A simple method for measuring signs of 1HN chemical shift differences between ground and excited protein states

Journal of Biomolecular NMR

Volumn 47, Issue 2, 2010, Pages 135-141

  Bouvignies, Guillaume ^a   Korzhnev, Dmitry M ^a   Neudecker, Philipp ^a   Hansen, D Flemming ^a   Cordes, Matthew H J ^b   Kay, Lewis E ^a  

^a UNIVERSITY OF TORONTO   (Canada)

^b University of Arizona   (United States)

Author keywords

Chemical exchange; Chemical shifts; Excited states; HMQC; HSQC

Indexed keywords

HYDROGEN;

ARTICLE; COMPARATIVE STUDY; DISPERSION; MAGNETIC FIELD; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTON NUCLEAR MAGNETIC RESONANCE; SPECTROSCOPY; STRUCTURE ANALYSIS; THERMODYNAMICS; TIME;

KINETICS; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; PROTONS; THERMODYNAMICS;

EID: 77954689925     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9418-8     Document Type: Article

References (41)

1. Anet FAL, Basus VJ (1978) Limiting equations for exchange broadening in two-site NMR systems with very unequal populations. J Magn Reson 32:339-343
2. Auer R, Hansen DF, Neudecker P, Korzhnev DM, Muhandiram DR, Konrat R, Kay LE (2009a) Measurement of signs of chemical shift differences between ground and excited protein states: a comparison between H(S/M)QC and R (1rho) methods. J Biomol NMR 46:205-216
3. Auer R, Neudecker P, Muhandiram DR, Lundstrom P, Hansen DF, Konrat R, Kay LE (2009b) Measuring the signs of 1H(alpha) chemical shift differences between ground and excited protein states by off-resonance spin-lock R(1rho) NMR spectroscopy. J Am Chem Soc 131:10832-10833
4. Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638-1642
5. Carr HY, Purcell EM (1954) Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys Rev 94:630-638
6. Frederick KK, Marlow MS, Valentine KG, Wand AJ (2007) Conformational entropy in molecular recognition by proteins. Nature 448:325-329
7. Hansen DF, Vallurupalli P, Lundstrom P, Neudecker P, Kay LE (2008) Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do? J Am Chem Soc 130:2667-2675
8. Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450:964-972
9. Igumenova TI, Brath U, Akke M, Palmer AG 3rd (2007) Characterization of chemical exchange using residual dipolar coupling. J Am Chem Soc 129:13396-13397
10. Ishima R, Torchia DA (2003) Extending the range of amide proton relaxation dispersion experiments in proteins using a constanttime relaxation-compensated CPMG approach. J Biomol NMR 25:243-248
11. Ishima R, Baber J, Louis JM, Torchia DA (2004) Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network. J Biomol NMR 29:187-198
12. Karplus M, Kuriyan J (2005) Molecular dynamics and protein function. Proc Natl Acad Sci USA 102:6679-6685
13. Korzhnev DM, Orekhov VY, Dahlquist FW, Kay LE (2003) Offresonance R1rho relaxation outside of the fast exchange limit: an experimental study of a cavity mutant of T4 lysozyme. J Biomol NMR 26:39-48
14. Korzhnev DM, Salvatella X, Vendruscolo M, Di Nardo AA, Davidson AR, Dobson CM, Kay LE (2004) Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature 430:586-590
15. Korzhnev DM, Neudecker P, Mittermaier A, Orekhov VY, Kay LE (2005a) Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutant. J Am Chem Soc 127:15602-15611 (Pubitemid 41572534)
16. Korzhnev DM, Orekhov VY, Kay LE (2005b) Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spinlock fields: an application to a Fyn SH3 domain. J Am Chem Soc 127:713-721
17. Korzhnev DM, Religa TL, Lundström P, Fersht AR, Kay LE (2007) The folding pathway of an FF domain: characterization of an onpathway intermediate state under folding conditions by (15)N, (13)C(alpha) and (13)C-methyl relaxation dispersion and (1)H/ (2)H-exchange NMR spectroscopy. J Mol Biol 372:497-512
