PDSFit: PDS data analysis in the presence of orientation selectivity, g-anisotropy, and exchange coupling.
DEER
EPR
PELDOR
RIDME
genetic algorithm
Journal
Magnetic resonance in chemistry : MRC
ISSN: 1097-458X
Titre abrégé: Magn Reson Chem
Pays: England
ID NLM: 9882600
Informations de publication
Date de publication:
Jan 2024
Jan 2024
Historique:
revised:
24
10
2023
received:
04
08
2023
accepted:
01
11
2023
medline:
22
12
2023
pubmed:
22
12
2023
entrez:
22
12
2023
Statut:
ppublish
Résumé
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS), encompassing techniques such as pulsed electron-electron double resonance (PELDOR or DEER) and relaxation-induced dipolar modulation enhancement (RIDME), is a valuable method in structural biology and materials science for obtaining nanometer-scale distance distributions between electron spin centers. An important aspect of PDS is the extraction of distance distributions from the measured time traces. Most software used for this PDS data analysis relies on simplifying assumptions, such as assuming isotropic g-factors of ~2 and neglecting orientation selectivity and exchange coupling. Here, the program PDSFit is introduced, which enables the analysis of PELDOR and RIDME time traces with or without orientation selectivity. It can be applied to spin systems consisting of up to two spin centers with anisotropic g-factors and to spin systems with exchange coupling. It employs a model-based fitting of the time traces using parametrized distance and angular distributions, and parametrized PDS background functions. The fitting procedure is followed by an error analysis for the optimized parameters of the distributions and backgrounds. Using five different experimental data sets published previously, the performance of PDSFit is tested and found to provide reliable solutions.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
37-60Subventions
Organisme : University of Bonn
Organisme : Deutsche Forschungsgemeinschaft
ID : 420322655
Organisme : Research Foundation
Informations de copyright
© 2023 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.
Références
A. D. Milov, K. M. Salikhov, M. D. Shchirov, Fiz. Tverd. Tela 1981, 23, 975.
R. E. Martin, M. Pannier, F. Diederich, V. Gramlich, M. Hubrich, H. W. Spiess, Angew. Chem., Int. Ed. 1998, 37, 2833.
P. P. Borbat, E. R. Georgieva, J. H. Freed, J. Phys. Chem. Lett. 2013, 4, 170.
P. E. Spindler, I. Waclawska, B. Endeward, J. Plackmeyer, C. Ziegler, T. F. Prisner, J. Phys. Chem. Lett. 2015, 6, 4331.
A. Doll, G. Jeschke, Phys. Chem. Chem. Phys. 2017, 19, 1039.
M. Di Valentin, M. Albertini, M. G. Dal Farra, E. Zurlo, L. Orian, A. Polimeno, M. Gobbo, D. Carbonera, Chem. - Eur. J. 2016, 22, 17204.
L. V. Kulik, S. A. Dzuba, I. A. Grigoryev, Y. Tsvetkov, Chem. Phys. Lett. 2001, 343, 315.
S. Milikisyants, F. Scarpelli, M. G. Finiguerra, M. Ubbink, M. Huber, J. Magn. Reson. 2009, 201, 48.
D. Abdullin, M. Suchatzki, O. Schiemann, Appl. Magn. Reson. 2022, 53, 539.
S. Saxena, J. H. Freed, Chem. Phys. Lett. 1996, 251, 102.
G. Jeschke, M. Pannier, A. Godt, H. W. Spiess, Chem. Phys. Lett. 2000, 331, 243.
D. Akhmetzyanov, P. Schöps, A. Marko, N. C. Kunjir, S. T. Sigurdsson, T. F. Prisner, Phys. Chem. Chem. Phys. 2015, 17, 24446.
O. Schiemann, T. F. Prisner, Q. Rev. Biophys. 2007, 40, 1.
G. Jeschke, eMagRes 2016, 5, 1459.
P. P. Borbat, J. H. Freed, eMagRes 2017, 6, 465.
C. R. Timmel, J. R. Harmer (Eds), Structure and Bonding, in Structural information from spin-labels and intrinsic paramagnetic centres in the biosciences, Vol. 152, Springer, Berlin Heidelberg 2013.
O. Schiemann, C. A. Heubach, D. Abdullin, K. Ackermann, M. Azarkh, E. G. Bagryanskaya, M. Drescher, B. Endeward, J. H. Freed, L. Galazzo, D. Goldfarb, T. Hett, L. Esteban Hofer, L. Fábregas Ibáñez, E. J. Hustedt, S. Kucher, I. Kuprov, J. E. Lovett, A. Meyer, S. Ruthstein, S. Saxena, S. Stoll, C. R. Timmel, M. Di Valentin, H. S. Mchaourab, T. F. Prisner, B. E. Bode, E. Bordignon, M. Bennati, G. Jeschke, J. Am. Chem. Soc. 2021, 143, 17875.
