PMID: 7536605Mar 1, 1995Paper

An improved NOESY simulation program for partially relaxed spectra: BIRDER

Journal of Magnetic Resonance. Series B
L Zhu, B R Reid

Abstract

An improved 2D NOESY simulation program, BIRDER (back-calculation considering incomplete recovery and differential external relaxation), has been developed. BIRDER has the following features: (1) It allows for differential external relaxation rates for protons with different chemical environments, (2) it automatically accounts for incomplete recovery of z magnetization between scans, and (3) it incorporates anisotropic tumbling motional modes for nonspherical molecules. It was found that a lower R factor is obtained if differential external relaxation rates are used in the NOESY spectrum simulation. The method for experimentally determining these external relaxation rates is discussed. In practice, the ability to account for incomplete recovery of z magnetization is very useful in the quantitative analysis of 2D NOESY spectra of spin systems with long longitudinal relaxation times (T1). For example, the T1's of some protons in RNA duplexes are approximately 4-6 s. Thus, a more than 15 s relaxation delay is needed to allow the z magnetization to return to thermal equilibrium between scans, requiring more than a week to obtain a single NOESY spectrum. Unless incomplete recovery of z magnetization is explicitly considered, distanc...Continue Reading

Citations

Nov 1, 1995·Nature Structural Biology·L ZhuB R Reid
Oct 29, 1996·Proceedings of the National Academy of Sciences of the United States of America·L ZhuB R Reid
May 25, 2004·Nucleic Acids Research·N B Fredrik EdfeldtBrian R Reid
May 25, 2004·Nucleic Acids Research·N B Fredrik EdfeldtBrian R Reid
Aug 15, 2014·Journal of Biomolecular NMR·Jakob Toudahl Nielsen, Niels Chr Nielsen
Mar 19, 1999·Journal of Molecular Biology·S H ChouS W Wang
Dec 13, 2005·Journal of Magnetic Resonance·Mikhail Veshtort, Robert G Griffin
Nov 25, 2004·American Journal of Physiology. Cell Physiology·Mehul ShahPravin B Sehgal

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