Related ArticlesFast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.
J Magn Reson. 2013 Aug 30;236C:83-88
Authors: Lee W, Hu K, Tonelli M, Bahrami A, Neuhardt E, Glass KC, Markley JL
Abstract
ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55h. Both experiments were carried out on a 500MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.
PMID: 24091140 [PubMed - as supplied by publisher]
[NMR paper] Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers
Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers
Publication date: Available online 30 August 2013
Source:Journal of Magnetic Resonance</br>
Author(s): Woonghee Lee , Kaifeng Hu , Marco Tonelli , Arash Bahrami , Elizabeth Neuhardt , Karen C. Glass , John L. Markley</br>
ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for -labeled proteins. Given the sequence of the protein and data for...
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Metabolomics. 2013 Jun;9(3):558-563
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Abstract Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone...
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Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10487-92
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J Mol Biol. 2002 May 24;319(1):209-27
Authors: Herrmann T, Güntert P, Wüthrich K
Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
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J Biomol NMR. 1997 Oct;10(3):207-19
Authors: Croft D, Kemmink J, Neidig KP, Oschkinat H
One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where...
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[U. of Ottawa NMR Facility Blog] Heat Dissipation in Bruker AVANCE Spectrometers
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It is very important that an NMR spectrometer operate within a fixed temperature range. To control the temperature, many units within the console are equipped with cooling fans which must be kept in good working order. Failure to do so will shorten the life of the spectrometer and cause instability or malfunctions. In the Bruker AVANCE series of spectrometers, the SGU (Signal Generation Unit) boards are particularly sensitive to temperature. Each SGU houses a DDS (Direct Digital Synthesizer) containing numerically controlled oscillators which...
Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.
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