Estimating side-chain order in [U-2H;13CH 3]-labeled high molecular weight proteins from analysis of HMQC/HSQC spectra

Journal of Physical Chemistry B

Volumn 117, Issue 13, 2013, Pages 3571-3577

  Tugarinov, Vitali ^a   Kay, Lewis E ^b,c  

^a University of Maryland   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR WEIGHT; QUANTUM THEORY;

CORRELATION MAPS; DEUTERATED PROTEINS; HIGH MOLECULAR WEIGHT; HIGH MOLECULAR WEIGHT PROTEIN; LABELED PROTEINS; MULTIPLE-QUANTUM COHERENCES; ORDER PARAMETER; RELAXATION RATES;

PROTEINS;

EID: 84875800477     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp401088c     Document Type: Article

References (37)

1. 15N-Labeled Protein: Potential in Structure Determination of Large Proteins by NMR J. Am. Chem. Soc. 1996, 118, 6800-1
2. Gardner, K. H.; Rosen, M. K.; Kay, L. E. Global Folds of Highly Deuterated, Methyl Protonated Proteins by Multidimensional NMR Biochemistry 1997, 36, 1389-401
3. Goto, N. K.; Kay, L. E. New Developments in Isotope Labeling Strategies for Protein Solution NMR Spectroscopy Curr. Opin. Struct. Biol. 2000, 10, 585-92
4. Tugarinov, V.; Kanelis, V.; Kay, L. E. Isotope Labeling Strategies for the Study of High-Molecular-Weight Proteins by Solution NMR Spectroscopy Nat. Protoc. 2006, 1, 749-54
5. Sprangers, R.; Velyvis, A.; Kay, L. E. Solution NMR of Supramolecular Complexes: Providing New Insights into Function Nat. Methods 2007, 4, 697-703
6. Ruschak, A. M.; Kay, L. E. Methyl Groups as Probes of Supra-Molecular Structure, Dynamics and Function J. Biomol. NMR 2010, 46, 75-87
7. 2H-Enriched Proteins J. Struct. Funct. Genomics 2010, 11, 223-32
8. Sheppard, D.; Sprangers, R.; Tugarinov, V. Experimental Approaches for NMR Studies of Sidechain Dynamics in High-Molecular-Weight Proteins Prog. Nucl. Magn. Reson. Spectrosc. 2010, 56, 1-45
9. Kay, L. E. Solution NMR Spectroscopy of Supra-Molecular Systems, Why Bother? A Methyl-Trosy View J. Magn. Reson. 2011, 210, 159-70
10. 13C NMR Spectroscopy of Methyl Groups in Very High Molecular Weight Proteins and Protein Complexes J. Am. Chem. Soc. 2003, 125, 10420-8
11. Tugarinov, V.; Hwang, P. M.; Kay, L. E. Nuclear Magnetic Resonance Spectroscopy of High-Molecular-Weight Proteins Annu. Rev. Biochem. 2004, 73, 107-46
12. 2 Methyl Isotopomers To Detect Slow Conformational Changes of Protein Side Chains J. Am. Chem. Soc. 1999, 121, 11589-90
13. 13C Longitudinal and Transverse Relaxation Rates Measured in the Same Protein Sample J. Am. Chem. Soc. 2001, 123, 6164-71
14. Tugarinov, V.; Ollerenshaw, J. E.; Kay, L. E. Probing Side-Chain Dynamics in High Molecular Weight Proteins by Deuterium NMR Spin Relaxation: An Application to an 82-kDa Enzyme J. Am. Chem. Soc. 2005, 127, 8214-25
15. 2H NMR Relaxation Experiment for the Measurement of the Time Scale of Methyl Side-Chain Dynamics in Large Proteins J. Am. Chem. Soc. 2006, 128, 12484-9
16. 2H NMR Relaxation Studies of the 723-Residue Enzyme Malate Synthase G Reveal a Dynamic Binding Interface Biochemistry 2005, 44, 15970-7
17. Sprangers, R.; Kay, L. E. Quantitative Dynamics and Binding Studies of the 20S Proteasome by NMR Nature 2007, 445, 618-22
18. Godoy-Ruiz, R.; Guo, C.; Tugarinov, V. Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins J. Am. Chem. Soc. 2010, 132, 18340-50
