1
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Sato M, Hariyama M, Komiya M, Suzuki K, Tozawa Y, Yamamoto H, Hirano-Iwata A. Model-free idealization: Adaptive integrated approach for idealization of ion-channel currents. Biophys J 2023; 122:3959-3975. [PMID: 37634080 PMCID: PMC10560676 DOI: 10.1016/j.bpj.2023.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/21/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023] Open
Abstract
Single-channel electrophysiological recordings provide insights into transmembrane ion permeation and channel gating mechanisms. The first step in the analysis of the recorded currents involves an "idealization" process, in which noisy raw data are classified into two discrete levels corresponding to the open and closed states of channels. This provides valuable information on the gating kinetics of ion channels. However, the idealization step is often challenging in cases of currents with poor signal-to-noise ratios and baseline drifts, especially when the gating model of the target channel is not identified. We report herein on a highly robust model-free idealization method for achieving this goal. The algorithm, called adaptive integrated approach for idealization of ion-channel currents (AI2), is composed of Kalman filter and Gaussian mixture model clustering and functions without user input. AI2 automatically determines the noise reduction setting based on the degree of separation between the open and closed levels. We validated the method on pseudo-channel-current datasets that contain either computed or experimentally recorded noise. We also investigated the relationship between the noise reduction parameter of the Kalman filter and the cutoff frequency of the low-pass filter. The AI2 algorithm was then tested on actual experimental data for biological channels including gramicidin A, a voltage-gated sodium channel, and other unidentified channels. We compared the idealization results with those obtained by the conventional methods, including the 50%-threshold-crossing method.
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Affiliation(s)
- Madoka Sato
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Masanori Hariyama
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.
| | - Maki Komiya
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, Sendai, Miyagi, Japan
| | - Kae Suzuki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan; Epsilon Molecular Engineering, Inc, Open Innovation Center in Saitama University, Saitama, Japan
| | - Yuzuru Tozawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Hideaki Yamamoto
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, Sendai, Miyagi, Japan
| | - Ayumi Hirano-Iwata
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Miyagi, Japan; Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, Sendai, Miyagi, Japan; Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Miyagi, Japan.
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2
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Ghosh M, Denkert N, Reuter M, Klümper J, Reglinski K, Peschel R, Schliebs W, Erdmann R, Meinecke M. Dynamics of the translocation pore of the human peroxisomal protein import machinery. Biol Chem 2023; 404:169-178. [PMID: 35977096 DOI: 10.1515/hsz-2022-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/05/2022] [Indexed: 01/15/2023]
Abstract
Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and imported in a posttranslational manner. Intricate protein import machineries have evolved that catalyze the different stages of translocation. In humans, PEX5L was found to be an essential component of the peroxisomal translocon. PEX5L is the main receptor for substrate proteins carrying a peroxisomal targeting signal (PTS). Substrates are bound by soluble PEX5L in the cytosol after which the cargo-receptor complex is recruited to peroxisomal membranes. Here, PEX5L interacts with the docking protein PEX14 and becomes part of an integral membrane protein complex that facilitates substrate translocation into the peroxisomal lumen in a still unknown process. In this study, we show that PEX5L containing complexes purified from human peroxisomal membranes constitute water-filled pores when reconstituted into planar-lipid membranes. Channel characteristics were highly dynamic in terms of conductance states, selectivity and voltage- and substrate-sensitivity. Our results show that a PEX5L associated pore exists in human peroxisomes, which can be activated by receptor-cargo complexes.
