Sensitivity Enhancement in 1H -13C HSQC Experiments on Aromatic Groups in Proteins

Abstract

Abstract:

含芳香环的氨基酸残基多处于蛋白质的疏水内核或者是蛋白质与配体的结合部位，这些残基间的非共价键相互作用对于蛋白质结构的稳定性和生物的特异性识
别有重要意义．因此，在蛋白质的核磁共振研究中，芳香基团被认为是一个研究蛋白质结构动力学的潜在探针．但是由于芳香基团的1H-13C HSQC谱的灵敏度较低，目前，利用核磁共振对其进行研究乏善可陈．造成这一现象的主要原因可能在于芳香环体积较大，往往存在慢的翻转运动，导致其NMR信号被展宽．作者利用CPMG-INEPT HSQC序列可以有效地减小慢运动影响的特征，将其应用到了GB1蛋白质芳香环的¹H-¹³CHSQC谱中，有效的增强了芳香基团HSQC谱信号的灵敏度，得到了部分在常规HSQC中无法观测的信号．

Key words: 核磁共振(NMR), CPMG-INEPT, 化学交换, 信号增强, 芳香环侧链

CLC Number:

O482.53

JIANG Xian-wang1,2，SUN Peng1,2，XIAO Nan1,2，JIANG Bin1，QIN Xian-guo1，LI Cong-gang1，LIU Mai-li1*，ZHANG Xu1*.

Sensitivity Enhancement in ¹H -13C HSQC Experiments on Aromatic Groups in Proteins

[J]. Chinese Journal of Magnetic Resonance.

References

[1] Hetzel R, Wuthrich K, Deisenhofer J, et al. Dynamics of aromatic amino-acid residues in globular conformation of basic pancreatic trypsin-inhibitor (Bpti). 2. semiempirical energy calculations[J]. Biophys Struct Mech, 1976, 2(2): 159－180.

[2] Wagner G, Demarco A, Wuthrich K. Dynamics of aromatic amino-acid residues in globular conformation of basic pancreatic trypsin-inhibitor (Bpti). 1. ¹H NMR studies[J]. Biophys Struct Mech, 1976, 2(2): 139－158.

[3] Wuthrich K, Wagner G. Internal motion in globular proteins[J]. Trends Biochem Sci, 1978, 3(10): 227－230.

[4] Wagner G. Characterization of the distribution of internal motions in the basic pancreatic trypsin-inhibitor using a large number of internal NMR probes[J]. Q Rev Biophys, 1983, 16(1): 1－57.

[5] Burley S K, Petsko G A. Aromatic-aromatic interaction - a mechanism of protein-structure stabilization[J]. Science, 1985, 229(4 708): 23－28.

[6] Weiss M A, Karplus M, Sauer R T. 1H NMR aromatic spectrum of the operator binding domain of the lambda-repressor -resonance assignment with application to structure and dynamics[J]. Biochemistry, 1987, 26(3): 890－897.

[7] Weiss M A, Nguyen D T, Khait I, et al. Two-dimensional NMR and photo-cidnp studies of theinsulin monomer -assignment of aromatic resonances with application to protein folding, structure, and dynamics[J]. Biochemistry, 1989, 28(25): 9 855－9 873.

[8] Dougherty D A. Cation-pi interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp[J]. Science, 1996, 271(5 246): 163－168.

[9] Smith B O, Ito Y, Raine A, et al. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types[J]. J Biomol NMR, 1996, 8(3): 360－368.

[10] Ma J C, Dougherty D A. The cation-pi interaction[J]. Chem Rev, 1997, 97(5): 1 303－1 324.

[11] Gallivan J P, Dougherty D A. Cation-pi interactions in structural biology[J]. Proc Nat Acad Sci US, 1999, 96(17): 9 459－9 464.

[12] Crowhurst K A, Forman-Kay J D. Aromatic and methyl NOES highlight hydrophobic clustering in the unfolded state of an SH3 domain[J]. Biochemistry, 2003, 42(29): 8 687－8 695.

[13] Meyer E A, Castellano R K, Diederich F. Interactions with aromatic rings in chemical and biological recognition[J]. Angew Chem Int Ed, 2003, 42(11): 1 210－1 250.

