Related ArticlesProtein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Nucleic Acids Res. 2015 Jan 13;
Authors: Collins KM, Oregioni A, Robertson LE, Kelly G, Ramos A
Abstract
Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding proteins. We show that PCA can be used to compare the changes in the nuclear magnetic resonance (NMR) spectrum of a protein upon binding a set of quasi-degenerate RNAs and define the nucleobase specificity. We couple this application of PCA to an automated NMR spectra recording and processing protocol and obtain an unbiased and high-throughput NMR method for the analysis of nucleobase preference in protein-RNA interactions. We test the method on the RNA binding domains of three important regulators of RNA metabolism.
PMID: 25586222 [PubMed - as supplied by publisher]
[NMR paper] Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Related Articles Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Magn Reson Chem. 2014 Sep 1;
Authors: Reddy JG, Kumar D, Hosur RV
Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The...
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09-03-2014 11:44 AM
Unravelling proton NMR spectra of foodstuffs with independent component analysis techniques
Unravelling proton NMR spectra of foodstuffs with independent component analysis techniques
http://www.spectroscopynow.com/common/images/thumbnails/144c151d9a0.jpgOverlapping signals in the proton NMR spectra of complex liquids, like foodstuffs and soft drinks, can be processed using a chemometric method, independent component analysis, to extract the spectra of pure components and determine their concentrations.
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03-14-2014 07:34 PM
Visualizing the principal component of 1H,15N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C
Visualizing the principal component of 1H,15N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C
Abstract Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding 1H,15N-HSQC NMR spectra for homologous proteins, we investigated whether structural information could be ascertained for a new homolog solely from its...
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09-30-2011 08:01 PM
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
J Biomol NMR. 2011 Sep;51(1-2):115-22
Authors: Robertson IM, Boyko RF, Sykes BD
Abstract
Laboratories often repeatedly determine the structure of a given protein under a variety of conditions,...
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09-30-2011 06:00 AM
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
Visualizing the principal component of (1)H, (15)N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C.
J Biomol NMR. 2011 Sep;51(1-2):115-22
Authors: Robertson IM, Boyko RF, Sykes BD
Abstract
Laboratories often repeatedly determine the structure of a given protein under a variety of conditions,...
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09-30-2011 05:59 AM
[NMR paper] NMR data collection and analysis protocol for high-throughput protein structure determination.
NMR data collection and analysis protocol for high-throughput protein structure determination.
Related Articles NMR data collection and analysis protocol for high-throughput protein structure determination.
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10487-92
Authors: Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that...
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12-01-2010 06:56 PM
[NMR paper] NMR analysis of in vitro-synthesized proteins without purification: a high-throughput
NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach.
Related Articles NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach.
FEBS Lett. 2002 Jul 31;524(1-3):159-62
Authors: Guignard L, Ozawa K, Pursglove SE, Otting G, Dixon NE
A cell-free protein expression system was established that provides protein samples of adequate concentration and purity for direct NMR analysis. The Escherichia coli peptidyl-prolyl cis-trans isomerase PpiB was expressed in this system...
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11-24-2010 08:58 PM
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
Naohiro Kobayashi, Junji Iwahara, Seizo Koshiba, Tadashi Tomizawa, Naoya Tochio, Peter Güntert, Takanori Kigawa and Shigeyuki Yokoyama
Journal of Biomolecular NMR; 2007; 39(1) pp 31 - 52
Abstract:
The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput...
Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
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