What is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR

Journal of Molecular Biology

Volumn 308, Issue 4, 2001, Pages 745-764

  Goto, Natalie K ^a,b   Skrynnikov, Nikolai R ^c   Dahlquist, Frederick W ^d   Kay, Lewis E ^a,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF OREGON   (United States)

Author keywords

Dipolar couplings; Domain orientation; NMR; T4 lysozyme

Indexed keywords

LYSOZYME;

ARTICLE; BACTERIOPHAGE T4; ENZYME ANALYSIS; ENZYME CONFORMATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; STRUCTURE ANALYSIS; X RAY ANALYSIS;

T4 BACTERIOPHAGE;

EID: 0034972906     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4614     Document Type: Article

References (97)

1. The specificity requirements of bacteriophage T4 lysozyme
2. Studies on the specificity of action of bacteriophage T4 lysozyme
3. A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme
4. Reexamination of the role of Asp20 in catalysis by bacteriophage T4 lysozyme
5. Crystallographic determination of the mode of binding of oligosaccharides to T4 bacteriophage lysozyme: Implications for the mechanism of catalysis
6. Structural basis of the conversion of T4 lysozyme into a transglycosidase by reengineering the active site
7. Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution
8. The three dimensional structure of the lysozyme from bacteriophage T4
9. The structure of phage T4 lysozyme in solution noticeably differs from its crystalline struction
10. Motion of spin-labeled side-chains in T4 lysozyme, correlation with protein structure and dynamics
11. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
12. A mutant T4 lysozyme displays five different crystal conformations
13. Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3 → Pro
14. 1H NMR assignments and secondary structure for T4-lysozyme
15. 15N NMR resonances of bacteriophage T4 lysozyme
16. Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme
17. Subdomain interactions as a determinant in the folding and stability of T4 lysozyme
18. Structure-based design of a lysozyme with altered catalytic activity
19. A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene
20. Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR
21. Use of differentially substituted selenomethionine proteins in X-ray structure determination
22. Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths
23. 15N isotopic labeling: Structural and dynamic studies of larger proteins
24. Polarization-enhanced NMR spectroscopy of biomolecules in frozen solution
25. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations
26. Protein dynamics derived from clusters of crystal structures
27. Motion of spin-labeled side-chains in T4 lysozyme: Effect of side-chain structure
28. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: Differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin
29. 13C couplings in the structure determination of magnetically oriented macromolecules in solution
30. 1JCH splittings from magnetic-field dependence of J modulation in two-dimensional NMR spectra
31. Molecular symmetry as an aid to geometry determination in ligand protein complexes
32. New techniques in structural NMR - Anisotropic interactions
33. Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis
34. The NMR structure of a DNA dodecamer in an aqueous dilute liquid crystalline phase
35. Global folds of proteins with low densities of NOEs using residual dipolar couplings: Application to the 370-residue maltodextrin-binding protein
36. Domain orientation and dynamics in multidomain proteins from residual dipolar couplings
37. Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization
38. Refining the overall structure and subdomain orientation of ribosomal protein S4 Δ41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases
39. 3+
40. Control of enzyme activity by an engineered disulfide bond
41. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
42. Use of a novel aqueous liquid crystalline medium for high-resolution NMR of macromolecules in solution
43. Characterization of surfactant liquid crystal phases suitable for molecular alignment and measurement of dipolar couplings
44. A sensitivity-enhanced method for measuring heteronuclear long-range coupling constants from the displacement of signals in two 1D subspectra
45. Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra
46. Identifying conformational changes with site-directed spin labeling
47. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling
48. Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme
49. Disulphide bridges in globular proteins
50. Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
51. Crystallography & NMR system: A new software suite for macromolecular structure determination
52. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage
53. Purple membrane induced alignment of biological macromolecules in the magnetic field
54. NMR measurement of dipolar couplings in proteins aligned by transient binding to purple membrane fragments
55. Order matrix analysis of residual dipolar couplings using singular value decomposition
56. Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
57. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
58. Nitroxide spin-spin interactions: Applications to protein structure and dynamics
59. Crystal structures of spin labeled T4 lysozyme mutants: Implications for the interpretation of EPR spectra in terms of structure
60. Understanding modem molecular dynamics: Techniques and applications
61. Modeling protein-small molecule interactions: Structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A
62. Purification of bacteriophage T4 lysozyme
63. Improved dilute bicelle solutions for high-resolution NMR of biological macromolecules
64. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients
65. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity
66. Coherence selection by gradients without signal attenuation: Application to the 3-dimensional HNCO experiment
67. Improved linear prediction for trtmcated signals of known phase
68. NMRPipe: A multidimensional spectral processing system based on UNIX pipes
69. Nmr view: A computer program for the visualization and analysis of NMR data
70. A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams
71. Structural studies of mutants of T4 lysozyme that alter hydrophobic stabilization
72. MOLMOL: A program for display and analysis of macromolecular structures
73. Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings
74. Satisfying hydrogen bonding potential in proteins
75. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
76. Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings
77. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation
78. 15N spectra of isotopically enriched proteins
79. Gradient-enhanced triple-resonance 3-dimensional NMR experiments with improved sensitivity
80. 13C labeled proteins
81. An improved sequence for broadband decoupling: WALTZ-16
82. Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins
83. Selective excitation by pulse shaping combined with phase modulation
84. Single- and multiple-frequency-shifted laminar pulses
85. 13C-carbonyl decoupling
86. Improved line-shape and sensitivity in the HNCO-family of triple resonance experiments
87. Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins
88. 2O
89. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences
90. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
91. Structural basis of amino-acid alpha-helix propensity
92. Structure of a thermostable disulfide-bridge mutant of phage T4 lysozyme shows that an engineered cross-link in a flexible region does not increase the rigidity of the folded protein
93. Crystal structure of T4-lysozyme generated from synthetic coding DNA expressed in Escherichia coli
94. Bicelle-based liquid crystals for NMR-measurement of dipolar couplings at acidic and basic pH values