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

J 2013

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

NOVÁČEK, Jiří, Lubomír JANDA, Radka DOPITOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ et. al.

Basic information

Original name

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

Authors

NOVÁČEK, Jiří (203 Czech Republic, belonging to the institution), Lubomír JANDA (203 Czech Republic, belonging to the institution), Radka DOPITOVÁ (203 Czech Republic, belonging to the institution), Lukáš ŽÍDEK (203 Czech Republic, guarantor, belonging to the institution) and Vladimír SKLENÁŘ (203 Czech Republic, belonging to the institution)

Edition

Journal of Biomolecular NMR, Dordrecht, Springer, 2013, 0925-2738

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.305

RIV identification code

RIV/00216224:14740/13:00066377

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1007/s10858-013-9761-7

UT WoS

000323661800001

Keywords in English

Nuclear magnetic resonance; Intrinsically disordered proteins; Microtubule-associated protein; Transient secondary structure; C-13 detection

Abstract

V originále

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 C-13-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek 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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GAP206/11/0758, research and development project

Name: Vývoj metodologie s vysokým rozlišením pro NMR studie neuspořádaných proteinů s vysoce degenerovanými rezonančními frekvencemi (Acronym: HIGHRES)

Investor: Czech Science Foundation

261863, interní kód MU

Name: BioNMR Facilities - Bio NMR (Acronym: BioNMR)

Investor: European Union, Capacities

Citovat

NOVÁČEK, Jiří, Lubomír JANDA, Radka DOPITOVÁ, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. 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. Dordrecht: Springer, 2013, vol. 56, No 4, p. 291-301. ISSN 0925-2738. Available from: https://dx.doi.org/10.1007/s10858-013-9761-7.

@article{1123258,
   author = {Nováček, Jiří and Janda, Lubomír and Dopitová, Radka and Žídek, Lukáš and Sklenář, Vladimír},
   article_location = {Dordrecht},
   article_number = {4},
   doi = {http://dx.doi.org/10.1007/s10858-013-9761-7},
   keywords = {Nuclear magnetic resonance; Intrinsically disordered proteins; Microtubule-associated protein; Transient secondary structure; C-13 detection},
   language = {eng},
   issn = {0925-2738},
   journal = {Journal of Biomolecular NMR},
   title = {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},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23877929},
   volume = {56},
   year = {2013}
}

TY  - JOUR
ID  - 1123258
AU  - Nováček, Jiří - Janda, Lubomír - Dopitová, Radka - Žídek, Lukáš - Sklenář, Vladimír
PY  - 2013
TI  - 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
JF  - Journal of Biomolecular NMR
VL  - 56
IS  - 4
SP  - 291-301
EP  - 291-301
PB  - Springer
SN  - 09252738
KW  - Nuclear magnetic resonance
KW  - Intrinsically disordered proteins
KW  - Microtubule-associated protein
KW  - Transient secondary structure
KW  - C-13 detection
UR  - http://www.ncbi.nlm.nih.gov/pubmed/23877929
L2  - http://www.ncbi.nlm.nih.gov/pubmed/23877929
N2  - 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 C-13-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek 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.
ER  -

NOVÁČEK, Jiří, Lubomír JANDA, Radka DOPITOVÁ, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. 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. \textit{Journal of Biomolecular NMR}. Dordrecht: Springer, 2013, vol.~56, No~4, p.~291-301. ISSN~0925-2738. Available from: https://dx.doi.org/10.1007/s10858-013-9761-7.

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