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Affiliation(s)
- Mausumi Ghosh
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany.,Institute for Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Niels Denkert
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany.,Institute for Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Maren Reuter
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Jessica Klümper
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Katharina Reglinski
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Michael Meinecke
- Biochemistry Center (BZH), Heidelberg University, D-69120 Heidelberg, Germany.,Institute for Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
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3
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Miller AN, Houlihan PR, Matamala E, Cabezas-Bratesco D, Lee GY, Cristofori-Armstrong B, Dilan TL, Sanchez-Martinez S, Matthies D, Yan R, Yu Z, Ren D, Brauchi SE, Clapham DE. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. eLife 2023; 12:e84477. [PMID: 36695574 PMCID: PMC9910834 DOI: 10.7554/elife.84477] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/25/2023] [Indexed: 01/26/2023] Open
Abstract
The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as viroporins. Here, we show that neither SARS-CoV-2 nor SARS-CoV-1 Orf3a form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a positively charged aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a's ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
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Affiliation(s)
| | | | - Ella Matamala
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
| | - Deny Cabezas-Bratesco
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
| | - Gi Young Lee
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | | | | | | | | | - Rui Yan
- Janelia Research CampusAshburnUnited States
| | - Zhiheng Yu
- Janelia Research CampusAshburnUnited States
| | - Dejian Ren
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Sebastian E Brauchi
- Janelia Research CampusAshburnUnited States
- Physiology Institute and Millennium Nucleus of Ion Channel-Associated Diseases, Universidad Austral de ChileValdiviaChile
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4
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Miller AN, Houlihan PR, Matamala E, Cabezas-Bratesco D, Lee GY, Cristofori-Armstrong B, Dilan TL, Sanchez-Martinez S, Matthies D, Yan R, Yu Z, Ren D, Brauchi SE, Clapham DE. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.02.506428. [PMID: 36263072 PMCID: PMC9580380 DOI: 10.1101/2022.09.02.506428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as a viroporin. Here we show that neither SARS-CoV-2 nor SARS-CoV-1 form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a basic aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.
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5
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Ball STM, Celik N, Sayari E, Abdul Kadir L, O’Brien F, Barrett-Jolley R. DeepGANnel: Synthesis of fully annotated single molecule patch-clamp data using generative adversarial networks. PLoS One 2022; 17:e0267452. [PMID: 35536793 PMCID: PMC9089889 DOI: 10.1371/journal.pone.0267452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/09/2022] [Indexed: 11/19/2022] Open
Abstract
Development of automated analysis tools for “single ion channel” recording is hampered by the lack of available training data. For machine learning based tools, very large training sets are necessary with sample-by-sample point labelled data (e.g., 1 sample point every 100microsecond). In an experimental context, such data are labelled with human supervision, and whilst this is feasible for simple experimental analysis, it is infeasible to generate the enormous datasets that would be necessary for a big data approach using hand crafting. In this work we aimed to develop methods to generate simulated ion channel data that is free from assumptions and prior knowledge of noise and underlying hidden Markov models. We successfully leverage generative adversarial networks (GANs) to build an end-to-end pipeline for generating an unlimited amount of labelled training data from a small, annotated ion channel “seed” record, and this needs no prior knowledge of theoretical dynamical ion channel properties. Our method utilises 2D CNNs to maintain the synchronised temporal relationship between the raw and idealised record. We demonstrate the applicability of the method with 5 different data sources and show authenticity with t-SNE and UMAP projection comparisons between real and synthetic data. The model would be easily extendable to other time series data requiring parallel labelling, such as labelled ECG signals or raw nanopore sequencing data.
