of biomolecular NMR.

[16]  G. Wagner,et al.  An optimized 3D NOESY-HSQC. , 1996, Journal of magnetic resonance. Series B.

[17]  F. Shewmaker,et al.  The Disordered Mobile Loop of GroES Folds into a Defined β-Hairpin upon Binding GroEL* , 2001, The Journal of Biological Chemistry.

[18]  A. Horwich,et al.  The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex , 1997, Nature.

[19]  T. James,et al.  A theoretical study of distance determinations from NMR. Two-dimensional nuclear overhauser effect spectra , 1984 .

[20]  Kurt Wüthrich,et al.  NMR analysis of a 900K GroEL–GroES complex , 2002, Nature.

[21]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[22]  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.

[23]  C. Georgopoulos,et al.  Interplay of structure and disorder in cochaperonin mobile loops. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Lila M. Gierasch,et al.  Characterization of a functionally important mobile domain of GroES , 1993, Nature.

[25]  L. Kay,et al.  NMR studies of protein structure and dynamics. , 2005, Journal of magnetic resonance.

[26]  M. Forster.  Comparison of compuational methods for simulating nuclear Overhauser effects in NMR spectroscopy , 1991 .

[27]  Gerhard Wagner,et al.  Two-dimensional relayed coherence transfer spectroscopy of a protein , 1983 .

[28]  NMR Assignment and Secondary Structure Determination of an Octameric 110 kDa Protein Using TROSY in Triple Resonance Experiments , 2000 .

[29]  Kurt Wüthrich,et al.  Processing of multi-dimensional NMR data with the new software PROSA , 1992 .

[30]  G. Wider,et al.  Dissection of heteronuclear NMR experiments for studies of magnetization transfer efficiencies. , 2003, Journal of magnetic resonance.

[31]  M. Goldman,et al.  Interference effects in the relaxation of a pair of unlike spin-1/2 nuclei , 1984 .

[32]  S. Grzesiek,et al.  The Importance of Not Saturating H2o in Protein NMR : application to Sensitivity Enhancement and Noe Measurements , 1993 .

[33]  Roger W. Hendrix,et al.  Homologous plant and bacterial proteins chaperone oligomeric protein assembly , 1988, Nature.

[34]  J. Deisenhofer,et al.  The crystal structure of the GroES co-chaperonin at 2.8 Å resolution , 1996, Nature.

[35]  B. Meier,et al.  Computer Simulations in Magnetic Resonance. An Object-Oriented Programming Approach , 1994 .

[36]  M. Konrad,et al.  Selective spin diffusion. A novel method for studying motional properties of biopolymers in solution , 1978, FEBS letters.

[37]  L. Kay,et al.  Improved lineshape and sensitivity in the HNCO-family of triple resonance experiments , 1999 .

[38]  G. Wider,et al.  Managing the solvent water polarization to obtain improved NMR spectra of large molecular structures , 2005, Journal of biomolecular NMR.

[39]  K Wüthrich,et al.  TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  F. A. Seiler,et al.  Numerical Recipes in C: The Art of Scientific Computing , 1989 .

[41]  A. Redfield,et al.  Cross relaxation and spin diffusion effects on the proton NMR of biopolymers in H2O. Solvent saturation and chemical exchange in superoxide dismutase. , 1978, FEBS letters.

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

[43]  Kurt Wüthrich,et al.  TROSY-TYPE TRIPLE-RESONANCE EXPERIMENTS FOR SEQUENTIAL NMR ASSIGNMENTS OF LARGE PROTEINS , 1999 .

[44]  Perunthiruthy K. Madhu,et al.  Cross-correlations in NMR , 2000 .

[45]  Zbyszek Otwinowski,et al.  The crystal structure of the bacterial chaperonln GroEL at 2.8 Å , 1994, Nature.

[46]  M. Page,et al.  Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from staphylococcus aureus , 1998, Nature Structural Biology.

[47]  K Wüthrich,et al.  Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations. , 1982, Journal of molecular biology.

[48]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .