Structure calculation from NMR data.

NMR calculation methods have kept pace with the rapid extension of NMR experiments to larger molecules. By including additional data and effects of local dynamics in the refinement, we can obtain a more complete picture of the molecule in solution. The structure determination process is being aided by new methods to solve some aspects of spectral assignment during the structure calculation.

[1]  D F Mierke,et al.  Coupling constants again: Experimental restraints in structure refinement , 1994, J. Comput. Aided Mol. Des..

[2]  M. Goldman,et al.  Off-Resonance ROESY for the Study of Dynamic Processes , 1994 .

[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]  R. Abseher,et al.  NMR cross-relaxation investigated by molecular dynamics simulation: a case study of ubiquitin in solution. , 1995, Journal of molecular biology.

[5]  M. Williamson,et al.  Application of 1H NMR chemical shifts to measure the quality of protein structures. , 1995, Journal of molecular biology.

[6]  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.

[7]  Patrice Koehl,et al.  Calculation of nuclear magnetic resonance order parameters in proteins by normal mode analysis , 1996 .

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

[9]  A. Bax,et al.  Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts , 1991 .

[10]  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.

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

[12]  R. Brüschweiler.  Connections between NMR Relaxation Measurements and Theoretical Models of Structural Dynamics of Biopolymers in Solution , 1994 .

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

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

[15]  W. F. Gunsteren,et al.  Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble , 1995, Journal of biomolecular NMR.

[16]  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.

[17]  C. Schiffer,et al.  Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. , 1994, Methods in enzymology.

[18]  K. Wüthrich,et al.  Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long‐time molecular dynamics calculations in explicit water , 1996, Proteins.

[19]  Andrew E. Torda,et al.  Parametrisation of time-averaged distance restraints in MD simulations , 1995, Journal of biomolecular NMR.

[20]  R. Brunne,et al.  Structure refinement using time-averaged J-coupling constant restraints , 1993, Journal of biomolecular NMR.

[21]  P. Domaille,et al.  An Approach to the Structure Determination of Larger Proteins Using Triple Resonance NMR Experiments in Conjunction with Random Fractional Deuteration , 1996 .

[22]  J. Markley,et al.  Comparison of the accuracy of protein solution structures derived from conventional and network‐edited NOESY data , 1995, Protein science : a publication of the Protein Society.

[23]  Makoto Demura,et al.  The relationship between amide proton chemical shifts and secondary structure in proteins , 1995, Journal of biomolecular NMR.

[24]  H Oschkinat,et al.  Automated assignment of multidimensional nuclear magnetic resonance spectra. , 1994, Methods in enzymology.

[25]  Ashok Kumar,et al.  Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution. , 1995, Biophysical journal.

[26]  J. Lefèvre,et al.  Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions. , 1996, Biochemistry.

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

[28]  T. James.  Relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra , 1991 .

[29]  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.

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

[31]  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.

[32]  E. Oldfield,et al.  Protein Structure Refinement Using Carbon- 13 Nuclear Magnetic Resonance Spectroscopic Chemical Shifts and Quantum Chemistry , 1995 .

[33]  H. Kalbitzer,et al.  A general Bayesian method for an automated signal class recognition in 2D NMR spectra combined with a multivariate discriminant analysis , 1995, Journal of biomolecular NMR.

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

[35]  T. L. James,et al.  Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure , 1993, Journal of biomolecular NMR.

[36]  A. Brünger,et al.  Conformational variability of solution nuclear magnetic resonance structures. , 1995, Journal of molecular biology.

[37]  A. Gronenborn,et al.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. , 1993, Science.

[38]  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.

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

[40]  Michael Nilges,et al.  Structure of the pleckstrin homology domain from β-spectrin , 1994, Nature.

[41]  D E Wemmer,et al.  Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors , 1995, Journal of biomolecular NMR.

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

[43]  M. Karplus,et al.  Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution , 1992 .

[44]  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.

[45]  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.

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

[47]  J. Prestegard,et al.  Refinement of the NMR structures for acyl carrier protein with scalar coupling data , 1990, Proteins.

[48]  Ping F. Yip.  A computationally efficient method for evaluating the gradient of 2D NOESY intensities , 1993 .

[49]  Rafael Brüschweiler,et al.  Characterization of biomolecular structure and dynamics by NMR cross relaxation , 1994 .

[50]  R A Smith,et al.  Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4. , 1992, Biochemistry.

[51]  Eric Oldfield,et al.  Chemical shifts and three-dimensional protein structures , 1995, Journal of biomolecular NMR.

[52]  Wilfred F. van Gunsteren,et al.  Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .

[53]  M. J. Dellwo,et al.  Computationally efficient gradients for relaxation matrix-based structure refinement including the accommodation of internal motions , 1993, Journal of biomolecular NMR.

[54]  H. Schwalbe,et al.  Conformation of valine side chains in ribonuclease T1 determined by NMR studies of homonuclear and heteronuclear 3J coupling constants. , 1994, Biochemistry.

[55]  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.

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

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

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

[59]  W. Taylor,et al.  Global fold determination from a small number of distance restraints. , 1995, Journal of molecular biology.

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

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

[62]  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.