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Affiliation(s)
- Sam T. M. Ball
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
| | - Numan Celik
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
| | - Elaheh Sayari
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
| | - Lina Abdul Kadir
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
| | - Fiona O’Brien
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
| | - Richard Barrett-Jolley
- Faculty of Health and Life Science, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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6
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Bücher A, Dette H, Heinrichs F. Are deviations in a gradually varying mean relevant? A testing approach based on sup-norm estimators. Ann Stat 2021. [DOI: 10.1214/21-aos2098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Axel Bücher
- Mathematisches Institut, Heinrich-Heine-Universität Düsseldorf
| | - Holger Dette
- Fakultät für Mathematik, Ruhr-Universität Bochum
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7
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Romano G, Rigaill G, Runge V, Fearnhead P. Detecting Abrupt Changes in the Presence of Local Fluctuations and Autocorrelated Noise. J Am Stat Assoc 2021. [DOI: 10.1080/01621459.2021.1909598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Gaetano Romano
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université Paris-Saclay, CNRS, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, Evry-Courcouronnes, France
| | - Vincent Runge
- Université Paris-Saclay, CNRS, Univ Evry, Laboratoire de Mathématiques et Modélisation d’Evry, Evry-Courcouronnes, France
| | - Paul Fearnhead
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
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8
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Pein F, Eltzner B, Munk A. Analysis of patchclamp recordings: model-free multiscale methods and software. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:187-209. [PMID: 33837454 PMCID: PMC8071803 DOI: 10.1007/s00249-021-01506-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/02/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
Analysis of patchclamp recordings is often a challenging issue. We give practical guidance how such recordings can be analyzed using the model-free multiscale idealization methodology JSMURF, JULES, and HILDE. We provide an operational manual how to use the accompanying software available as an R-package and as a graphical user interface. This includes selection of the right approach and tuning of parameters. We also discuss advantages and disadvantages of model-free approaches in comparison to hidden Markov model approaches and explain how they complement each other.
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Affiliation(s)
- Florian Pein
- Statistical Laboratory, DPMMS, University of Cambridge, Cambridge, UK.
| | - Benjamin Eltzner
- Institute for Mathematical Stochastics, Georg-August-University of Goettingen, Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, Georg-August-University of Goettingen, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, Göttingen, Germany
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9
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Pein F, Bartsch A, Steinem C, Munk A. Heterogeneous Idealization of Ion Channel Recordings - Open Channel Noise. IEEE Trans Nanobioscience 2020; 20:57-78. [PMID: 33052850 DOI: 10.1109/tnb.2020.3031202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose a new model-free segmentation method for idealizing ion channel recordings. This method is designed to deal with heterogeneity of measurement errors. This in particular applies to open channel noise which, in general, is particularly difficult to cope with for model-free approaches. Our methodology is able to deal with lowpass filtered data which provides a further computational challenge. To this end we propose a multiresolution testing approach, combined with local deconvolution to resolve the lowpass filter. Simulations and statistical theory confirm that the proposed idealization recovers the underlying signal very accurately at presence of heterogeneous noise, even when events are shorter than the filter length. The method is compared to existing approaches in computer experiments and on real data. We find that it is the only one which allows to identify openings of the PorB porine at two different temporal scales. An implementation is available as an R package.
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10
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Enikeeva F, Munk A, Pohlmann M, Werner F. Bump detection in the presence of dependency: Does it ease or does it load? BERNOULLI 2020. [DOI: 10.3150/20-bej1226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Hrd1 forms the retrotranslocation pore regulated by auto-ubiquitination and binding of misfolded proteins. Nat Cell Biol 2020; 22:274-281. [DOI: 10.1038/s41556-020-0473-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/20/2020] [Indexed: 01/01/2023]
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12
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Bartsch A, Llabrés S, Pein F, Kattner C, Schön M, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C. High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB. Sci Rep 2019; 9:1264. [PMID: 30718567 PMCID: PMC6362148 DOI: 10.1038/s41598-018-37066-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
The permeation of most antibiotics through the outer membrane of Gram-negative bacteria occurs through porin channels. To design drugs with increased activity against Gram-negative bacteria in the face of the antibiotic resistance crisis, the strict constraints on the physicochemical properties of the permeants imposed by these channels must be better understood. Here we show that a combination of high-resolution electrophysiology, new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding events between the β-lactam antibiotic ampicillin and the porin PorB from the pathogenic bacterium Neisseria meningitidis. In particular, an asymmetry often seen in the electrophysiological characteristics of ligand-bound channels is utilised to characterise the binding site and molecular interactions in detail, based on the principles of electro-osmotic flow through the channel. Our results provide a rationale for the determinants that govern the binding and permeation of zwitterionic antibiotics in porin channels.
