Literature DB >> 19553148

OPTESIM, a versatile toolbox for numerical simulation of electron spin echo envelope modulation (ESEEM) that features hybrid optimization and statistical assessment of parameters.

Li Sun1, Jessica Hernandez-Guzman, Kurt Warncke.   

Abstract

Electron spin echo envelope modulation (ESEEM) is a technique of pulsed-electron paramagnetic resonance (EPR) spectroscopy. The analyis of ESEEM data to extract information about the nuclear and electronic structure of a disordered (powder) paramagnetic system requires accurate and efficient numerical simulations. A single coupled nucleus of known nuclear g value (g(N)) and spin I=1 can have up to eight adjustable parameters in the nuclear part of the spin Hamiltonian. We have developed OPTESIM, an ESEEM simulation toolbox, for automated numerical simulation of powder two- and three-pulse one-dimensional ESEEM for arbitrary number (N) and type (I, g(N)) of coupled nuclei, and arbitrary mutual orientations of the hyperfine tensor principal axis systems for N>1. OPTESIM is based in the Matlab environment, and includes the following features: (1) a fast algorithm for translation of the spin Hamiltonian into simulated ESEEM, (2) different optimization methods that can be hybridized to achieve an efficient coarse-to-fine grained search of the parameter space and convergence to a global minimum, (3) statistical analysis of the simulation parameters, which allows the identification of simultaneous confidence regions at specific confidence levels. OPTESIM also includes a geometry-preserving spherical averaging algorithm as default for N>1, and global optimization over multiple experimental conditions, such as the dephasing time (tau) for three-pulse ESEEM, and external magnetic field values. Application examples for simulation of (14)N coupling (N=1, N=2) in biological and chemical model paramagnets are included. Automated, optimized simulations by using OPTESIM lead to a convergence on dramatically shorter time scales, relative to manual simulations.

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Year:  2009        PMID: 19553148      PMCID: PMC3058049          DOI: 10.1016/j.jmr.2009.05.012

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  12 in total

1.  Numerical simulation of one- and two-dimensional ESEEM experiments.

Authors:  Z L Madi; S Van Doorslaer; A Schweiger
Journal:  J Magn Reson       Date:  2002-02       Impact factor: 2.229

2.  Rapid construction of solid-state magnetic resonance powder spectra from frequencies and amplitudes as applied to ESEEM.

Authors:  Stefan Stoll; Arthur Schweiger
Journal:  J Magn Reson       Date:  2003-08       Impact factor: 2.229

3.  XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra.

Authors:  Graeme R Hanson; Kevin E Gates; Christopher J Noble; Mark Griffin; Anthony Mitchell; Simon Benson
Journal:  J Inorg Biochem       Date:  2004-05       Impact factor: 4.155

4.  EasySpin, a comprehensive software package for spectral simulation and analysis in EPR.

Authors:  Stefan Stoll; Arthur Schweiger
Journal:  J Magn Reson       Date:  2005-09-26       Impact factor: 2.229

5.  Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features.

Authors:  Li Sun; Kurt Warncke
Journal:  Proteins       Date:  2006-08-01

6.  Optimization by simulated annealing.

Authors:  S Kirkpatrick; C D Gelatt; M P Vecchi
Journal:  Science       Date:  1983-05-13       Impact factor: 47.728

7.  Electron spin-echo studies of the composition of the paramagnetic intermediate formed during the deamination of propanolamine by ethanolamine ammonia-lyase, and AdoCbl-dependent enzyme.

Authors:  S L Tan; M G Kopczynski; W W Bachovchin; W H Orme-Johnson; B M Babior
Journal:  J Biol Chem       Date:  1986-03-15       Impact factor: 5.157

8.  Characterization of the product radical structure in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase by using three-pulse 2H ESEEM spectroscopy.

Authors:  Kurt Warncke
Journal:  Biochemistry       Date:  2005-03-08       Impact factor: 3.162

9.  Critical role of arginine 160 of the EutB protein subunit for active site structure and radical catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase.

