Dynamic 15 N{ 1 H} NOE measurements: a tool for studying protein dynamics
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ARTICLE
Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics Vladlena Kharchenko1 · Michal Nowakowski1,2 · Mariusz Jaremko1 · Andrzej Ejchart3 · Łukasz Jaremko1 Received: 1 May 2020 / Accepted: 12 August 2020 © The Author(s) 2020
Abstract Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature. Keywords NMR · Protein dynamics · Heteronuclear NOE · Dynamic NOE · Errors of NOE measurements
Introduction Since its first use of magnetic relaxation measurements of 15 N nuclei applied to the protein, the staphylococcal nuclease (Kay et al. 1989), this method has become indispensable in the determination of molecular motions in biopolymers (Jarymowycz and Stone 2006; Kempf and Loria 2003; Palmer, III 2004; Reddy and Rayney 2010; Stetz et al. 2019). Electronic supplementary material The online version of this article (doi:https://doi.org/10.1007/s10858-020-00346-6) contains supplementary material, which is available to authorized users. * Łukasz Jaremko [email protected] 1
Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955‑6900, Saudi Arabia
2
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02‑089 Warsaw, Poland
3
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02‑106, Warsaw, Poland
The canonical triad of relaxation parameters—longitudinal (R1) and transverse (R2) relaxation rates accompanied by the 15 N{1H} nuclear Overhauser effect (NOE)—have been most often used in studies investigating the mobility of backbone in proteins. It is a common opinion that 15N{1H} NOE is unique among the mentioned three relaxation parameters because it is regarded as essential for the accurate estimation of the spectral density function at high frequencies (ωH ± ωN), and it is crucial for the identification of fast backbone motions. (Idiyatullin et al. 2001; Gong and Ish
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