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Affiliation(s)
- Annika Bartsch
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK
| | - Florian Pein
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Christof Kattner
- ZIK HALOmem, Membrane Protein Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes Straße 3, 06120, Halle (Saale), Germany
- Juno Therapeutics GmbH, Göttingen, Germany
| | - Markus Schön
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Manuel Diehn
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Mikio Tanabe
- Institute of Materials Structure Science, Structural Biology Research Center, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Nethergate, Dundee, DD1 5EH, UK.
- Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee, DD1 4NH, UK.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany.
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13
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Diehn M, Munk A, Rudolf D. Maximum likelihood estimation in hidden Markov models with inhomogeneous noise. ESAIM-PROBAB STAT 2019. [DOI: 10.1051/ps/2018017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We consider parameter estimation in finite hidden state space Markov models with time-dependent inhomogeneous noise, where the inhomogeneity vanishes sufficiently fast. Based on the concept of asymptotic mean stationary processes we prove that the maximum likelihood and a quasi-maximum likelihood estimator (QMLE) are strongly consistent. The computation of the QMLE ignores the inhomogeneity, hence, is much simpler and robust. The theory is motivated by an example from biophysics and applied to a Poisson- and linear Gaussian model.
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14
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Affiliation(s)
- Paul Fearnhead
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
- Laboratoire de Mathématiques at Modélisation d’Evry (LaMME), Université d’Evry Val d’Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Paris, France
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15
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Pein F, Tecuapetla-Gomez I, Schutte OM, Steinem C, Munk A. Fully Automatic Multiresolution Idealization for Filtered Ion Channel Recordings: Flickering Event Detection. IEEE Trans Nanobioscience 2018; 17:300-320. [PMID: 29994220 DOI: 10.1109/tnb.2018.2845126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We propose a new model-free segmentation method, JULES, which combines recent statistical multiresolution techniques with local deconvolution for idealization of ion channel recordings. The multiresolution criterion takes into account scales down to the sampling rate enabling the detection of flickering events, i.e., events on small temporal scales, even below the filter frequency. For such small scales the deconvolution step allows for a precise determination of dwell times and, in particular, of amplitude levels, a task which is not possible with common thresholding methods. This is confirmed theoretically and in a comprehensive simulation study. In addition, JULES can be applied as a preprocessing method for a refined hidden Markov analysis. Our new methodology allows us to show that gramicidin A flickering events have the same amplitude as the slow gating events. JULES is available as an R function jules in the package clampSeg.
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16
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Yi T, Wang Z. Bayesian sieve method for piece-wise smooth regression. Stat Probab Lett 2017. [DOI: 10.1016/j.spl.2017.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Denkert N, Schendzielorz AB, Barbot M, Versemann L, Richter F, Rehling P, Meinecke M. Cation selectivity of the presequence translocase channel Tim23 is crucial for efficient protein import. eLife 2017; 6. [PMID: 28857742 PMCID: PMC5578737 DOI: 10.7554/elife.28324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/31/2017] [Indexed: 01/09/2023] Open
Abstract
Virtually all mitochondrial matrix proteins and a considerable number of inner membrane proteins carry a positively charged, N-terminal presequence and are imported by the TIM23 complex (presequence translocase) located in the inner mitochondrial membrane. The voltage-regulated Tim23 channel constitutes the actual protein-import pore wide enough to allow the passage of polypeptides with a secondary structure. In this study, we identify amino acids important for the cation selectivity of Tim23. Structure based mutants show that selectivity is provided by highly conserved, pore-lining amino acids. Mutations of these amino acid residues lead to reduced selectivity properties, reduced protein import capacity and they render the Tim23 channel insensitive to substrates. We thus show that the cation selectivity of the Tim23 channel is a key feature for substrate recognition and efficient protein