Abstract We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni2+-chelated DO2A. In proton-detected 1H-15N SOFAST-HMQC and carbon-detected (H-flip)13CO-15N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line broadening effects. At 40 mmol·Lâ??1 of the PRE agent, we obtain a 1.7- to 1.9-fold larger signal to noise (S/N) for the respective 2D NMR experiments. High solvent accessibility of intrinsically disordered protein (IDP) residues renders this class of proteins particularly amenable to the outlined approach.
Content Type Journal Article
Category Article
Pages 1-9
DOI 10.1007/s10858-011-9577-2
Authors
François-Xavier Theillet, Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle Str. 10, 13125 Berlin, Germany
Andres Binolfi, Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle Str. 10, 13125 Berlin, Germany
Stamatis Liokatis, Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle Str. 10, 13125 Berlin, Germany
Silvia Verzini, Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle Str. 10, 13125 Berlin, Germany
Philipp Selenko, Department of NMR-assisted Structural Biology, In-cell NMR Group, Leibniz Institute of Molecular Pharmacology (FMP), Robert-Roessle Str. 10, 13125 Berlin, Germany
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
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...
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09-26-2011 06:42 AM
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins.
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins.
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins.
J Biol Chem. 2011 Apr 20;
Authors: Iwasa H, Meshitsuka S, Hongo K, Mizobata T, Kawata Y
Co-chaperonin GroES from E. coli works with chaperonin GroEL to mediate the folding reactions of various proteins. However, under specific conditions, i. e., the...
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04-22-2011 02:00 PM
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
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH
Abstract Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970â??2978, 2001). The chemical shifts are...
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01-17-2011 02:40 AM
[Question from NMRWiki Q&A forum] Relaxation editing vr paramagnetic relaxation enhancement experiments - 13C CP-MAS NM
Relaxation editing vr paramagnetic relaxation enhancement experiments - 13C CP-MAS NMR
I am a beginner in NMR spectroscopy and I would like to learn more about relaxation editing experiments vs PRE. A colleague of mine is doing the 13C CP-MAS NMR experim. and he using cellulose II powder, regenerated cellulose and milled reg cellulose. We are interested in C4 resonance of cellulose II, good resolved resonance, to better understand the supramolecular structure of cellulose II. As experiments: long relaxation experiments - PRE with aqueous CuSO4 solution of certain concentration, does the...
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10-15-2010 05:16 PM
[Question from NMRWiki Q&A forum] Does anyone know something about paramagnetic relaxation enhancement (PRE)?
Does anyone know something about paramagnetic relaxation enhancement (PRE)?
Does anyone know something about paramagnetic relaxation enhancement (PRE)? i would like to try this method on my cellulose materials. What info can you take out of it? Thank you very much.
Check if somebody has answered this question on NMRWiki QA forum
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins
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