18. LeFevre KR, Cordes MH (2003) Retroevolution of lambda Cro toward a stable monomer. Proc Natl Acad Sci U S A 100:2345-2350
19. Loria JP, Rance M, Palmer AG (1999) A relaxation compensated CPMG sequence for characterizing chemical exchange. J Am Chem Soc 121:2331-2332
20. Lundstrom P, Vallurupalli P, Religa TL, Dahlquist FW, Kay LE (2007) A single-quantum methyl C-13-relaxation dispersion experiment with improved sensitivity. J Biomol NMR 38:79-88
21. Lundstrom P, Hansen DF, Kay LE (2008) Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: comparison between uniformly and selectively (13)C labeled samples. J Biomol NMR 42:35-47
22. Lundstrom P, Hansen DF, Vallurupalli P, Kay LE (2009a) Accurate measurement of alpha proton chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy. J Am Chem Soc 131:1915-1926
23. Lundstrom P, Lin H, Kay LE (2009b) Measuring 13Cbeta chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy. J Biomol NMR 44:139-155
24. Massi F, Johnson E, Wang C, Rance M, Palmer AG 3rd (2004) NMR R1 rho rotating-frame relaxation with weak radio frequency fields. J Am Chem Soc 126:2247-2256
25. McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430-431
26. Meiboom S, Gill D (1958) Modified spin-echo method for measuring nuclear relaxation times. Rev Sci Instrum 29:688-691
27. Neudecker P, Zarrine-Afsar A, Choy W-Y, Muhandiram DR, Davidson AR, Kay LE (2006) Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy. J Mol Biol 363:958-976
28. Orekhov VY, Korzhnev DM, Kay LE (2004) Double- and zeroquantum NMR relaxation dispersion experiments sampling millisecond time scale dynamics in proteins. J Am Chem Soc 126:1886-1891
29. Palmer AG, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 339:204-238
30. Popovych N, Sun S, Ebright RH, Kalodimos CG (2006) Dynamically driven protein allostery. Nat Struct Mol Biol 13:831-838
31. Press W, Teukolsky S, Vetterling W, Flannery B (2007) Numerical recipes 3rd edition: the art of scientific computing. Cambridge University Press, New-York, NY
32. Roessler CG, Hall BM, Anderson WJ, Ingram WM, Roberts SA, Montfort WR, Cordes MH (2008) Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proc Natl Acad Sci U S A 105:2343-2348
33. Skrynnikov NR, Mulder FAA, Hon B, Dahlquist FW, Kay LE (2001) Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 123:4556-4566 (Pubitemid 32923384)
34. Skrynnikov NR, Dahlquist FW, Kay LE (2002) Reconstructing NMR spectra of ''invisible'' excited protein states using HSQC and HMQC experiments. J Am Chem Soc 124:12352-12360
35. Sugase K, Dyson HJ, Wright PE (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021-1025
36. Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) Using dipolar 1H-15 N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct Biol 4:732-738
37. Tollinger M, Skrynnikov NR, Mulder FAA, Forman-Kay JD, Kay LE (2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123:11341-11352
38. Trott O, Palmer AG (2002) R-1 rho relaxation outside of the fastexchange limit. J Magn Reson 154:157-160
39. Vallurupalli P, Hansen DF, Stollar E, Meirovitch E, Kay LE (2007) Measurement of bond vector orientations in invisible excited states of proteins. Proc Natl Acad Sci USA 104: 18473-18477
40. Vallurupalli P, Hansen DF, Kay LE (2008) Probing structure in invisible protein states with anisotropic NMR chemical shifts. J Am Chem Soc 130:2734-2735
41. Wishart DS, Bigam CG, Holm A, Hodges RS, Sykes BD (1995) 1H, 13C and 15 N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 5:67-81