import. The cells of animals, plants and other eukaryotic organisms contain compartments known as organelles that play many different roles. For example, compartments called mitochondria are responsible for supplying the chemical energy cells need to survive and grow. Two membranes surround each mitochondrion and energy is converted on the surface of the inner one. Mitochondria contain over 1,000 different proteins, most of which are produced in the main part of the cell and have to be transported into the mitochondria. A transport protein called Tim23 is part of a larger group or ‘complex’ of proteins that helps to import many other proteins into the mitochondria. This complex sits in the inner membrane, with the Tim23 protein forming a large, water-filled pore through its core that provides a route for proteins to pass through the membrane. Proteins are made of building blocks called amino acids. The proteins transported by the complex containing Tim23 all have a short chain of amino acids at one end known as an N-terminal presequence. However, it is not clear how the inside of the Tim23 channel identifies and transports this presequence to allow the right proteins to pass through the inner membrane. Denkert, Schendzielorz et al. studied the normal and mutant versions of a Tim23 channel from yeast to find out which parts of the protein are involved in detecting the N-terminal presequence after it enters the pore. The experiments show that there are several amino acids in Tim23 that play important roles in this process. Furthermore, mitochondria containing mutant Tim23 channels, that are less able to identify the N-terminal presequence, are impaired in their ability to import proteins. Tim23 proteins in humans and other organisms also contain most or all of the specific amino acids identified in this study, suggesting that the findings of Denkert, Schendzielorz et al. will also apply to other species. Furthermore, the experimental strategy used in this study could be adapted to investigate transport proteins in other cell compartments.
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Affiliation(s)
- Niels Denkert
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Mariam Barbot
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Lennart Versemann
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Frank Richter
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Göttinger Zentrum für Molekulare Biowissenschaften, Göttingen, Germany
| | - Michael Meinecke
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Göttinger Zentrum für Molekulare Biowissenschaften, Göttingen, Germany.,European Neuroscience Institute Göttingen, Göttingen, Germany
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Gnanasambandam R, Nielsen MS, Nicolai C, Sachs F, Hofgaard JP, Dreyer JK. Unsupervised Idealization of Ion Channel Recordings by Minimum Description Length: Application to Human PIEZO1-Channels. Front Neuroinform 2017; 11:31. [PMID: 28496407 PMCID: PMC5406404 DOI: 10.3389/fninf.2017.00031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/05/2017] [Indexed: 12/04/2022] Open
Abstract
Researchers can investigate the mechanistic and molecular basis of many physiological phenomena in cells by analyzing the fundamental properties of single ion channels. These analyses entail recording single channel currents and measuring current amplitudes and transition rates between conductance states. Since most electrophysiological recordings contain noise, the data analysis can proceed by idealizing the recordings to isolate the true currents from the noise. This de-noising can be accomplished with threshold crossing algorithms and Hidden Markov Models, but such procedures generally depend on inputs and supervision by the user, thus requiring some prior knowledge of underlying processes. Channels with unknown gating and/or functional sub-states and the presence in the recording of currents from uncorrelated background channels present substantial challenges to such analyses. Here we describe and characterize an idealization algorithm based on Rissanen's Minimum Description Length (MDL) Principle. This method uses minimal assumptions and idealizes ion channel recordings without requiring a detailed user input or a priori assumptions about channel conductance and kinetics. Furthermore, we demonstrate that correlation analysis of conductance steps can resolve properties of single ion channels in recordings contaminated by signals from multiple channels. We first validated our methods on simulated data defined with a range of different signal-to-noise levels, and then showed that our algorithm can recover channel currents and their substates from recordings with multiple channels, even under conditions of high noise. We then tested the MDL algorithm on real experimental data from human PIEZO1 channels and found that our method revealed the presence of substates with alternate conductances.
