NMR-based structural characterization of large protein-ligand interactions

Genomic research on target identification and validation has created a great need for methods that rapidly provide detailed structural information on protein-ligand interactions. We developed a suite of NMR experiments as rapid and efficient tools to provide descriptive structural information on protein-ligand complexes. The methods work with large proteins and in particular cases also without the need for a complete three-dimensional structure. We will show applications with two tetrameric enzymes of 120 and 170 kDa.

[1]  Ray Freeman,et al.  Band-selective radiofrequency pulses , 1991 .

[2]  H. Kalbitzer,et al.  Protein NMR Spectroscopy. Principles and Practice , 1997 .

[3]  F. Young Biochemistry , 1955, The Indian Medical Gazette.

[4]  R. London,et al.  The inter-ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands , 1999, Journal of biomolecular NMR.

[5]  David Neuhaus,et al.  The Nuclear Overhauser Effect in Structural and Conformational Analysis , 1989 .

[6]  G. Scapin,et al.  Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. , 1997, Biochemistry.

[7]  D. Knighton,et al.  Structure-based design of novel, urea-containing FKBP12 inhibitors. , 1996, Journal of medicinal chemistry.

[8]  C. Gilvarg,et al.  The reduction step in diaminopimelic acid biosynthesis. , 1965, Journal of Biological Chemistry.

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

[10]  Shunji Takahashi,et al.  Characterization of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase, an Enzyme Involved in Isopentenyl Diphosphate Biosynthesis, and Identification of Its Catalytic Amino Acid Residues* , 2000, The Journal of Biological Chemistry.

[11]  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.

[12]  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 .

[13]  I. Shimada,et al.  Carbon-13 NMR study of switch variant anti-dansyl antibodies: antigen binding and domain-domain interactions. , 1991, Biochemistry.

[14]  G. Bodenhausen,et al.  Measurement of Cross-Relaxation between Amide Protons in 15N-Enriched Proteins with Suppression of Spin Diffusion , 1996 .

[15]  M. Sundström,et al.  Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water* , 2000, Journal of biomolecular NMR.

[16]  Jens Klein,et al.  DETECTING BINDING AFFINITY TO IMMOBILIZED RECEPTOR PROTEINS IN COMPOUND LIBRARIES BY HR-MAS STD NMR , 1999 .

[17]  Stephen W. Fesik,et al.  The Use of Differential Chemical Shifts for Determining the Binding Site Location and Orientation of Protein-Bound Ligands , 2000 .

[18]  K. Wüthrich,et al.  Torsion angle dynamics for NMR structure calculation with the new program DYANA. , 1997, Journal of molecular biology.

[19]  L. Kay,et al.  Comparison of different modes of two-dimensional reverse-correlation NMR for the study of proteins , 1990 .

[20]  S. Fesik,et al.  Heteronuclear three-dimensional nmr spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra , 1988 .

[21]  R. Stevens,et al.  Global Efforts in Structural Genomics , 2001, Science.

[22]  L. Kay,et al.  New developments in isotope labeling strategies for protein solution NMR spectroscopy. , 2000, Current opinion in structural biology.

[23]  M. Rance,et al.  Characterization of the binding interface between the E-domain of Staphylococcal protein A and an antibody Fv-fragment. , 2000, Biochemistry.

[24]  A. J. Shaka,et al.  Computer-optimized decoupling scheme for wideband applications and low-level operation , 1985 .