Publication date: December 2014 Source:Journal of Magnetic Resonance, Volume 249
Author(s): Elena Schmidt , Teppei Ikeya , Mitsuhiro Takeda , Frank Löhr , Lena Buchner , Yutaka Ito , Masatsune Kainosho , Peter Güntert
The automated chemical shift assignment algorithm FLYA has been extended for use with stereo-array isotope labeled (SAIL) proteins to determine the sequence-specific resonance assignments of large proteins. Here we present the assignment of the backbone and sidechain chemical shifts of the 21kDa thioldisulfide oxidoreductase DsbA from Escherichia coli that were determined with the SAIL-FLYA algorithm in conjunction with automated peak picking. No manual corrections of peak lists or assignments were applied. The assignments agreed with manually determined reference assignments in 95.4% of the cases if 16 input spectra were used, 94.1% if only 3D 13C/15N-resolved NOESY, CBCA(CO)NH, and 2D [13C/15N,1H]-HSQC were used, and 86.8% if exclusively 3D 13C/15N-resolved NOESY spectra were used. Considering only the assignments that are classified as reliable by the SAIL-FLYA algorithm, the degrees of agreement increased to 97.5%, 96.5%, and 94.2%, respectively. With our approach it is thus possible to automatically obtain almost complete and correct assignments of proteins larger than 20kDa. Graphical abstract
Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10
Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10
Abstract
A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly -labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3Â*mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila ...
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[NMR paper] Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.
Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.
Related Articles Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.
J Biomol NMR. 2013 May 21;
Authors: Schmidt E, Gath J, Habenstein B, Ravotti F, Székely K, Huber M, Buchner L, Böckmann A, Meier BH, Güntert P
Abstract
Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very...
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05-22-2013 04:43 PM
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
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
J Comput Biol. 2011 Mar;18(3):347-63
Authors: Jang R, Gao X, Li M
Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...
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03-10-2011 03:51 PM
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation.
J Bioinform Comput Biol. 2011 Feb;9(1):15-41
Authors: Alipanahi B, Gao X, Karakoc E, Li SC, Balbach F, Feng G, Donaldson L, Li M
Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable...
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02-18-2011 08:07 PM
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
J Am Chem Soc. 2010 Dec 16;
Authors: Gossert AD, Hiller S, Ferna?ndez C
The detection and structural characterization of protein-ligand interactions by solution NMR is central to functional biology research as well as to drug discovery. Here we present a robust and highly automated procedure for obtaining the resonance assignments necessary for studies of such...
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12-18-2010 12:00 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain
Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77
Authors: Li KB, Sanctuary BC
A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...
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08-22-2010 03:31 PM
[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain
Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.
J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77
Authors: Li KB, Sanctuary BC
A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures...
Automated resonance assignment of the 21kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA
Linear Mode
