Literature DB >> 17031954

Targeted acquisition for real-time NMR spectroscopy.

Victor A Jaravine1, Vladislav Yu Orekhov.   

Abstract

A target-oriented approach for the acquisition of information in biomolecular NMR spectroscopy is being developed. This approach combines concurrent data accumulation, processing, and monitoring of spectral quality. Real-time estimation of parameters allows acquisition to be stopped when results are complete and have a specified precision. The technique is based on multidimensional decomposition, which can process incomplete data. An incremental nonuniform sampling scheme ensures the optimization of resolution sensitivity. To validate this method, 3D HNCO spectra of three biomolecular systems (8 kDa ubiquitin, 22 kDa barstar-barnase complex, and 82 kDa malate synthase G) are processed incrementally at small acquisition time steps. The range of molecular sizes illustrates applicability in both sample- and sensitivity-limited regimes. In each case, the target was to acquire all backbone resonances in the spectra. For the three systems, the targets are achieved after 4.5 min, 1.6 h, and 22 h of acquisition time, respectively. A number of other targets that can be similarly monitored as a function of time are discussed.

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Year:  2006        PMID: 17031954     DOI: 10.1021/ja062146p

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  26 in total

1.  NMR protein structure determination in living E. coli cells using nonlinear sampling.

Authors:  Teppei Ikeya; Atsuko Sasaki; Daisuke Sakakibara; Yoshiki Shigemitsu; Junpei Hamatsu; Tomomi Hanashima; Masaki Mishima; Masatoshi Yoshimasu; Nobuhiro Hayashi; Tsutomu Mikawa; Daniel Nietlispach; Markus Wälchli; Brian O Smith; Masahiro Shirakawa; Peter Güntert; Yutaka Ito
Journal:  Nat Protoc       Date:  2010-05-13       Impact factor: 13.491

2.  Random phase detection in multidimensional NMR.

Authors:  Mark W Maciejewski; Matthew Fenwick; Adam D Schuyler; Alan S Stern; Vitaliy Gorbatyuk; Jeffrey C Hoch
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-26       Impact factor: 11.205

3.  Highly automated protein backbone resonance assignment within a few hours: the "BATCH" strategy and software package.

Authors:  Ewen Lescop; Bernhard Brutscher
Journal:  J Biomol NMR       Date:  2009-04-15       Impact factor: 2.835

4.  Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data.

Authors:  Leo E Wong; James E Masse; Victor Jaravine; Vladislav Orekhov; Konstantin Pervushin
Journal:  J Biomol NMR       Date:  2008-09-11       Impact factor: 2.835

5.  Fast multi-dimensional NMR acquisition and processing using the sparse FFT.

Authors:  Haitham Hassanieh; Maxim Mayzel; Lixin Shi; Dina Katabi; Vladislav Yu Orekhov
Journal:  J Biomol NMR       Date:  2015-06-30       Impact factor: 2.835

6.  A non-uniform sampling approach enables studies of dilute and unstable proteins.

Authors:  Tomas Miljenović; Xinying Jia; Peter Lavrencic; Bostjan Kobe; Mehdi Mobli
Journal:  J Biomol NMR       Date:  2017-02-10       Impact factor: 2.835

7.  Pitfalls in compressed sensing reconstruction and how to avoid them.

Authors:  Alexandra Shchukina; Paweł Kasprzak; Rupashree Dass; Michał Nowakowski; Krzysztof Kazimierczuk
Journal:  J Biomol NMR       Date:  2016-11-11       Impact factor: 2.835

8.  Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.

Authors:  Daniel Y L Mao; Dante Neculai; Michael Downey; Stephen Orlicky; Yosr Z Haffani; Derek F Ceccarelli; Jenny S L Ho; Rachel K Szilard; Wei Zhang; Cynthia S Ho; Leo Wan; Christophe Fares; Sigrun Rumpel; Igor Kurinov; Cheryl H Arrowsmith; Daniel Durocher; Frank Sicheri
Journal:  Mol Cell       Date:  2008-10-24       Impact factor: 17.970

9.  Spectroscopy by integration of frequency and time domain information for fast acquisition of high-resolution dark spectra.

Authors:  Yoh Matsuki; Matthew T Eddy; Judith Herzfeld
Journal:  J Am Chem Soc       Date:  2009-04-08       Impact factor: 15.419

10.  Coupled decomposition of four-dimensional NOESY spectra.

Authors:  Sebastian Hiller; Ilghis Ibraghimov; Gerhard Wagner; Vladislav Y Orekhov
Journal:  J Am Chem Soc       Date:  2009-09-16       Impact factor: 15.419

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