Authors:  Li Sun; Olivia A Groover; Jeffrey M Canfield; Kurt Warncke
Journal:  Biochemistry       Date:  2008-04-30       Impact factor: 3.162

10.  Carboxylate binding in copper histidine complexes in solution and in zeolite Y: X- and W-band pulsed EPR/ENDOR combined with DFT calculations.

Authors:  Debbie Baute; Dafna Arieli; Frank Neese; Herbert Zimmermann; Bert M Weckhuysen; Daniella Goldfarb
Journal:  J Am Chem Soc       Date:  2004-09-22       Impact factor: 15.419

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  9 in total

1.  Copper(II)-bis-histidine coordination structure in a fibrillar amyloid β-peptide fragment and model complexes revealed by electron spin echo envelope modulation spectroscopy.

Authors:  Jessica Hernández-Guzmán; Li Sun; Anil K Mehta; Jijun Dong; David G Lynn; Kurt Warncke
Journal:  Chembiochem       Date:  2013-09-06       Impact factor: 3.164

2.  Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy.

Authors:  Daniel Mayo; Andy Zhou; Indra Sahu; Robert McCarrick; Parker Walton; Adam Ring; Kaylee Troxel; Aaron Coey; Jaclyn Hawn; Abdul-Hamid Emwas; Gary A Lorigan
Journal:  Protein Sci       Date:  2011-06-02       Impact factor: 6.725

3.  Local structure and global patterning of Cu2+ binding in fibrillar amyloid-β [Aβ(1-40)] protein.

Authors:  William A Gunderson; Jessica Hernández-Guzmán; Jesse W Karr; Li Sun; Veronika A Szalai; Kurt Warncke
Journal:  J Am Chem Soc       Date:  2012-10-24       Impact factor: 15.419

Review 4.  Use of electron paramagnetic resonance to solve biochemical problems.

Authors:  Indra D Sahu; Robert M McCarrick; Gary A Lorigan
Journal:  Biochemistry       Date:  2013-08-20       Impact factor: 3.162

5.  Measuring the orientation of taurine in the active site of the non-heme Fe(II)/α-ketoglutarate-dependent taurine hydroxylase (TauD) using electron spin echo envelope modulation (ESEEM) spectroscopy.

Authors:  Thomas M Casey; Piotr K Grzyska; Robert P Hausinger; John McCracken
Journal:  J Phys Chem B       Date:  2013-08-29       Impact factor: 2.991

6.  Pulsed EPR study of amino acid and tetrahydropterin binding in a tyrosine hydroxylase nitric oxide complex: evidence for substrate rearrangements in the formation of the oxygen-reactive complex.

Authors:  Matthew D Krzyaniak; Bekir E Eser; Holly R Ellis; Paul F Fitzpatrick; John McCracken
Journal:  Biochemistry       Date:  2013-11-14       Impact factor: 3.162

7.  Heterogeneous ordered-disordered structure of the mesodomain in frozen sucrose-water solutions revealed by multiple electron paramagnetic resonance spectroscopies.

Authors:  Hanlin Chen; Li Sun; Kurt Warncke
Journal:  Langmuir       Date:  2013-03-19       Impact factor: 3.882

8.  Design and implementation of an FPGA-based timing pulse programmer for pulsed-electron paramagnetic resonance applications.

Authors:  Li Sun; Joshua J Savory; Kurt Warncke
Journal:  Concepts Magn Reson Part B Magn Reson Eng       Date:  2013-08-01       Impact factor: 1.176

9.  Identification of the valence and coordination environment of the particulate methane monooxygenase copper centers by advanced EPR characterization.

Authors:  Megen A Culpepper; George E Cutsail; William A Gunderson; Brian M Hoffman; Amy C Rosenzweig
Journal:  J Am Chem Soc       Date:  2014-08-08       Impact factor: 15.419

  9 in total

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