Ambiguous distance data in the calculation of NMR structures.

The use of molecular dynamics for simulated annealing optimization of structures calculated from NMR data is reviewed. I focus on ways of directly using and automatically assigning ambiguous peaks from nuclear Overhauser enhancement experiments during the structure calculation.

[1]  M. Nilges,et al.  A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13. , 1994, Journal of molecular biology.

[2]  M. Levitt.  Protein folding by restrained energy minimization and molecular dynamics. , 1983, Journal of molecular biology.

[3]  Stephen W. Fesik,et al.  A computer-based protocol for semiautomated assignments and 3D structure determination of proteins , 1994, Journal of biomolecular NMR.

[4]  M. Weiss.  Distinguishing symmetry-related intramolecular and intermolecular nuclear overhauser effects in a protein by asymmetric isotopic labeling , 1990 .

[5]  C. Sander,et al.  Quality control of protein models : directional atomic contact analysis , 1993 .

[6]  A. Gronenborn,et al.  Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. , 1988, Protein engineering.

[7]  T. Gibson,et al.  Three-Dimensional Structure and Stability of the KH Domain: Molecular Insights into the Fragile X Syndrome , 1996, Cell.

[8]  M Wilmanns,et al.  Structure of the binding site for inositol phosphates in a PH domain. , 1995, The EMBO journal.

[9]  T. Gibson,et al.  Structure of the dsRNA binding domain of E. coli RNase III. , 1995, The EMBO journal.

[10]  M. Nilges,et al.  Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy , 1993, Quarterly Reviews of Biophysics.

[11]  H Oschkinat,et al.  Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. , 1997, Journal of molecular biology.

[12]  A. Gronenborn,et al.  Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations , 1988, FEBS letters.

[13]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[14]  C. W. Hilbers,et al.  Solution structure of the single‐stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single‐stranded nucleic acids. , 1995, The EMBO journal.

[15]  P Herzyk,et al.  A reduced representation of proteins for use in restraint satisfaction calculations , 1993, Proteins.

[16]  A. Brünger,et al.  Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement , 1994, Proteins.

[17]  A T Brünger,et al.  Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. , 1997, Journal of magnetic resonance.

[18]  W F van Gunsteren,et al.  A protein structure from nuclear magnetic resonance data. lac repressor headpiece. , 1985, Journal of molecular biology.

[19]  I. Kuntz,et al.  [9] Distance geometry , 1989 .

[20]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[21]  K Wüthrich,et al.  Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints , 1991, Journal of biomolecular NMR.

[22]  M Nilges,et al.  Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. , 1995, Journal of molecular biology.

[23]  J. Thornton,et al.  Stereochemical quality of protein structure coordinates , 1992, Proteins.

[24]  Kurt Wüthrich,et al.  The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination , 1993 .

[25]  Timothy F. Havel.  An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. , 1991, Progress in biophysics and molecular biology.

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

[27]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[28]  Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor. , 1990, Biochemistry.

[29]  A. Gronenborn,et al.  Determination of three‐dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms Circumventing problems associated with folding , 1988, FEBS letters.

[30]  M Karplus,et al.  Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[31]  M Karplus,et al.  Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance and restrained molecular dynamics. , 1985, Journal of molecular biology.

[32]  M. Nilges,et al.  Sampling Properties of Simulated Annealing and Distance Geometry , 1991 .

[33]  Alan S. Stern,et al.  A method for determining overall protein fold from NMR distance restraints , 1992 .

[34]  W. Braun,et al.  Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. , 1995, Journal of molecular biology.

[35]  P. Kraulis,et al.  Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach. , 1994, Journal of molecular biology.

[36]  H Nakamura,et al.  Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties , 1993, Journal of biomolecular NMR.

[37]  C. Hilbers,et al.  Overcoming the ambiguity problem encountered in the analysis of nuclear overhauser magnetic resonance spectra of symmetric dimer proteins , 1993 .

[38]  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.

[39]  M Nilges,et al.  A calculation strategy for the structure determination of symmetric demers by 1H NMR , 1993, Proteins.

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

[41]  L. Kay,et al.  Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy , 1995 .

[42]  W. Braun,et al.  Pattern recognition and self‐correcting distance geometry calculations applied to myohemerythrin , 1994, FEBS letters.

[43]  M. Nilges,et al.  Calculation of symmetric multimer structures from NMR data using a priori knowledge of the monomer structure, co-monomer restraints, and interface mapping: The case of leucine zippers , 1996, Journal of biomolecular NMR.

[44]  A T Brünger,et al.  Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. , 1991, Journal of molecular biology.

[45]  I D Kuntz,et al.  Application of distance geometry to the proton assignment problem , 1993, Biopolymers.

[46]  W F van Gunsteren,et al.  A structure refinement method based on molecular dynamics in four spatial dimensions. , 1993, Journal of molecular biology.