Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results.
[NMR paper] An Approach to NMR Assignment of Intrinsically Disordered Proteins.
An Approach to NMR Assignment of Intrinsically Disordered Proteins.
An Approach to NMR Assignment of Intrinsically Disordered Proteins.
Chemphyschem. 2015 Jan 30;
Authors: Goradia N, Wiedemann C, Herbst C, Görlach M, Heinemann SH, Ohlenschläger O, Ramachandran R
Abstract
An efficient approach to NMR assignments in intrinsically disordered proteins is presented, making use of the good dispersion of cross peaks observed in - and -correlation spectra. The method involves the simultaneous collection of {3D (H)NCO(CAN)H and 3D...
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02-03-2015 12:16 PM
â??CON-CONâ?? assignment strategy for highly flexible intrinsically disordered proteins
â??CON-CONâ?? assignment strategy for highly flexible intrinsically disordered proteins
Abstract
Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the...
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10-21-2014 11:31 PM
New 13C-detected experiments for the assignment of intrinsically disordered proteins
New 13C-detected experiments for the assignment of intrinsically disordered proteins
Abstract
NMR assignment of intrinsically disordered proteins (IDPs) by conventional HN-detected methods is hampered by the small dispersion of the amide protons chemical shifts and exchange broadening of amide proton signals. Therefore several alternative assignment strategies have been proposed in the last years. Attempting to seize that dispersion of 13Câ?˛ and 15N chemical shifts holds even in IDPs, we recently proposed two 13C-detected experiments to directly...
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06-19-2014 10:21 PM
[NMR paper] High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
Related Articles High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins.
J Biomol NMR. 2013 Nov 8;
Authors: Bermel W, Felli IC, Gonnelli L, Ko?mi?ski W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A
Abstract
We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and...
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11-11-2013 01:30 AM
An assignment of intrinsically disordered regions of proteins based on NMR structures
An assignment of intrinsically disordered regions of proteins based on NMR structures
January 2013
Publication year: 2013
Source:Journal of Structural Biology, Volume 181, Issue 1</br>
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Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as...
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02-03-2013 10:13 AM
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
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...
Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins
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