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Affiliation(s)
| | - Morten S. Nielsen
- Department of Biomedical Sciences and The Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Christopher Nicolai
- Department of Physiology and Biophysics, State University of New YorkBuffalo, NY, USA
| | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New YorkBuffalo, NY, USA
| | - Johannes P. Hofgaard
- Department of Biomedical Sciences and The Danish National Research Foundation Centre for Cardiac Arrhythmia, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Jakob K. Dreyer
- Center for Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
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Tecuapetla-Gómez I, Munk A. Autocovariance Estimation in Regression with a Discontinuous Signal and m-Dependent Errors: A Difference-Based Approach. Scand Stat Theory Appl 2016. [DOI: 10.1111/sjos.12256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Axel Munk
- Institute for Mathematical Stochastics; University of Goettingen
- Max Planck Institute for Biophysical Chemistry at Goettingen
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20
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Pein F, Sieling H, Munk A. Heterogeneous change point inference. J R Stat Soc Series B Stat Methodol 2016. [DOI: 10.1111/rssb.12202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Axel Munk
- Georg-August-Universität Göttingen and Max Planck Institute for Biophysical Chemistry; Göttingen Germany
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22
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Siekmann I, Sneyd J, Crampin EJ. Statistical analysis of modal gating in ion channels. Proc Math Phys Eng Sci 2014. [DOI: 10.1098/rspa.2014.0030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ion channels regulate the concentrations of ions within cells. By stochastically opening and closing its pore, they enable or prevent ions from crossing the cell membrane. However, rather than opening with a constant probability, many ion channels switch between several different levels of activity even if the experimental conditions are unchanged. This phenomenon is known as modal gating: instead of directly adapting its activity, the channel seems to mix sojourns in active and inactive modes in order to exhibit intermediate open probabilities. Evidence is accumulating that modal gating rather than modulation of opening and closing at a faster time scale is the primary regulatory mechanism of ion channels. However, currently, no method is available for reliably calculating sojourns in different modes. In order to address this challenge, we develop a statistical framework for segmenting single-channel datasets into segments that are characteristic for particular modes. The algorithm finds the number of mode changes, detects their locations and infers the open probabilities of the modes. We apply our approach to data from the inositol-trisphosphate receptor. Based upon these results, we propose that mode changes originate from alternative conformational states of the channel protein that determine a certain level of channel activity.
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Affiliation(s)
- Ivo Siekmann
- National ICT Australia, Victorian Research Laboratory, Melbourne, Australia
- Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Melbourne, Australia
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand
| | - Edmund J. Crampin
- National ICT Australia, Victorian Research Laboratory, Melbourne, Australia
- Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Melbourne, Australia
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Affiliation(s)
- Klaus Frick
- Interstate University of Applied Sciences of Technology; Buchs Switzerland
| | - Axel Munk
- University of Göttingen; Göttingen Germany
- Max Planck Institute for Biophysical Chemistry; Göttingen Germany
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Qian H, Kou SC. Statistics and Related Topics in Single-Molecule Biophysics. ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION 2014; 1:465-492. [PMID: 25009825 PMCID: PMC4084599 DOI: 10.1146/annurev-statistics-022513-115535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Since the universal acceptance of atoms and molecules as the fundamental constituents of matter in the early twentieth century, molecular physics, chemistry and molecular biology have all experienced major theoretical breakthroughs. To be able to actually "see" biological macromolecules, one at a time in action, one has to wait until the 1970s. Since then the field of single-molecule biophysics has witnessed extensive growth both in experiments and theory. A distinct feature of single-molecule biophysics is that the motions and interactions of molecules and the transformation of molecular species are necessarily described in the language of stochastic processes, whether one investigates equilibrium or nonequilibrium living behavior. For laboratory measurements following a biological process, if it is sampled over time on individual participating molecules, then the analysis of experimental data naturally calls for the inference of stochastic processes. The theoretical and experimental developments of single-molecule biophysics thus present interesting questions and unique opportunity for applied statisticians and probabilists. In this article, we review some important statistical developments in connection to single-molecule biophysics, emphasizing the application of stochastic-process theory and the statistical questions arising from modeling and analyzing experimental data.
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Affiliation(s)
- Hong Qian
- Department of Applied Mathematics, University of Washington Seattle, WA 98195
| | - S C Kou
- Department of Statistics, Harvard University, MA 02138
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