Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints

SummaryA new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985)J. Mol. Biol.,186, 611) is described, which makes use of redundant dihedral angle constraints (REDAC) derived from preliminary calculations of the complete structure. The REDAC approach reduces the computation time for obtaining a group of acceptable conformers with the program DIANA 5-100-fold, depending on the complexity of the protein structure, and retains good sampling of conformation space.

[1]  Werner Braun,et al.  Automated stereospecific 1H NMR assignments and their impact on the precision of protein structure determinations in solution , 1989 .

[2]  K. Wüthrich,et al.  Structure determination of the Antp (C39----S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. , 1991, Journal of molecular biology.

[3]  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.

[4]  Kurt Wüthrich,et al.  Determination of the Three-dimensional Structure of the Antennapedia Homeodomain from Drosophila in Solution by 1H Nuclear Magnetic Resonance Spectroscopy , 1993 .

[5]  Gottfried Otting,et al.  Determination of the three-dimensional structure of theAntennapedia homeodomain fromDrosophila in solution by1H nuclear magnetic resonance spectroscopy , 1990 .

[6]  A. Mclachlan Gene duplications in the structural evolution of chymotrypsin. , 1979, Journal of molecular biology.

[7]  N. Go,et al.  Refined structure of melittin bound to perdeuterated dodeclylphoscholine micelles as studied by 2D‐NMR and distance geometry calculation , 1991, Proteins.

[8]  K. Wüthrich,et al.  Three-dimensional structure of rabbit liver [Cd7]metallothionein-2a in aqueous solution determined by nuclear magnetic resonance. , 1991, Journal of molecular biology.

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

[10]  K Wüthrich,et al.  Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. , 1984, Journal of molecular biology.

[11]  W. J. Gehring,et al.  The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: Comparison with prokaryotic repressors , 1989, Cell.

[12]  H. Scheraga,et al.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[13]  K Wüthrich,et al.  Comparison of the high-resolution structures of the alpha-amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. , 1989, Journal of molecular biology.

[14]  N. Go,et al.  Tertiary structure of mouse epidermal growth factor determined by two-dimensional 1H NMR. , 1988, Journal of biochemistry.

[15]  W. Braun,et al.  Distance geometry and related methods for protein structure determination from NMR data , 1987, Quarterly Reviews of Biophysics.

[16]  G. Wider,et al.  The NMR structure of the activation domain isolated from porcine procarboxypeptidase B. , 1991, The EMBO journal.

[17]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

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

[19]  K Wüthrich,et al.  Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. , 1991, Journal of molecular biology.

[20]  M. Billeter,et al.  Three‐dimensional structure of the neurotoxin ATX Ia from Anemonia sulcata in aqueous solution determined by nuclear magnetic resonance spectroscopy , 1989, Proteins.

[21]  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.

[22]  G. Wider,et al.  Sequence-specific 1H NMR assignments and determination of the secondary structure for the activation domain isolated from pancreatic procarboxypeptidase B. , 1990, Biochemistry.