Study of protein dynamics in solution by measurement of 13C?-13CO NOE and 13CO longitudinal relaxation

Zeng, Lei; Fischer, Mark W. F.; Zuiderweg, Erik R. P.

doi:10.1007/bf00203826

Cited by 48 publications

(36 citation statements)

References 26 publications

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“…Furthermore, C a detection is expected to be better than the detection of CO at high fields, as CO relaxation is dominated by the chemical-shift anisotropy (CSA) interaction that increases with the square of the magnetic field. [29,30] The detailed pulse sequence is reported in the Supporting Information. Figure 2 b shows that the DIPAP building block is quite effective.…”

mentioning

confidence: 99%

Complete Assignment of Heteronuclear Protein Resonances by Protonless NMR Spectroscopy

Bermel¹,

Bertini²,

Duma³

et al. 2005

Angew Chem Int Ed

171

224

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The complete assignment of the resonances of a protein is key to the determination of its solution structure by NMR spectroscopy and for the study of protein-protein and protein-ligand interactions. The proton-based assignment strategy usually starts with the correlation of individual resonances of each amino acid residue through scalar connectivities followed by linking them one after the other. [1,2] Although many different triple-resonance NMR spectroscopy experiments have been designed for full assignments, [2] spectral overlap can still lead to ambiguities. This poses a significant limiting factor in the cases of large and/or paramagnetic biomolecules. [3] After the pioneering report of 13 C NMR spin-system assignments of 13 C-enriched Anabaena 7120 ferredoxin by Markley and co-workers, [4] heteronuclear NMR spectroscopy experiments were progressively abandoned in favor of 1 Hdetection experiments. However, as was recently pointed out, heteronuclear NMR spectroscopy decreases the effect of detrimental transverse relaxation, which is typical of large or paramagnetic proteins. [5][6][7][8][9][10][11][12][13][14][15][16][17] For this reason, several heteronuclear NMR spectroscopy experiments for backbone assignment have been proposed for fully 13 C-and 15 N-enriched proteins. [13,14,17] Furthermore, backbone sequence-specific assignment by the recently-designed CANCO experiment has also been reported. [18] We present herein an extension of the set of exclusively heteronuclear experiments to protein side chain resonances for the complete heteronuclear assignment of a protein. With a novel CBCACO experiment the carbonyl carbon (CO) is linked to the C b and to the C a nuclei; the connection to the rest of the amino acid side chain is achieved through a 13 C-13 C TOCSY experiment with C a detection. In these experiments, we have successfully implemented spin-state selection methods for the removal of signal splitting in the acquisition dimension which is caused by multiple 13 C-13 C scalar couplings. This makes 13 C detection an amenable tool for high-resolution NMR spectroscopy. The proposed assignment strategy is summarized in Figure 1. A Figure 1. Illustration of the assignment procedure for 13 C NMR spectroscopy experiments. The assignment starts with analysis of the CACO experiment, which provides the correlation between the carbonyl carbon (CO) and the C a nuclei of each amino acid. The spin-system assignment is extended to the C b nuclei with the CBCACO experiment, and the process is completed with the TOCSY experiment, which provides correlation between the C a and the other carbon nuclei of the amino acid side chain. The amino acid spin systems are finally assigned in a sequence-specific manner with the aid of a CANCO experiment, [18] which provides the correlation of each CO to the two neighboring C a nuclei.

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mentioning

confidence: 99%

Complete Assignment of Heteronuclear Protein Resonances by Protonless NMR Spectroscopy

Bermel¹,

Bertini²,

Duma³

et al. 2005

Angew Chem Int Ed

171

224

View full text Add to dashboard Cite

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“…Other less commonly used nuclei are 13 C′ and/or 13 C α . (Chang and Tjandra 2005;Pang et al 2002;Wang et al 2005;Wang et al 2006;Zeng et al 1996) However the accurate measurement and interpretation of 13 C relaxation is more complicated. A less commonly known approach uses the interference effects of cross-correlated relaxation mechanisms, which have been utilized to great advantage in TROSY (Pervushin et al 1997;Riek et al 1999;Salzmann et al 1998) and Methyl-TROSY methodology (Tugarinov et al 2003;Kay 2004a, 2004b;Tugarinov et al 2004) for the study of large molecular weight systems.…”

Section: Cross-correlated Relaxation (Ccr) To Define Backbone Conformmentioning

confidence: 99%

NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins

Kurzbach

Kontaxis

Coudevylle

et al. 2015

Advances in Experimental Medicine and Biology

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Intrinsically disordered proteins (IDPs) are characterized by substantial conformational flexibility and thus not amenable to conventional structural biology techniques. Given their inherent structural flexibility NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This chapter will summarize key advances in NMR methodology. Despite the availability of efficient (multi-dimensional) NMR experiments for signal assignment of IDPs it is discussed that NMR of larger and more complex IDPs demands spectral simplification strategies capitalizing on specific isotope-labeling strategies. Prototypical applications of isotope labeling-strategies are described. Since IDP-ligand association and dissociation processes frequently occur on time scales that are amenable to NMR spectroscopy we describe in detail the application of CPMG relaxation dispersion techniques to studies of IDP protein binding. Finally, we demonstrate that the complementary usage of NMR and EPR data provide a more comprehensive picture about the conformational states of IDPs and can be employed to analyze the conformational ensembles of IDPs.

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“…These two methods can also be implemented for the measurement of 13Ca-~3CO crossrelaxation rates. In an accompanying paper, Zeng et al (1996) determine the 13Ca-13CO steady-state NOE and convert it into cross-relaxation rates using an independent measure of the ~3CO longitudinal relaxation (T]). In this communication, we present a method for direct measurement of the ~3Ca-~3CO cross-relaxation rate as the initial slope of a buildup curve.…”

Section: Waltz16mentioning

confidence: 99%

Measurement of 13C?-13CO cross-relaxation rates in 15N-/13C-labelled proteins

1996

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Internal motions play an important role in the biological function of proteins and NMR relaxation studies may characterize them over a wide range of frequencies. An experimental pulse scheme is proposed for the measurement of the (13)CO-(13)C(α) cross-relaxation rate. For sensitivity reasons, this measurement is performed in an indirect manner through several coherence transfer steps, which should thus be calibrated independently. Contributions of other relaxation pathways can be eliminated by the determination of the initial slope of the buildup curve. The cross-relaxation rates have been determined on a (15)N-/(13)C-labelled 116-residue protein and the significant variations along the sequence have been interpreted as evidence of an increased amount of fast local motion.

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Study of protein dynamics in solution by measurement of 13C?-13CO NOE and 13CO longitudinal relaxation

Cited by 48 publications

References 26 publications

Complete Assignment of Heteronuclear Protein Resonances by Protonless NMR Spectroscopy

Complete Assignment of Heteronuclear Protein Resonances by Protonless NMR Spectroscopy

NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins

Measurement of 13C?-13CO cross-relaxation rates in 15N-/13C-labelled proteins

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