Related ArticlesStrategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10.
J Biomol NMR. 2014 Aug;59(4):231-40
Authors: Krähenbühl B, Lukavsky P, Wider G
Abstract
A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-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 0.3*mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80*% of the resonances of the (13)C-(1)H moieties at the 1', 2', 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY.
Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments
Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments
Abstract
A fast, robust and reliable strategy for automated sequential resonance assignment for uniformly -labeled RNA via its phosphodiester backbone is presented. It is based on a series of high-dimensional through-bond APSY experiments: a 5D HCP-CCH COSY, a 4D H1â?²C1â?²CH TOCSY for ribose resonances, a 5D HCNCH for ribose-to-base connection, a 4D H6C6C5H5 TOCSY for pyrimidine resonances, and a 4D...
nmrlearner
Journal club
0
06-19-2014 10:21 PM
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 ...
nmrlearner
Journal club
0
06-19-2014 10:21 PM
A novel strategy for NMR resonance assignment and protein structure determination
A novel strategy for NMR resonance assignment and protein structure determination
Abstract The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution â?? especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a...
nmrlearner
Journal club
0
12-18-2010 01:31 AM
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
J Biomol NMR. 2010 Dec 14;
Authors: Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH
The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed...
nmrlearner
Journal club
0
12-17-2010 11:23 AM
[NMR paper] Automated protein fold determination using a minimal NMR constraint strategy.
Automated protein fold determination using a minimal NMR constraint strategy.
Related Articles Automated protein fold determination using a minimal NMR constraint strategy.
Protein Sci. 2003 Jun;12(6):1232-46
Authors: Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] Full 1H NMR assignment of a 24-nucleotide RNA hairpin: application of the 1H 3D-NOE/2
Full 1H NMR assignment of a 24-nucleotide RNA hairpin: application of the 1H 3D-NOE/2QC experiment.
Related Articles Full 1H NMR assignment of a 24-nucleotide RNA hairpin: application of the 1H 3D-NOE/2QC experiment.
J Biomol NMR. 1998 Apr;11(3):319-28
Authors: Nooren IM, Wang KY, Borer PN, Pelczer I
The subject RNA models the binding site for the coat protein of the R17 virus, as well as the ribosome recognition sequence for the R17 replicase gene. With an RNA of this size, overlaps among the sugar protons complicate assignments of the 1H NMR...
nmrlearner
Journal club
0
11-17-2010 11:06 PM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
nmrlearner
Journal club
0
08-22-2010 03:33 AM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10.
Linear Mode
