Computational Modeling and Least‐Squares Fittingof EPR Spectra

Stoll, Stefan

doi:10.1002/9783527672431.ch3

Cited by 24 publications

(22 citation statements)

References 433 publications

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“…To quantify the correlation between increasing IR survival and an increasing population of H-Mn 2+ complexes revealed in Fig. 1 , Upper and Lower , a simple “quantitation by simulation” procedure ( 34 , 35 ) using the EasySpin program ( 36 ) was developed to decompose the cellular Mn 2+ 35-GHz absorption-display EPR spectra into fractional contributions from spectra that represent the L- and H-pools ( SI Appendix , Materials and Methods ). The contribution of the H-Mn 2+ pool to the EPR spectrum of a cell type was modeled as an optimized sum of a simulated exemplar spectrum that corresponds to that of the Pi complex of Mn 2+ ( SI Appendix , Fig.…”

Section: Resultsmentioning

confidence: 99%

Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance

Sharma

Gaidamakova

Grichenko

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

107

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SignificanceDecades of functional genomic efforts have failed to predict the ability of cells to survive ionizing radiation (IR). Evidence is mounting that small high-symmetry antioxidant complexes of manganous ions with metabolites (H-Mn2+) are responsible for cellular IR resistance, and that H-Mn2+ protects the proteome, not the genome, from IR-induced reactive oxygen species. We show that the amount of H-Mn2+ in nonirradiated living cells is readily gauged by electron paramagnetic resonance (EPR) spectroscopy and highly diagnostic of their DNA repair efficiency and survival after gamma-radiation exposure. This spectroscopic measure of cellular H-Mn2+ content is the strongest known biological indicator of cellular IR resistance between and within organisms across the three domains of the tree of life, with potential applications including optimization of radiotherapy.

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Section: Resultsmentioning

confidence: 99%

Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance

Sharma

Gaidamakova

Grichenko

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

107

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“…On the positive side, the most recent review by Stoll [141] on the computational modeling and fitting techniques of EPR spectra may be mentioned. This review contains a concise presentation of various terms in SHs, while utilizing proper terminology, and may be consulted for clarification of the problems identified in recent EMR-related textbooks surveyed in Section 4.…”

Section: Confusion Between the Cf (Lf) And Sh (Zfs) Quantities In Thementioning

confidence: 99%

“…(3). An interesting notational aspect is brought up by Stoll [141]instead of the customary form, S Á D Á S, where the dots (.) indicate a scalar product, the 'quadratic' ZFS term may be alternatively written in vector and matrix representations of S and D, as S T DS, where the subscript T denotes the transpose of the spin vector and the dot is omitted.…”

Section: Confusion Between the Cf (Lf) And Sh (Zfs) Quantities In Thementioning

confidence: 99%

Terminological confusions and problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians—Survey of the CF=ZFS confusion in recent literature

Rudowicz¹,

Karbowiak²

2014

Physica B: Condensed Matter

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“…(1) the fast motion limit (τC ~ 0), (2) the fast-motion regime (τC -1 >>   ), (3) the slow and intermediate motion regime (τC -1 is similar to   within two (2) orders of magnitude), and (4) the rigid limit (no rotation) [30].…”

Section: Applications Of Cw Epr To Study the Mobility Of Spin Labelsmentioning

confidence: 99%

“…An extensive summary on the approaches of computational simulation of EPR spectra, as well as related software packages with implementations and references was provided by S. Stoll [30] and many other researchers [35,36]. Thus, only a brief summary with principal equations is provided in this section.…”

Section: Applications Of Cw Epr To Study the Mobility Of Spin Labelsmentioning

confidence: 99%

Applications of electron paramagnetic resonance in biomedicine

Motygullina¹

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Spectroscopy and imaging are widely used to characterise systems structurally and functionally, and this information allows for the rational development of novel drugs and theranostics in many diverse areas of medicine. This thesis focuses on applying Electron Paramagnetic Resonance (EPR) techniques to determine the structure and function of protein molecules. A feasibility study to develop paramagnetic probes for EPR imaging is also presented.In EPR the probe is a paramagnetic centre and information is obtained by measuring interactions of this probe with its environment. In this thesis continuous wave (CW) EPR and Double Electron Electron Resonance (DEER) in conjunction with a site-directed spin labelling (SDSL) were employed to study structure and function of spin-labelled protein molecules. The techniques allow examination of molecular systems that cannot be crystallised or are too big for efficient NMR investigation. DEER provides information on distance distributions between two spin labels located on Cys-mutated residues of the protein molecule and can access longer distances in comparison with NMR. CW EPR provides information about the mobility of a single spin label which can be used to characterise protein dynamics. Structural modelling was used to combine the crystal structures and Molecular Dynamics (MD) simulations with DEER distance constraints to present a DEER-based structural model of the conformational variability of the protein molecule. Chapters 2 and 3 focus on characterising two metal ion substrate binding proteins (SBP), Zn 2+binding AdcA and Mn 2+ -binding PsaA, using DEER and CW EPR. The ATP-Binding Cassette (ABC) permeases, with which the SBPs are associated, are a primary importer used by bacteria to scavenge the essential first-row metal ions (e.g. iron, zinc, manganese) from a host environment. The process is essential for bacterial survival and propagation. Understanding the metal ion acquisition mechanisms by these SBPs can provide new opportunities for targeted drug development.Collectively, the CW EPR and DEER data along with crystal structures, differential scanning fluorimetry (DSF), Molecular Dynamics simulation, and smFRET microscopy, were able to determine a structural model for Zn 2+ -binding in the AdcA protein referred to as "trap-door" mechanism. Our data show that the "trap-door" mechanism employed by AdcA is different from the "spring-hammer" mechanism employed by PsaA.Non-Ribosomal Peptide Synthetase (NRPS) are the topic of chapter 4. NRPS's are a family of mega enzymes that produce a diverse range of pharmaceuticals, yet how these molecular machines operate to produce such complex chemicals is very poorly understood. This project will investigate module 7 of the teicoplanin NRPS, a 200 kDa protein, which is the last step in the production of the glycopeptide antibiotics (GPA). A comprehensive structural and functional understanding of the teicoplanin NRPS machinery will provide a paradigm for this enzyme family, enabling the tailored iv Publications included in this t...

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Computational Modeling and Least‐Squares Fittingof EPR Spectra

Cited by 24 publications

References 433 publications

Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance

Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance

Terminological confusions and problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians—Survey of the CF=ZFS confusion in recent literature

Applications of electron paramagnetic resonance in biomedicine

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Computational Modeling and Least‐Squares Fittingof EPR Spectra

Cited by 24 publications

References 433 publications

Across the tree of life, radiation resistance is governed by antioxidant Mn 2+ , gauged by paramagnetic resonance

Across the tree of life, radiation resistance is governed by antioxidant Mn 2+ , gauged by paramagnetic resonance

Terminological confusions and problems at the interface between the crystal field Hamiltonians and the zero-field splitting Hamiltonians—Survey of the CF=ZFS confusion in recent literature

Applications of electron paramagnetic resonance in biomedicine

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Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance

Across the tree of life, radiation resistance is governed by antioxidant Mn ²⁺ , gauged by paramagnetic resonance