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Wiechers H, Kehl A, Hiller M, Eltzner B, Huckemann SF, Meyer A, Tkach I, Bennati M, Pokern Y. Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. J Magn Reson 2023; 353:107491. [PMID: 37301045 DOI: 10.1016/j.jmr.2023.107491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
ENDOR spectroscopy is a fundamental method to detect nuclear spins in the vicinity of paramagnetic centers and their mutual hyperfine interaction. Recently, site-selective introduction of 19F as nuclear labels has been proposed as a tool for ENDOR-based distance determination in biomolecules, complementing pulsed dipolar spectroscopy in the range of angstrom to nanometer. Nevertheless, one main challenge of ENDOR still consists of its spectral analysis, which is aggravated by a large parameter space and broad resonances from hyperfine interactions. Additionally, at high EPR frequencies and fields (⩾94 GHz/3.4 Tesla), chemical shift anisotropy might contribute to broadening and asymmetry in the spectra. Here, we use two nitroxide-fluorine model systems to examine a statistical approach to finding the best parameter fit to experimental 263 GHz 19F ENDOR spectra. We propose Bayesian optimization for a rapid, global parameter search with little prior knowledge, followed by a refinement by more standard gradient-based fitting procedures. Indeed, the latter suffer from finding local rather than global minima of a suitably defined loss function. Using a new and accelerated simulation procedure, results for the semi-rigid nitroxide-fluorine two and three spin systems lead to physically reasonable solutions, if minima of similar loss can be distinguished by DFT predictions. The approach also delivers the stochastic error of the obtained parameter estimates. Future developments and perspectives are discussed.
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Affiliation(s)
- H Wiechers
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - B Eltzner
- Research Group Computational Biomolecular Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - S F Huckemann
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany
| | - I Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany.
| | - Y Pokern
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom.
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Robertson IM, Klein BA, Sykes BD. Optimizing fluorine labelling for 19F solid-state NMR in oriented biological systems. J Biomol NMR 2020; 74:1-7. [PMID: 31912345 DOI: 10.1007/s10858-019-00296-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
When planning a fluorine labeling strategy for 19F solid state NMR (ssNMR) studies of the structure and/or mobility of fluorine labeled compounds in situ in an oriented biological system, it is important to characterize the NMR properties of the label. This manuscript focuses on the characterization of a selection of aromatic fluorine compounds in dimyristoylphosphatidylcholine bilayers using 19F ssNMR from the standpoint of determining the optimum arrangement of fluorine nuclei on a pendant aromatic ring before incorporation into more complex biological systems.
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Affiliation(s)
- Ian M Robertson
- Ministry of Health, Government of Alberta, Edmonton, AB, T5J 1S6, Canada
| | - Brittney A Klein
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada.
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