R. D. Britt (Ed), Advances in biomolecular EPR, Elsevier, Cambridge 2022.
G. Jeschke, V. Chechik, P. Ionita, A. Godt, H. Zimmermann, J. Banham, C. R. Timmel, D. Hilger, H. Jung, Appl. Magn. Reson. 2006, 30, 473.
S. G. Worswick, J. A. Spencer, G. Jeschke, I. Kuprov, Sci. Adv. 2018, 4, eaat5218.
L. Fábregas Ibáñez, G. Jeschke, S. Stoll, Magn. Reson. 2020, 1, 209.
R. A. Stein, A. H. Beth, E. J. Hustedt, Methods Enzymol. 2015, 563, 531.
C. J. López, Z. Yang, C. Altenbach, W. L. Hubbell, Proc. Nat. Acad. Sci. U.S.A. 2013, 110, E4306.
O. Schiemann, P. Cekan, D. Margraf, T. F. Prisner, S. T. Sigurdsson, Angew. Chem., Int. Ed. 2009, 48, 3292.
B. Endeward, J. A. Butterwick, R. MacKinnon, T. F. Prisner, J. Am. Chem. Soc. 2009, 131, 15246.
C. Abé, D. Klose, F. Dietrich, W. H. Ziegler, Y. Polyhach, G. Jeschke, H.-J. Steinhoff, J. Magn. Reson. 2012, 216, 53.
I. Tkach, S. Pornsuwan, C. Höbartner, F. Wachowius, S. T. Sigurdsson, T. Y. Baranova, U. Diederichsen, G. Sicoli, M. Bennati, Phys. Chem. Chem. Phys. 2013, 15, 3433.
M. Kerzhner, D. Abdullin, J. Więcek, H. Matsuoka, G. Hagelueken, O. Schiemann, M. Famulok, Chem. - Eur. J. 2016, 22, 12113.
Y. Polyhach, A. Godt, C. Bauer, G. Jeschke, J. Magn. Reson. 2007, 185, 118.
V. P. Denysenkov, T. F. Prisner, J. Stubbe, M. Bennati, Proc. Nat. Acad. Sci. U.S.a. 2006, 103, 13386.
V. P. Denysenkov, D. Biglino, W. Lubitz, T. F. Prisner, M. Bennati, Angew. Chem., Int. Ed. 2008, 47, 1224.
I. M. C. van Amsterdam, M. Ubbink, G. W. Canters, M. Huber, Angew. Chem., Int. Ed. 2003, 42, 62.
J. E. Lovett, A. M. Bowen, C. R. Timmel, M. W. Jones, J. R. Dilworth, D. Caprotti, S. G. Bell, L. L. Wong, J. Harmer, Phys. Chem. Chem. Phys. 2009, 11, 6840.
M. M. Roessler, M. S. King, A. J. Robinson, F. A. Armstrong, J. Harmer, J. Hirst, Proc. Nat. Acad. Sci. U.S.a. 2010, 107, 1930.
Z. Yang, M. R. Kurpiewski, M. Ji, J. E. Townsend, P. Mehta, L. Jen-Jacobson, S. Saxena, Proc. Nat. Acad. Sci. U.S.a. 2012, 109, E993.
D. Abdullin, N. Florin, G. Hagelueken, O. Schiemann, Angew. Chem., Int. Ed. 2015, 54, 1827.
A. M. Bowen, E. O. D. Johnson, F. Mercuri, N. J. Hoskins, R. Qiao, J. S. O. McCullagh, J. E. Lovett, S. G. Bell, W. Zhou, C. R. Timmel, L. L. Wong, J. R. Harmer, J. Am. Chem. Soc. 2018, 140, 2514.
D. Margraf, B. E. Bode, A. Marko, O. Schiemann, T. F. Prisner, Mol. Phys. 2007, 105, 2153.
B. E. Bode, J. Plackmeyer, T. F. Prisner, O. Schiemann, J. Phys. Chem. A 2008, 112, 5064.
B. E. Bode, J. Plackmeyer, M. Bolte, T. F. Prisner, O. Schiemann, J. Organomet. Chem. 2009, 694, 1172.
Z. Yang, D. Kise, S. Saxena, J. Phys. Chem. B 2010, 114, 6165.
D. Abdullin, G. Hagelueken, R. I. Hunter, G. M. Smith, O. Schiemann, Mol. Phys. 2015, 113, 544.
A. M. Bowen, M. W. Jones, J. E. Lovett, T. G. Gaule, M. J. McPherson, J. R. Dilworth, C. R. Timmel, J. R. Harmer, Phys. Chem. Chem. Phys. 2016, 18, 5981.
