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Syryamina VN, Matveeva AG, Bowman MK. Confidence limits in pulse dipolar EPR spectroscopy: estimates for individual measurements. Phys Chem Chem Phys 2024; 26:5537-5547. [PMID: 38284165 DOI: 10.1039/d3cp05797f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
The distribution of inter-label distances obtained by electron paramagnetic resonance (EPR) pulse dipolar spectroscopies (PDS), such as DEER aka PELDOR, gives a valuable characterization of structure on the nanometer scale. The impact of random experimental noise on such experiments is examined for three independent methods for analysing PDS data: the model-free method with Tikhonov regularization, model-free with Mellin-transformation, and a model-based method. All three methods show negative bias for the mean distance and positive bias for the distribution width. Both biases grow with increasing noise levels. The estimated confidence bands and the uncertainties obtained from a single experimental measurement by the standard bootstrapping or χ2-surface scanning approaches are inconsistent and can exclude the true distance distribution. Yet, both approaches can provide quite valuable support for hypothesis testing in PDS studies.
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Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
| | - Anna G Matveeva
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
| | - Michael K Bowman
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
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2
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Matveeva AG, Syryamina VN, Nekrasov VM, Bowman MK. Non-uniform sampling in pulse dipolar spectroscopy by EPR: the redistribution of noise and the optimization of data acquisition. Phys Chem Chem Phys 2021; 23:10335-10346. [PMID: 33881433 DOI: 10.1039/d1cp00705j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pulse dipolar spectroscopy (PDS) in Electron Paramagnetic Resonance (EPR) is the method of choice for determining the distance distribution function for mono-, bi- or multi- spin-labeled macromolecules and nanostructures. PDS acquisition schemes conventionally use uniform sampling of the dipolar trace, but non-uniform sampling (NUS) schemes can decrease the total measurement time or increase the accuracy of the resulting distance distributions. NUS requires optimization of the data acquisition scheme, as well as changes in data processing algorithms to accommodate the non-uniformly sampled data. We investigate in silico the applicability of the NUS approach in PDS, considering its effect on random, truncation and sampling noise in the experimental data. Each type of noise in the time-domain data propagates differently and non-uniformly into the distance spectrum as errors in the distance distribution. NUS schemes seem to be a valid approach for increasing sensitivity and/or throughput in PDS by decreasing and redistributing noise in the distance spectrum so that it has less impact on the distance spectrum.
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Affiliation(s)
- Anna G Matveeva
- Institute of Solid State Chemistry and Mechanochemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vyacheslav M Nekrasov
- Novosibirsk State University, 630090 Novosibirsk, Russia and Voevodsky Institute of Chemical Kinetics and Combustion of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Michael K Bowman
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA.
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Fábregas Ibáñez L, Jeschke G, Stoll S. DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:209-224. [PMID: 34568875 PMCID: PMC8462493 DOI: 10.5194/mr-1-209-2020] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/21/2020] [Indexed: 05/09/2023]
Abstract
Dipolar EPR spectroscopy (DEER and other techniques) enables the structural characterization of macromolecular and biological systems by measurement of distance distributions between unpaired electrons on a nanometer scale. The inference of these distributions from the measured signals is challenging due to the ill-posed nature of the inverse problem. Existing analysis tools are scattered over several applications with specialized graphical user interfaces. This renders comparison, reproducibility, and method development difficult. To remedy this situation, we present DeerLab, an open-source software package for analyzing dipolar EPR data that is modular and implements a wide range of methods. We show that DeerLab can perform one-step analysis based on separable non-linear least squares, fit dipolar multi-pathway models to multi-pulse DEER data, run global analysis with non-parametric distributions, and use a bootstrapping approach to fully quantify the uncertainty in the analysis.