19. 1H Transitions in Methyl Groups of Proteins as Reporters of Side-Chain Dynamics J. Am. Chem. Soc. 2006, 128, 7299-308
20. Tugarinov, V.; Sprangers, R.; Kay, L. E. Probing Side-Chain Dynamics in the Proteasome by Relaxation Violated Coherence Transfer NMR Spectroscopy J. Am. Chem. Soc. 2007, 129, 1743-50
21. Sun, H.; Kay, L. E.; Tugarinov, V. An Optimized Relaxation-Based Coherence Transfer NMR Experiment for the Measurement of Side-Chain Order in Methyl-Protonated, Highly Deuterated Proteins J. Phys. Chem. B 2011, 115, 14878-84
22. Ollerenshaw, J. E.; Tugarinov, V.; Kay, L. E. Methyl Trosy: Explanation and Experimental Verification Magn. Reson. Chem. 2003, 41, 843-52
23. Korzhnev, D. M.; Kloiber, K.; Kanelis, V.; Tugarinov, V.; Kay, L. E. Probing Slow Dynamics in High Molecular Weight Proteins by Methyl-Trosy NMR Spectroscopy: Application to a 723-Residue Enzyme J. Am. Chem. Soc. 2004, 126, 3964-73
24. Bax, A.; Griffey, R. H.; Hawkings, B. L. Correlation of Proton and Nitrogen-15 Chemical Shifts by Multiple Quantum NMR J. Magn. Reson. 1983, 55, 301-15
25. Mueller, L. Sensitivity Enhanced Detection of Weak Nuclei Using Heteronuclear Multiple Quantum Coherence J. Am. Chem. Soc. 1979, 101, 4481-4
26. Bodenhausen, G.; Ruben, J. Natural Abundance Nitrogen-15 NMR by Enhanced Heteronuclear Spectroscopy Chem. Phys. Lett. 1980, 69, 185-9
27. 2 Relaxation by Mutual Cancellation of Dipole-Dipole Coupling and Chemical Shift Anisotropy Indicates an Avenue to NMR Structures of Very Large Biological Macromolecules in Solution Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 12366-71
28. 13C-labeled Proteins J. Am. Chem. Soc. 1998, 120, 6394-400
29. Miclet, E.; Williams, D. C., Jr; Clore, G. M.; Bryce, D. L.; Boisbouvier, J.; Bax, A. Relaxation-Optimized NMR Spectroscopy of Methylene Groups in Proteins and Nucleic Acids J. Am. Chem. Soc. 2004, 126, 10560-70
30. Howard, B. R.; Endrizzi, J. A.; Remington, S. J. Crystal Structure of Escherichia coli Malate Synthase G Complexed with Magnesium and Glyoxylate at 2.0 Å Resolution: Mechanistic Implications Biochemistry 2000, 39, 3156-68
31. Löwe, J.; Stock, D.; Jap, B.; Zwickl, P.; Baumeister, W.; Huber, R. Crystal Structure of the 20S Proteasome from the Archaeon T. Acidophilum at 3.4 Å Resolution Science 1995, 268, 533-9
32. Guo, C.; Zhang, D.; Tugarinov, V. An NMR Experiment for Simultaneous Trosy-Based Detection of Amide and Methyl Groups in Large Proteins J. Am. Chem. Soc. 2008, 130, 10872-73
33. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. NMRpipe: A Multidimensional Spectral Processing System Based on Unix Pipes J. Biomol. NMR 1995, 6, 277-93
34. Kamith, U.; Shriver, J. W. Characterization of the Thermotropic State Changes in Myosin Subfragment-1 and Heavy Meromyosin by UV Difference Spectroscopy J. Biol. Chem. 1989, 264, 5586-92
35. Tugarinov, V.; Kay, L. E. Methyl Groups as Probes of Structure and Dynamics in NMR Studies of High-Molecular-Weight Proteins ChemBioChem 2005, 6, 1567-77
36. Sun, H.; Godoy-Ruiz, R.; Tugarinov, V. Estimating Side-Chain Order in Methyl-Protonated, Perdeuterated Proteins Via Multiple-Quantum Relaxation Violated Coherence Transfer NMR Spectroscopy J. Biomol. NMR 2012, 52, 233-43
37. 1H CSA Values (Δσ) in Proteins from Cross-Correlated Spin Relaxation J. Biomol. NMR 2004, 30, 397-406