Narrow peaks and high dimensionalities: Exploiting the advantages of random sampling

Kazimierczuk, Krzysztof; Zawadzka, Anna; Koźmiński, Wiktor

doi:10.1016/j.jmr.2009.01.003

Cited by 76 publications

(97 citation statements)

References 33 publications

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“…Multidimensional Fourier transform with iterative algorithm for artifact suppression (73) was employed to process indirect dimensions in three-dimensional experiments. Indirect dimensions in five-dimensional experiments were processed using the sparse multidimensional Fourier transform (74). Spectral analysis was done using the software Sparky 3.115 (T. D. Goddard and D. G. Kneller, University of California, San Francisco).…”

Section: Nmr Spectroscopymentioning

confidence: 99%

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Jansen

Melková

Trošanová

et al. 2017

Journal of Biological Chemistry

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Edited by Norma AllewellMicrotubule-associated protein 2c (MAP2c) is involved in neuronal development and is less characterized than its homolog Tau, which has various roles in neurodegeneration. Using NMR methods providing single-residue resolution and quantitative comparison, we investigated molecular interactions important for the regulatory roles of MAP2c in microtubule dynamics. We found that MAP2c and Tau significantly differ in the position and kinetics of sites that are phosphorylated by cAMP-dependent protein kinase (PKA), even in highly homologous regions. We determined the binding sites of unphosphorylated and phosphorylated MAP2c responsible for interactions with the regulatory protein 14-3-3 . Differences in phosphorylation and in charge distribution between MAP2c and Tau suggested that both MAP2c and Tau respond to the same signal (phosphorylation by PKA) but have different downstream effects, indicating a signaling branch point for controlling microtubule stability. Although the interactions of phosphorylated Tau with 14-3-3 are supposed to be a major factor in microtubule destabilization, the binding of 14-3-3 to MAP2c enhanced by PKA-mediated phosphorylation is likely to influence microtubule-MAP2c binding much less, in agreement with the results of our tubulin co-sedimentation measurements. The specific location of the major MAP2c phosphorylation site in a region homologous to the muscarinic receptor-binding site of Tau suggests that MAP2c also may regulate processes other than microtubule dynamics.Cytoskeletal microtubule-associated proteins (MAPs) 3 are proteins of critical importance for regulating the stability and dynamics of microtubules (1). MAP2 and Tau represent MAP subfamilies expressed in neurons; MAP2 is localized in dendrites, whereas Tau is found mainly in axons (2). Tau and MAP2 belong to the class of intrinsically disordered proteins (IDPs), which lack a unique structure and which exist in multiple, quickly interconverting conformations (3-7). NMR is the method of choice for structural investigation of this type of protein. Tau and MAP2 differ in their N-terminal projection domains, which contain acidic and proline-rich subdomains, whereas the C-terminal parts, containing the microtubulebinding domain (MTBD) and the C-terminal region, are homologous (8). Tau is expressed in several splice variants. The human brain isoforms differ in the number of microtubulebinding regions (MTBRs) in the C-terminal portion and in the presence of two inserts near the N terminus. For the sake of simplicity, only the 441-residue variant lacking exons 6, 8, and 10 (9) is discussed in this paper. This variant has been studied in detail and was shown to form paired helical filaments and neurofibillary tangles in brains of patients suffering from Alzheimer's disease (10). The MAP2 family is composed of two high-molecular-weight proteins, MAP2a and MAP2b, each consisting of 1830 amino acids, and two low-molecular-weight proteins, MAP2c and MAP2d, consisting of 467 and 498 amino acids, respectively. The ...

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Section: Nmr Spectroscopymentioning

confidence: 99%

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Jansen

Melková

Trošanová

et al. 2017

Journal of Biological Chemistry

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“…The non-uniformly sampled data were processed using Sparse Multidimensional Fourier Transform (SMFT) (Kazimierczuk et al 2009). This method does not recover the full high-dimensional spectrum.…”

Section: Resultsmentioning

confidence: 99%

4D Non-uniformly sampled HCBCACON and 1 J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

et al. 2012

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A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

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“…Exploiting improved instrumental sensitivities substantial improvements were made (Chap. 3) due to: (i) non-uniform sampling technologies enabling high-dimensionality (> 4D) experiments (Kazimierczuk et al 2009), (ii) faster acquisition of NMR experiments making use of longitudinal relaxation enhancements (Schanda et al 2006) and (iii) direct heteronuclei ( 13 C) detection using cryoprobe technology (avoiding exchange problems) (Bermel et al 2012;Bertini et al 2011;Novacek et al 2011). The problems of poor signal dispersion and extensive signal overlap found for IDPs are overcome by high-dimensionality spectra (> 4D) using non-uniform sampling (NUS) of indirect dimensions together with appropriate processing schemes, e.g., Sparse Multidimensional Fourier Transform (SMFT) processing (Kazimierczuk et al 2010a;Kazimierczuk et al 2010b;Motackova et al 2010;Zawadzka-Kazimierczuk et al 2012).…”

Section: Nmr Spectral Assignment Of Idpsmentioning

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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Narrow peaks and high dimensionalities: Exploiting the advantages of random sampling

Cited by 76 publications

References 33 publications

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau

4D Non-uniformly sampled HCBCACON and 1 J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins

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