Abstract Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to the â??z direction, Larmor precession is impeded since magnetization becomes spin-locked, which is a potentially useful feature for the investigation of microsecond to millisecond dynamics. A major drawback of these pulses as theoretical prediction is concerned, however, results from their time-dependent offset: simulations of spin density matrices under the influence of a time-dependent Hamiltonian with non-commuting elements are costly in terms of computational time, rendering data analysis impracticable. In this paper we suggest several ways to reduce the computational time without compromising accuracy with respect to effects such as cross-correlated relaxation and modulation of the chemical shift.
Content Type Journal Article
Category Article
Pages 35-47
DOI 10.1007/s10858-011-9539-8
Authors
Renate Auer, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
Martin Tollinger, Department of Organic Chemistry, Leopold Franzens Universitaet Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
Ilya Kuprov, Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford, OX1 3QG UK
Robert Konrat, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
Karin Kloiber, Department of Organic Chemistry, Leopold Franzens Universitaet Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Yi Xue, Joshua M. Ward, Tairan Yuwen, Ivan S. Podkorytov and Nikolai R. Skrynnikov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja206442c/aop/images/medium/ja-2011-06442c_0001.gif
Journal of the American Chemical Society
DOI: 10.1021/ja206442c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
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Water proton spin saturation affects measured protein backboneN spin relaxation rates
Water proton spin saturation affects measured protein backboneN spin relaxation rates
Publication year: 2011
Source: Journal of Magnetic Resonance, Available online 1 October 2011</br>
Kang*Chen, Nico*Tjandra</br>
Protein backboneN NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses....
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relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
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J Biomol NMR. 2011 May 27;
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Investigation of protein dynamics on the ps-ns and ?s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying...
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