Determining the structures of large proteins and protein complexes by NMR.

Recent advances in multidimensional NMR methodology to obtain 1H, 15N and 13C resonance assignments, interproton-distance and torsion-angle restraints, and restraints that characterize long-range order have, coupled with new methods of structure refinement, permitted solution structure of proteins in excess of 250 residues to be solved. These developments may permit the determination by NMR of the structures of macromolecules up to 50-60kDa, thereby bringing into reach numerous systems of considerable biological interest, including a large variety of protein-protein and protein-nucleic-acid complexes.

[1]  G. Marius Clore,et al.  Applications of three- and four-dimensional heteronuclear NMR spectroscopy to protein structure determination , 1991 .

[2]  P. Kraulis,et al.  Three-dimensional NMR spectroscopy of a protein in solution , 1988, Nature.

[3]  A. Ullrich,et al.  Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos , 1994, Nature Structural Biology.

[4]  T. Schall,et al.  Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C type. , 1995, Biochemistry.

[5]  A M Gronenborn,et al.  Solution structure of the DNA binding domain of HIV-1 integrase. , 1995, Biochemistry.

[6]  C. Arrowsmith,et al.  Solution structure of the tetrameric minimum transforming domain of p53 , 1995, Nature Structural Biology.

[7]  A three-dimensional NMR experiment with improved sensitivity for carbonyl–carbonyl J correlation in proteins , 1997, Journal of biomolecular NMR.

[8]  Haruki Nakamura,et al.  Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices , 1994, Cell.

[9]  R. Kaptein,et al.  Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. , 1994, Journal of molecular biology.

[10]  Y. Thériault,et al.  Solution structure of the cyclosporin A/cyclophilin complex by NMR , 1993, Nature.

[11]  D. G. Davis,et al.  Solution structure of the human pp60c-src SH2 domain complexed with a phosphorylated tyrosine pentapeptide. , 1995, Biochemistry.

[12]  L. Kay,et al.  Four-dimensional carbon-13/carbon-13-edited nuclear Overhauser enhancement spectroscopy of a protein in solution: application to interleukin 1.beta. , 1991 .

[13]  A M Gronenborn,et al.  NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. , 1993, Science.

[14]  Jeffrey R. Huth,et al.  The solution structure of an HMG-I(Y)–DNA complex defines a new architectural minor groove binding motif , 1997, Nature Structural Biology.

[15]  A. Bax,et al.  2D and 3D NMR Study of Phenylalanine Residues in Proteins by Reverse Isotopic Labeling , 1994 .

[16]  A M Gronenborn,et al.  1H‐Nmr stereospecific assignments by conformational data‐base searches , 1990, Biopolymers.

[17]  O. Jardetzky,et al.  The solution structures of the trp repressor-operator DNA complex. , 1994, Journal of molecular biology.

[18]  D. S. Garrett,et al.  Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system by multidimensional NMR. , 1997, Biochemistry.

[19]  L. Kay,et al.  Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. , 1997, Biochemistry.

[20]  D. S. Garrett,et al.  Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy , 1997, Nature Structural Biology.

[21]  T. L. James,et al.  CHAPTER 2 – PRINCIPLES OF NUCLEAR MAGNETIC RESONANCE , 1975 .

[22]  A. Gronenborn,et al.  High-resolution structure of the oligomerization domain of p53 by multidimensional NMR. , 1994, Science.

[23]  Angela M. Gronenborn,et al.  The Impact of Direct Refinement against 13Cα and 13Cβ Chemical Shifts on Protein Structure Determination by NMR , 1995 .

[24]  A. Gronenborn,et al.  High-resolution three-dimensional structure of interleukin 1 beta in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. , 1992, Biochemistry.

[25]  G. Bodenhausen,et al.  Principles of nuclear magnetic resonance in one and two dimensions , 1987 .

[26]  A. Gronenborn,et al.  Solution structure of a calmodulin-target peptide complex by multidimensional NMR. , 1994, Science.

[27]  K. Wüthrich NMR of proteins and nucleic acids , 1988 .

[28]  T. Pawson,et al.  Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-γ1 complexed with a high affinity binding peptide , 1994, Cell.

[29]  A M Gronenborn,et al.  Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 beta in solution. , 1990, Science.

[30]  S. Grzesiek,et al.  Two-Dimensional NMR Methods for Determining χ1 Angles of Aromatic Residues in Proteins from Three-Bond JC‘Cγ and JNCγ Couplings , 1997 .

[31]  A M Gronenborn,et al.  Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids. , 1997, Journal of magnetic resonance.

[32]  A. Gronenborn,et al.  Three-dimensional structure of interleukin 8 in solution. , 1991, Biochemistry.

[33]  Hongtao Yu,et al.  Structural basis for the binding of proline-rich peptides to SH3 domains , 1994, Cell.

[34]  G. Wider,et al.  Determination of the NMR solution structure of the cyclophilin A-cyclosporin A complex , 1994, Journal of biomolecular NMR.

[35]  G. Clore,et al.  Determination of the secondary structure and global topology of the 44 kDa ectodomain of gp41 of the simian immunodeficiency virus by multidimensional nuclear magnetic resonance spectroscopy. , 1997, Journal of molecular biology.

[36]  Ad Bax,et al.  Methodological advances in protein NMR , 1993 .

[37]  A. Bax,et al.  Optimized recording of heteronuclear multidimensional NMR spectra using pulsed field gradients , 1992 .

[38]  A. Gronenborn,et al.  Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases , 1996, Protein science : a publication of the Protein Society.

