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.
Content Type Journal Article
DOI 10.1007/s10858-010-9447-3
Authors
Veronika MotáÄ?ková, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, KotláÅ?ská 2, 611 37 Brno, Czech Republic
JiÅ?Ã* NováÄ?ek, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, KotláÅ?ská 2, 611 37 Brno, Czech Republic
Anna Zawadzka-Kazimierczuk, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
Krzysztof Kazimierczuk, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
Lukáš ŽÃ*dek, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, KotláÅ?ská 2, 611 37 Brno, Czech Republic
Hana Å*anderová, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology, Academy of Sciences of the Czech Republic, VÃ*deÅ?ská 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, VÃ*deÅ?ská 1083, 142 20 Prague, Czech Republic
Wiktor KoźmiÅ?ski, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02 093 Warsaw, Poland
VladimÃ*r SklenáÅ?, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, KotláÅ?ská 2, 611 37 Brno, Czech Republic
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
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02-21-2012 03:40 AM
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins
iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 9 November 2011</br>
Sophie*Feuerstein, Michael J.*Plevin, Dieter*Willbold, Bernhard*Brutscher</br>
An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing theH-N correlations into 7 different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard...
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11-10-2011 07:38 AM
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
Bioinformatics. 2011 Mar 3;
Authors: Tamiola K, Mulder FA
SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of...
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03-05-2011 01:02 PM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13C� and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13C� spins offer superior chemical shift dispersion in comparison to 13Cα and 13Cβ spins. However, HN-detected experiments...
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01-29-2011 05:31 AM
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Jie, Wen , Jihui, Wu , Pei, Zhou</br>
Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
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01-05-2011 11:03 AM
A simple strategy for 13C,1H labeling at the Ile-γ2 methyl position in highly deuter
A simple strategy for 13C,1H labeling at the Ile-γ2 methyl position in highly deuterated proteins
Abstract A straightforward approach for the production of highly deuterated proteins labeled with 13C and 1H at Ile-γ2 methyl positions is described. The utility of the methodology is illustrated with an application involving the half proteasome (360 kDa). High quality 2D Ile 13Cγ2,1Hγ2 HMQC data sets, exploiting the methyl-TROSY principle, are recorded with excellent sensitivity and resolution, that compare favorably with Ile 13Cδ1,1Hδ1 spectra. This labeling scheme adds to a growing...
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10-20-2010 06:50 AM
Strategy for complete NMR assignment of disordered proteins with highly repetitive se
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments.
J Biomol NMR. 2010 Oct 2;
Authors: MotáÄ?ková V, NováÄ?ek J, Zawadzka-Kazimierczuk A, Kazimierczuk K, ZÃ*dek L, Sanderová H, Krásný L, KoźmiÅ?ski W, SklenáÅ? V
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly...
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10-05-2010 12:11 PM
HA-detected experiments for the backbone assignment of intrinsically disordered prote
Abstract We propose a new alpha proton detection based approach for the sequential assignment of natively unfolded proteins. The proposed protocol superimposes on following features: HA-detection (1) enables assignment of natively unfolded proteins at any pH, i.e., it is not sensitive to rapid chemical exchange undergoing in natively unfolded proteins even at moderately high pH. (2) It allows straightforward assignment of proline-rich polypeptides without additional proline-customized experiments. (3) It offers more streamlined and less ambiguous assignment based on solely intraresidual...
Strategy for complete NMR assignment of disordered proteins with highly repetitive se
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