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Affiliation(s)
- Luis Fábregas Ibáñez
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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Sweger SR, Pribitzer S, Stoll S. Bayesian Probabilistic Analysis of DEER Spectroscopy Data Using Parametric Distance Distribution Models. J Phys Chem A 2020; 124:6193-6202. [PMID: 32614584 PMCID: PMC7846514 DOI: 10.1021/acs.jpca.0c05026] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Double electron-electron resonance (DEER) spectroscopy measures distance distributions between spin labels in proteins, yielding important structural and energetic information about conformational landscapes. Analysis of an experimental DEER signal in terms of a distance distribution is a nontrivial task due to the ill-posed nature of the underlying mathematical inversion problem. This work introduces a Bayesian probabilistic inference approach to analyze DEER data, using a multi-Gauss mixture model for the distance distribution. The method uses Markov chain Monte Carlo (MCMC) sampling to determine a posterior probability distribution over model parameter space. This distribution contains all the information available from the data, including a full quantification of the uncertainty about the parameters. The corresponding uncertainty about the distance distribution is captured via an ensemble of posterior predictive distributions. Several synthetic examples illustrate the method. An experimental example shows the importance of model checking and comparison using residual analysis and Bayes factors. Overall, the Bayesian approach allows for more robust inference about protein conformations from DEER spectroscopy.
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Affiliation(s)
- Sarah R Sweger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stephan Pribitzer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Kuznetsova AA, Matveeva AG, Milov AD, Vorobjev YN, Dzuba SA, Fedorova OS, Kuznetsov NA. Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway. Nucleic Acids Res 2019; 46:11454-11465. [PMID: 30329131 PMCID: PMC6265485 DOI: 10.1093/nar/gky912] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Human apurinic/apyrimidinic (AP) endonuclease APE1 catalyses the hydrolysis of phosphodiester bonds on the 5′ side of an AP-site (in the base excision repair pathway) and of some damaged nucleotides (in the nucleotide incision repair pathway). The range of substrate specificity includes structurally unrelated damaged nucleotides. Here, to examine the mechanism of broad substrate specificity of APE1, we performed pulsed electron–electron double resonance (PELDOR) spectroscopy and pre-steady-state kinetic analysis with Förster resonance energy transfer (FRET) detection of DNA conformational changes during DNA binding and lesion recognition. Equilibrium PELDOR and kinetic FRET data revealed that DNA binding by APE1 leads to noticeable damage-dependent bending of a DNA duplex. Molecular dynamics simulations showed that the damaged nucleotide is everted from the DNA helix and placed into the enzyme’s binding pocket, which is formed by Asn-174, Asn-212, Asn-229, Ala-230, Phe-266 and Trp-280. Nevertheless, no damage-specific contacts were detected between these amino acid residues in the active site of the enzyme and model damaged substrates containing 1,N6-ethenoadenosine, α-adenosine, 5,6-dihydrouridine or F-site. These data suggest that the substrate specificity of APE1 is controlled by the ability of a damaged nucleotide to flip out from the DNA duplex in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna G Matveeva
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander D Milov
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yuri N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Worswick SG, Spencer JA, Jeschke G, Kuprov I. Deep neural network processing of DEER data. SCIENCE ADVANCES 2018; 4:eaat5218. [PMID: 30151430 PMCID: PMC6108566 DOI: 10.1126/sciadv.aat5218] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/20/2018] [Indexed: 05/24/2023]
Abstract
The established model-free methods for the processing of two-electron dipolar spectroscopy data [DEER (double electron-electron resonance), PELDOR (pulsed electron double resonance), DQ-EPR (double-quantum electron paramagnetic resonance), RIDME (relaxation-induced dipolar modulation enhancement), etc.] use regularized fitting. In this communication, we describe an attempt to process DEER data using artificial neural networks trained on large databases of simulated data. Accuracy and reliability of neural network outputs from real experimental data were found to be unexpectedly high. The networks are also able to reject exchange interactions and to return a measure of uncertainty in the resulting distance distributions. This paper describes the design of the training databases, discusses the training process, and rationalizes the observed performance. Neural networks produced in this work are incorporated as options into Spinach and DeerAnalysis packages.
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Affiliation(s)
- Steven G. Worswick
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - James A. Spencer
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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