A. Potapov, J. Magn. Reson. 2020, 316, 106769.
A. Godt, M. Schulte, H. Zimmermann, G. Jeschke, Angew. Chem., Int. Ed. 2006, 45, 7560.
P. E. Spindler, P. Schöps, W. Kallies, S. J. Glaser, T. F. Prisner, J. Magn. Reson. 2017, 280, 30.
A. Doll, G. Jeschke, J. Magn. Reson. 2017, 280, 46.
D. Abdullin, F. Duthie, A. Meyer, E. S. Müller, G. Hagelueken, O. Schiemann, J. Phys. Chem. B 2015, 119, 13534.
A. V. Astashkin, B. O. Elmore, W. Fan, J. G. Guillemette, C. Feng, J. Am. Chem. Soc. 2010, 132, 12059.
D. Abdullin, H. Matsuoka, M. Yulikov, N. Fleck, C. Klein, S. Spicher, G. Hagelueken, S. Grimme, A. Lützen, O. Schiemann, Chem. - Eur. J. 2019, 25, 8820.
D. Abdullin, P. Brehm, N. Fleck, S. Spicher, S. Grimme, O. Schiemann, Chem. - Eur. J. 2019, 25, 14388.
D. Abdullin, Appl. Magn. Reson. 2020, 51, 725.
A. Weber, O. Schiemann, B. Bode, T. F. Prisner, J. Magn. Reson. 2002, 157, 277.
G. W. Reginsson, R. I. Hunter, P. A. S. Cruickshank, D. R. Bolton, S. T. Sigurdsson, G. M. Smith, O. Schiemann, J. Magn. Reson. 2012, 216, 175.
N. C. Kunjir, G. W. Reginsson, O. Schiemann, S. T. Sigurdsson, Phys. Chem. Chem. Phys. 2013, 15, 19673.
A. Meyer, J. J. Jassoy, S. Spicher, A. Berndhäuser, O. Schiemann, Phys. Chem. Chem. Phys. 2018, 20, 13858.
D. Margraf, P. Cekan, T. F. Prisner, S. T. Sigurdsson, O. Schiemann, Phys. Chem. Chem. Phys. 2009, 11, 6708.
G. Jeschke, Macromol. Rapid Commun. 2002, 23, 227.
K. Keller, I. Ritsch, H. Hintz, M. Hülsmann, M. Qi, F. D. Breitgoff, D. Klose, Y. Polyhach, M. Yulikov, A. Godt, G. Jeschke, Phys. Chem. Chem. Phys. 2020, 22, 21707.
A. Meyer, D. Abdullin, G. Schnakenburg, O. Schiemann, Phys. Chem. Chem. Phys. 2016, 18, 9262.
C. Wuebben, S. Blume, D. Abdullin, D. Brajtenbach, F. Haege, S. Kath-Schorr, O. Schiemann, Molecules 2019, 24, 4482.
L. M. Stratmann, Y. Kutin, M. Kasanmascheff, G. H. Clever, Angew. Chem., Int. Ed. 2021, 60, 4939.
D. Abdullin, G. Hagelueken, O. Schiemann, Phys. Chem. Chem. Phys. 2016, 18, 10428.
A. D. Milov, A. G. Maryasov, Y. D. Tsvetkov, Appl. Magn. Reson. 1998, 15, 107.
A. D. Milov, A. B. Ponomarev, Y. Tsvetkov, Chem. Phys. Lett. 1984, 110, 67.
A. D. Milov, Y. D. Tsvetkov, Appl. Magn. Reson. 1997, 12, 495.
K. Keller, M. Qi, C. Gmeiner, I. Ritsch, A. Godt, G. Jeschke, A. Savitsky, M. Yulikov, Phys. Chem. Chem. Phys. 2019, 21, 8228.
D. Abdullin, O. Schiemann, ChemPlusChem 2020, 85, 353.
A. Marko, D. Margraf, H. Yu, Y. Mu, G. Stock, T. Prisner, J. Chem. Phys. 2009, 130, 64102.
A. V. Astashkin, Methods Enzymol. 2015, 563, 251.
D. Abdullin, T. Hett, P. Rauh Corro, O. Schiemann, PDSFit manual, https://github.com/dinarabdullin/PDSFit, 2023.
E. J. Hustedt, F. Marinelli, R. A. Stein, J. D. Faraldo-Gómez, H. S. Mchaourab, Biophys. J. 2018, 115, 1200.
F. Gao, L. Han, Comput. Optim. Appl. 2012, 51, 259.
W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, Numerical recipes in C: the art of scientific computing, second ed., Cambridge University Press, Cambridge 1992.
T. H. Edwards, S. Stoll, J. Magn. Reson. 2016, 270, 87.
N. Florin, O. Schiemann, G. Hagelueken, BMC Struct. Biol. 2014, 14, 16.
C. A. Heubach, Z. Hasanbasri, D. Abdullin, A. Reuter, B. Korzekwa, S. Saxena, O. Schiemann, Chem. - Eur. J. 2023. https://doi.org/10.1002/chem.202302541