Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings

Journal of Magnetic Resonance

Volumn 154, Issue 2, 2002, Pages 329-335

  Clore, G Marius ^a   Bewley, Carole A ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; BACTERIAL PROTEIN; CARRIER PROTEIN; CYANOVIRIN N;

ARTICLE; CHEMISTRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN TERTIARY STRUCTURE;

ANTI-HIV AGENTS; BACTERIAL PROTEINS; CARRIER PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN STRUCTURE, TERTIARY;

EID: 0036018868     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmre.2001.2489     Document Type: Editorial

References (33)

1. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
2. Measurement of residual dipolar couplings of macromolecules aligned in the nematic phase of a colloidal suspension of rod-shaped viruses
3. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions
4. NMR structures of biomolecules using field oriented media and residual dipolar couplings
5. −13 C couplings in the structure determination of magnetically oriented macromolecules in solution
6. Rapid determination of protein folds using residual dipolar couplings
7. Protein structure determination using molecular fragment replacement and NMR dipolar couplings
8. Determination of protein backbone structure using only residual dipolar couplings
9. Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints
10. Solution structure of cyanovirin-N, a potent HIV-inactivating protein
11. Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: An application to maltose binding protein
12. Determining DNA global structure and DNA bending by application of NMR residual dipolar couplings
13. The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase
14. Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions
15. Solution structure of the 40, 000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr
16. Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization
17. Glucose of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system
18. Solution structure of the MEF2A-DNA complex: Structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors
19. Structural basis for SRY-dependent 46-X, Y sex reversal: Modulation of DNA bending by a naturally occuring point mutation
20. Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization
21. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: Differences in solution and crystal forms of maltodextrin binding protein loaded with β-cyclodextrin
22. What is the average conformation of bacteriophage T4 Lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR
23. Global structure of RNA determined with residual dipolar couplings
24. Internal coordinates for molecular dynamics and minimization in structure determination and refinement
25. Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping
26. Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
27. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments
28. Order matrix analysis of residual dipolar couplings using singular value decomposition
29. R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures
30. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
31. Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force
32. The solution structure of a specific GAGA factor/DNA complex reveals a modular binding mode