[14] Eletsky A, Atreya H S, Liu G H, et al. Probing structure and functional dynamics of (large) proteins with aromatic rings: L-GFT-TROSY (4,3)D HCCH NMR spectroscopy[J]. J Am Chem Soc, 2005, 127(42): 14 578－14 579.

[15] Teilum K, Brath U, Lundstrom P, et al. Biosynthetic C-13 labeling of aromatic side chains in proteins for NMR relaxation measurements[J]. J Am Chem Soc, 2006, 128(8): 2 506－2 507.

[16] Mok K H, Kuhn L T, Goez M, et al. A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein[J]. Nature, 2007, 447(7 140): 106－109.

[17] Esfandiary R, Hunjan J S, Lushington G H, et al. Temperature dependent 2(nd) derivative absorbance spectroscopy of aromatic amino acids as a probe of protein dynamics[J]. Protein Science, 2009, 18(12): 2 603－2 614.

[18] Wiesler S C, Weinzierl R O, Buck M. An aromatic residue switch in enhancer-dependent bacterial RNA polymerase controls transcription intermediate complex activity[J]. Nucleic Acids Res, 2013, [Epub ahead of print, doi: 10.1093/nar/gkt271].

[19] Williams J K, Zhang Y, Schmidt-Rohr K, et al. pH-dependent conformation, dynamics and aromatic interaction of the gating tryptophan residue of the influenza M2 proton channel from solid state NMR[J]. Biophys J, 2013, 104(8): 1 698－1 708.

[20] Wuthrich K. NMR of Proteins and Nucleic[M]. New York: Acids Wiley, 1986.

[21] Vuister G W, Kim S J, Wu C, et al. 2D and 3D NMR-study of phenylalanine residues in proteins by reverse isotopic labeling[J]. J Am Chem Soc, 1994, 116(20): 9 206－9 210.

[22] Kay L E, Gardner K H. Solution NMR spectroscopy beyond 25 kDa[J]. Curr Opin Struc Biol, 1997, 7(5): 722－731.

[23] Aghazadeh B, Zhu K, Kubiseski T J, et al. Structure and mutagenesis of the Dbl homology domain[J]. Nat Struct Biol, 1998, 5(12): 1 098－1 107.

[24] Gardner K H, Kay L E. The use of H-2, C-13, N-15 multidimensional NMR to study the structure and dynamics of proteins[J]. Annu Rev Bioph Biom, 1998, 27: 357－406.

[25] Clore G M, Starich M R, Bewley C A, et al. Impact of residual dipolar couplings on the accuracy of NMR structures determined from a minimal number of NOE restraints[J]. J Am Chem Soc, 1999, 121(27): 6 513－6 514.

[26] Medek A, Olejniczak E T, Meadows R P, et al. An approach for high-throughput structure determination of proteins by NMR spectroscopy[J]. J Biomol NMR, 2000, 18(3): 229－238.

[27] Ab E, Pugh D J R, Kaptein R, et al. Direct use of unassigned resonances in NMR structure calculations with proxy residues[J]. J Am Chem Soc, 2006, 128(23): 7 566－7 571.

[28] Kainosho M, Torizawa T, Iwashita Y, et al. Optimal isotope labelling for NMR protein structure determinations[J]. Nature, 2006, 440(7 080): 52－57.

[29] Yamazaki T, Formankay J D, Kay L E. 2-Dimensional NMR experiments for correlating C-13-beta and H-1-delta/epsilon chemical-shifts of aromatic residues in C-13-labeled proteins via scalar couplings[J]. J Am Chem Soc, 1993, 115(23): 11 054－11 055.

[30] Grzesiek S, Bax A. Audio-frequency NMR in a nutating frame - application to the assignment of phenylalanine residues in isotopically enriched proteins[J]. J Am Chem Soc, 1995, 117(24): 6 527－6 531.

[31] Simorre J P, Zimmermann G R, Pardi A, et al. Triple resonance HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine and uridine base protons in RNA[J]. J Biomol NMR, 1995, 6(4): 427－432.

[32] Carlomagno T, Maurer M, Sattler M, et al. PLUSH TACSY: Homonuclear planar TACSY with two-band selective shaped pulses applied to C-alpha,C' transfer and C-beta, C-aromatic correlations[J]. J Biomol NMR, 1996, 8(2): 161－170.

