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Nováček J, Janda L, Dopitová R, Žídek L, Sklenář V. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. JOURNAL OF BIOMOLECULAR NMR 2013; 56:291-301. [PMID: 23877929 DOI: 10.1007/s10858-013-9761-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/07/2013] [Indexed: 05/21/2023]
Abstract
Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional (13)C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Nováček et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Nováček J, Haba NY, Chill JH, Zídek L, Sklenář V. 4D non-uniformly sampled HCBCACON and ¹J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 53:139-48. [PMID: 22580891 DOI: 10.1007/s10858-012-9631-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/11/2012] [Indexed: 05/23/2023]
Abstract
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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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Zídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V. 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. JOURNAL OF BIOMOLECULAR NMR 2011; 50:1-11. [PMID: 21424579 DOI: 10.1007/s10858-011-9496-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 02/28/2011] [Indexed: 05/21/2023]
Abstract
Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of (13)C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum.
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Affiliation(s)
- Jiří Nováček
- Faculty of Science, NCBR, and CEITEC, Masaryk University, Brno, Czech Republic
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Motáčková V, Nováček J, Zawadzka-Kazimierczuk A, Kazimierczuk K, Žídek L, Šanderová H, Krásný L, Koźmiński W, Sklenář V. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. JOURNAL OF BIOMOLECULAR NMR 2010; 48:169-77. [PMID: 20890634 PMCID: PMC2966349 DOI: 10.1007/s10858-010-9447-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/01/2010] [Indexed: 05/11/2023]
Abstract
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.
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Affiliation(s)
- Veronika Motáčková
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jiří Nováček
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | | | - Lukáš Žídek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Šanderová
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Libor Krásný
- Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
| | - Vladimír Sklenář
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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