[39]  Paul A. Keifer,et al.  Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity , 1992 .

[40]  A M Gronenborn,et al.  Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. , 1991, Science.

[41]  A M Gronenborn,et al.  Determination of three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy. , 1987, Protein engineering.

[42]  G. Marius Clore,et al.  The solution structure of a specific GAGA factor–DNA complex reveals a modular binding mode , 1997, Nature Structural Biology.

[43]  K Wüthrich,et al.  Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. , 1993, Journal of molecular biology.

[44]  G W Vuister,et al.  The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR. , 1994, Journal of magnetic resonance. Series B.

[45]  D. S. Garrett,et al.  High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR. , 1994, Science.

[46]  M. Wittekind,et al.  Incorporation of 1H/13C/15N-{Ile, Leu, Val} into a Perdeuterated, 15N-Labeled Protein: Potential in Structure Determination of Large Proteins by NMR , 1996 .

[47]  Jeffrey R. Huth,et al.  Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NFκB , 1995 .

[48]  S. Grzesiek,et al.  Multiple-Quantum Line Narrowing for Measurement of H.alpha.-H.beta. J Couplings in Isotopically Enriched Proteins , 1995 .

[49]  A. Bax,et al.  Determination of φ and χ1 Angles in Proteins from 13C−13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond? , 1997 .

[50]  M Nilges,et al.  The solution structure of the Tyr41-->His mutant of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13. , 1994, Journal of molecular biology.

[51]  D. Case,et al.  Three-dimensional solution structure of the reduced form of Escherichia coli thioredoxin determined by nuclear magnetic resonance spectroscopy. , 1990, Biochemistry.

[52]  L. Kay,et al.  A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin , 1990 .

[53]  L. Kay,et al.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. , 1990, Biochemistry.

[54]  A. Gronenborn,et al.  Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex , 1995, Cell.

[55]  David A. Case,et al.  Structural basis for DNA bending by the architectural transcription factor LEF-1 , 1995, Nature.

[56]  Bennett T. Farmer,et al.  Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. , 1994 .

[57]  A M Gronenborn,et al.  The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. , 1995, Journal of magnetic resonance. Series B.

[58]  A M Gronenborn,et al.  Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. , 1989, Critical reviews in biochemistry and molecular biology.

[59]  A. Gronenborn,et al.  Three‐dimensional solution structure of the 44 kDa ectodomain of SIV gp41 , 1998, The EMBO journal.

[60]  A. Gronenborn,et al.  Complete resonance assignment for the polypeptide backbone of interleukin 1 beta using three-dimensional heteronuclear NMR spectroscopy. , 1990, Biochemistry.

[61]  A. Gronenborn,et al.  The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal. , 1996, Structure.

[62]  W. Fairbrother,et al.  The solution structure of melanoma growth stimulating activity. , 1994, Journal of molecular biology.

[63]  D. S. Garrett,et al.  Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. , 1997, Biochemistry.

[64]  R. Sauer,et al.  Solution structure of dimeric Mnt repressor (1-76). , 1994, Biochemistry.

[65]  S. Grzesiek,et al.  Measurement of homo- and heteronuclear J couplings from quantitative J correlation. , 1994, Methods in enzymology.

[66]  A. Petros,et al.  Three-dimensional structure of the FK506 binding protein/ascomycin complex in solution by heteronuclear three- and four-dimensional NMR. , 1993, Biochemistry.

[67]  Ad Bax,et al.  Four-Dimensional 15N-Separated NOESY of Slowly Tumbling Perdeuterated 15N-Enriched Proteins. Application to HIV-1 Nef , 1995 .

[68]  G. Marius Clore,et al.  Refined solution structure of the oligomerization domain of the tumour suppressor p53 , 1995, Nature Structural Biology.

[69]  R. R. Ernst,et al.  Correlation of connected transitions by two‐dimensional NMR spectroscopy , 1986 .

[70]  M. Billeter,et al.  The nuclear magnetic resonance solution structure of the mixed disulfide between Escherichia coli glutaredoxin(C14S) and glutathione. , 1994, Journal of molecular biology.

[71]  A M Gronenborn,et al.  A potential involving multiple proton chemical-shift restraints for nonstereospecifically assigned methyl and methylene protons. , 1996, Journal of magnetic resonance. Series B.

[72]  A M Gronenborn,et al.  Interhelical angles in the solution structure of the oligomerization domain of p53: correction , 1995, Science.

[73]  R. Boelens,et al.  The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site. , 1997, Structure.

[74]  G. Marius Clore,et al.  Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution , 1997, Nature Structural Biology.

[75]  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.

[76]  Bennett T. Farmer,et al.  Use of 1HN-1HN NOEs to Determine Protein Global Folds in Perdeuterated Proteins , 1995 .

[77]  A. Gronenborn,et al.  Solution structure of the N-terminal zinc binding domain of HIV-1 integrase , 1997, Nature Structural Biology.

[78]  Rolf Boelens,et al.  The DNA-binding domain of HIV-1 integrase has an SH3-like fold , 1995, Nature Structural Biology.

[79]  V. P. Chuprina,et al.  Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. , 1994, Journal of Molecular Biology.

[80]  High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution. , 1992 .

[81]  S. Schreiber,et al.  Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. , 1995, Science.

[82]  A. Gronenborn,et al.  Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. , 1995, Critical reviews in biochemistry and molecular biology.

[83]  B. Roques,et al.  NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline-rich peptide from Sos , 1994, Nature Structural Biology.