[33] Zerbe O, Szyperski T, Ottiger M, et al. Three-dimensional H-1-TOCSY-relayed ct- C-13, H-1 - HMQC for aromatic spin system identification in uniformly C-13-labeled proteins[J]. J Biomol NMR, 1996, 7(2): 99－106.

[34] Whitehead B, Tessari M, Dux P, et al. A N-15-filtered 2D H-1 TOCSY experiment for assignment of aromatic ring resonances and selective identification of tyrosine ring resonances in proteins: Description and application to photoactive yellow protein[J]. J Biomol NMR, 1997, 9(3): 313－316.

[35] Prompers J J, Groenewegen A, Hilbers C W, et al. Two-dimensional NMR experiments for the assignment of aromatic side chains in C-13-labeled proteins[J]. J Magn Reson, 1998, 130(1): 68－75.

[36] Slupsky C M, Gentile L N, McIntosh L P. Assigning the NMR spectra of aromatic amino acids in proteins: analysis of two Ets pointed domains[J]. Biochem Cell Biol, 1998, 76(2-3): 379－390.

[37] Sattler M, Schleucher J, Griesinger C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients[J]. Prog Nucl Mag Res Sp, 1999, 34(2): 93－158.

[38] Lohr F, Katsemi V, Betz M, et al. Sequence-specific assignment of histidine and tryptophan ring H-1, C-13 and N-15 resonances in C-13/N-15- and H-2/C-13/N-15-labelled proteins[J]. J Biomol NMR, 2002, 22(2): 153－164.

[39] Lohr F, Rogov V V, Shi M C, et al. Triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues[J]. J Biomol NMR, 2005, 32(4): 309－328.

[40] Lohr F, Hansel R, Rogov V V, et al. Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins[J]. J Biomol NMR, 2007, 37(3): 205－224.

[41] Rajesh S, Nietlispach D, Nakayama H, et al. A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp[J]. J Biomol NMR, 2003, 27(1): 81－86.

[42] Schlorb C, Ackermann K, Richter C, et al. Heterologous expression of hen egg white lysozyme and resonance assignment of tryptophan side chains in its non-native states[J]. J Biomol NMR, 2005, 33(2): 95－104.

[43] Ohki S Y, Kainosho M. Stable isotope labeling methods for protein NMR spectroscopy[J]. Prog Nucl Mag Res Sp, 2008, 53(4): 208－226.

[44] Ikeya T, Takeda M, Yoshida H, et al. Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system[J]. J Biomol NMR, 2009, 44(4): 261－272.

[45] Takeda M, Ono A M, Terauchi T, et al. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination[J]. J Biomol NMR, 2010, 46(1): 45－49.

[46] Skalicky J J, Mills J L, Sharma S, et al. Aromatic ring-flipping in supercooled water: Implications for NMR-based structural biology of proteins[J]. J Am Chem Soc, 2001, 123(3): 388－397.

[47] Mills J L, Szyperski T. Protein dynamics in supercooled water: The search for slow motional modes[J]. J Biomol NMR, 2002, 23(1): 63－67.

[48] Seifert M H, Ksiazek D, Azim M K, et al. Slow exchange in the chromophore of a green fluorescent protein variant[J]. J Am Chem Soc, 2002, 124(27): 7 932－7 942.

[49] Rao D K, Bhuyan A K. Complexity of aromatic ring-flip motions in proteins: Y97 ring dynamics in cytochrome cobserved by cross-relaxation suppressed exchange NMR spectroscopy[J]. J Biomol NMR, 2007, 39(3): 187－196.

[50] Boyer J A, Lee A L. Monitoring aromatic picosecond to nanosecond dynamics in proteins via C-13 relaxation: Expanding perturbation mapping of the rigidifying core mutation, V54A, in Eglin C[J]. Biochemistry, 2008, 47(17): 4 876－4 886.

[51] Boyer J A, Clay C J, Luce K S, et al. Detection of native-state nonadditivity in double mutant cycles via hydrogen exchange[J]. J Am Chem Soc, 2010, 132(23): 8 010－8 019.

[52] Zhuravleva A, Orekhov V Y. Divided evolution: A scheme for suppression of line broadening induced by conformational exchange[J]. J Am Chem Soc, 2008, 130(11): 3 260－3 261.

