Abstract Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of 13C and 1H chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their 13C chemical shifts with that of the neighboring, directly attached, 13C nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D 1H-TOCSY-HCCH and (c) (4,3)D 13C-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.
Content Type Journal Article
DOI 10.1007/s10858-010-9444-6
Authors
Garima Jaipuria, NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
Anushikha Thakur, NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
Patrick Dâ??Silva, Department of Biochemistry, Indian Institute of Science, Bangalore, 560012 India
Hanudatta S. Atreya, NMR Research Centre, Indian Institute of Science, Bangalore, 560012 India
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
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins
Abstract Well-resolved 2Hâ??13C correlation spectra, reminiscent of 1Hâ??13C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of 2H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T 1, allowing for high repetition rates and enabling 3D experiments with a 2Hâ??13C transfer step in a reasonable time....
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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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[NMR paper] Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-
Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins.
Related Articles Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins.
J Am Chem Soc. 2004 Aug 11;126(31):9584-91
Authors: Van Melckebeke H, Simorre JP, Brutscher B
New NMR experiments are presented for the measurement of methyl-methyl distances in (13)C-labeled proteins from a series of amino acid-type separated 2D or 3D NOESY spectra. Hadamard amino acid-type encoding of the proximal methyl...
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11-24-2010 10:01 PM
[NMR paper] NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypep
NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: application to the human prion protein hPrP(23-230).
Related Articles NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: application to the human prion protein hPrP(23-230).
J Biomol NMR. 2000 Feb;16(2):127-38
Authors: Liu A, Riek R, Wider G, von Schroetter C, Zahn R, Wüthrich K
A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15N,...
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11-18-2010 09:15 PM
High-resolution methyl edited GFT NMR experiments for protein resonance assignments a
High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination.
Related Articles High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination.
J Biomol NMR. 2010 Sep 14;
Authors: Jaipuria G, Thakur A, D'Silva P, Atreya HS
Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile,...
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09-15-2010 02:26 PM
[NMR paper] High resolution 2D-NMR studies indicating complete assignments and conformational cha
High resolution 2D-NMR studies indicating complete assignments and conformational characteristics of the NF-kappa B binding enhancer element of HIV-LTR.
Related Articles High resolution 2D-NMR studies indicating complete assignments and conformational characteristics of the NF-kappa B binding enhancer element of HIV-LTR.
J Biomol Struct Dyn. 1995 Oct;13(2):269-84
Authors: Singh MP, Fregeau NL, Pon RT, Lown JW
The asymmetrical DNA duplex . has been studied by one- and two-dimensional NMR techniques. The sequence is comprised of the actual 10...
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High Resolution 1H Detected 1H,13C Correlation Spectra in MAS Solid-State NMR using Deuterated Proteins with Selective 1H,2H Isotopic Labeling of Methyl Groups
High Resolution <SUP>1</SUP>H Detected <SUP>1</SUP>H,<SUP>13</SUP>C Correlation Spectra in MAS Solid-State NMR using Deuterated Proteins with Selective <SUP>1</SUP>H,<SUP>2</SUP>H Isotopic Labeling of Methyl Groups
Vipin Agarwal, Anne Diehl, Nikolai Skrynnikov, and Bernd Reif
J. Am. Chem. Soc.; 2006; 128(39) pp 12620 - 12621;
Abstract:
MAS solid-state NMR experiments applied to biological solids are still hampered by low sensitivity and resolution. In this work, we employ a deuteration scheme in which individual methyl groups are selectively protonated. This labeling scheme...
High-resolution methyl edited GFT NMR experiments for protein resonance assignments a
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