[53] Henzler-Wildman K, Kern D. Dynamic personalities of proteins[J]. Nature, 2007, 450(7 172): 964－972.

[54] Henzler-Wildman K A, Lei M, Thai V, et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis[J]. Nature, 2007, 450(7 171): 913－927.

[55] Baldwin A J, Kay L E. NMR spectroscopy brings invisible protein states into focus[J]. Nat Chem Biol, 2009, 5(11): 808－814.

[56] Mittermaier A K, Kay L E. Observing biological dynamics at atomic resolution using NMR[J]. Trends Biochem Sci, 2009, 34(12): 601－611.

[57] Bernado P, Blackledge M. Structural biology proteins in dynamic equilibrium[J]. Nature, 2010, 468(7 327): 1 046－1 048.

[58] Villali J, Kern D. Choreographing an enzyme's dance[J]. Curr Opin Chem Biol, 2010, 14(5): 636－643.

[59] Eisenmesser E Z, Millet O, Labeikovsky W, et al. Intrinsic dynamics of an enzyme underlies catalysis[J]. Nature, 2005, 438(7 064): 117－121.

[60] Korzhnev D M, Salvatella X, Vendruscolo M, et al. Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR[J]. Nature, 2004, 430(6 999): 586－590.

[61] Luz Z, Meiboom S. Nuclear Magnetic Resonance study of protolysis of trimethylammonium Ion in aqueous solution -order of reaction with respect to solvent[J]. J Chem Phys, 1963, 39(2): 366－370.

[62] Allerhand A, Gutowsky H S. Spin-echo NMR studies of chemical exchange .1. some general aspects[J]. J Chem Phys, 1964, 41(7): 2 115－2 126.

[63] Krishnan V V, Rance M. Influence of chemical-exchange among homonuclear spins in heteronuclear coherence-transfer experiments in liquids[J]. J Magn Reson Ser A, 1995, 116(1): 97－106.

[64] Li Y, Palmer A G, 3rd. Narrowing of protein NMR spectral lines broadened by chemical exchange[J]. J Am Chem Soc, 2010, 132(26): 8 856－8 857.

[65] Gullion T, Baker D B, Conradi M S. New, compensated Carr-Purcell sequences[J]. J Magn Reson, 1990, 89(3): 479－484.

[66] Ellett J D, Waugh J S. Chemical-shift concertina[J]. J Chem Phys, 1969, 51(7): 2 851.

[67] Mueller L, Legault P, Pardi A. Improved RNA structure determination by detection of NOE contacts to exchangebroadended amino protons[J]. J Am Chem Soc, 1995, 117(45): 11 043－11 048.

[68] Mulder F A A, Spronk C, Slijper M, et al. Improved HSQC experiments for the observation of exchange broadened signals[J]. J Biomol NMR, 1996, 8(2): 223－228.

[69] Davis A L, Keeler J, Laue E D, et al. Experiments for recording pure-sbsorption heteronuclear correlation spectra using pulsed field gradients[J]. J Magn Reson, 1992, 98(1): 207－216.

[70] Muhandiram D R, Farrow N A, Xu G Y, et al. A gradient C-13 NOESY-HSQC experiment for recording NOESY spectra of C-13-labeled proteins dissolved in H2O[J]. J Magn Reson Ser B, 1993, 102(3): 317－321.

[71] Kay L E, Xu G Y, Singer A U, et al. A gradient-enhanced HCCH TOCSY experiment for recording side-chain H-1 and C-13 correlations in H2O samples of proteins[J]. J Magn Reson Ser B, 1993, 101(3): 333－337.

[72] Delaglio F, Grzesiek S, Vuister G W, et al. Nmrpipe - a multidimensional spectral processing system based on Unix Pipes[J]. J Biomol NMR, 1995, 6(3): 277－293.

[73] Johnson B A, Blevins R A. NMR view - a computer-program for the visualization and analysis of NMR data[J]. J Biomol NMR, 1994, 4(5): 603－614.

[74] Gronenborn A M, Filpula D R, Essig N Z, et al. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein-G[J]. Science, 1991, 253(5020): 657－661.

Sensitivity Enhancement in ¹H -13C HSQC Experiments on Aromatic Groups in Proteins

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