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  1. AU="Jeschke, Gunnar"
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  1. Article ; Online: Protein ensemble modeling and analysis with MMMx.

    Jeschke, Gunnar

    Protein science : a publication of the Protein Society

    2024  Volume 33, Issue 3, Page(s) e4906

    Abstract: Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support ... ...

    Abstract Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support the design of experiments to characterize the distributed structure of such proteins, starting from AlphaFold2 predictions or folded domain structures. Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained. The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain. The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor. Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.
    MeSH term(s) Models, Molecular ; Proteins/chemistry ; Protein Conformation
    Chemical Substances Proteins
    Language English
    Publishing date 2024-02-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4906
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  2. Article ; Online: Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches.

    Jeschke, Gunnar

    Biomolecules

    2022  Volume 12, Issue 10

    Abstract: Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium- ... ...

    Abstract Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium-sized protein complexes. Such measurements do not require long-range ordering and are therefore applicable to systems with partial disorder. Data from spin-label-based measurements can be processed into distance distributions that provide information about the extent of such disorder. Using such information in modelling presents several challenges, including a small number of restraints, the influence of the label itself on the measured distance and distribution width, and balancing the fitting quality of the long-range restraints with the fitting quality of other restraint subsets. Starting with general considerations about integrative and hybrid structural modelling, this review provides an overview of recent approaches to these problems and identifies where further progress is needed.
    MeSH term(s) Models, Molecular ; Electron Spin Resonance Spectroscopy/methods ; Spin Labels ; Proteins/chemistry
    Chemical Substances Spin Labels ; Proteins
    Language English
    Publishing date 2022-09-25
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom12101369
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  3. Article: The contribution of modern EPR to structural biology.

    Jeschke, Gunnar

    Emerging topics in life sciences

    2021  Volume 2, Issue 1, Page(s) 9–18

    Abstract: Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is ... ...

    Abstract Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.
    Language English
    Publishing date 2021-01-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20170143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Rotational Coupling in Methyl-Tunneling Electron Spin Echo Envelope Modulation.

    Jeschke, Gunnar

    Applied magnetic resonance

    2021  Volume 53, Issue 3-5, Page(s) 635–651

    Abstract: Coherence between tunnel-split states of a methyl quantum rotor can be generated and observed in stimulated and spin-locked echo experiments, if hyperfine coupling of a nearby electron spin to the methyl protons breaks ... ...

    Abstract Coherence between tunnel-split states of a methyl quantum rotor can be generated and observed in stimulated and spin-locked echo experiments, if hyperfine coupling of a nearby electron spin to the methyl protons breaks C
    Language English
    Publishing date 2021-07-14
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 1480644-7
    ISSN 1613-7507 ; 0937-9347
    ISSN (online) 1613-7507
    ISSN 0937-9347
    DOI 10.1007/s00723-021-01375-6
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  5. Article ; Online: Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches

    Jeschke, Gunnar

    Biomolecules, 12 (10)

    2022  

    Abstract: Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium- ... ...

    Abstract Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium-sized protein complexes. Such measurements do not require long-range ordering and are therefore applicable to systems with partial disorder. Data from spin-label-based measurements can be processed into distance distributions that provide information about the extent of such disorder. Using such information in modelling presents several challenges, including a small number of restraints, the influence of the label itself on the measured distance and distribution width, and balancing the fitting quality of the long-range restraints with the fitting quality of other restraint subsets. Starting with general considerations about integrative and hybrid structural modelling, this review provides an overview of recent approaches to these problems and identifies where further progress is needed.

    ISSN:2218-273X
    Keywords EPR spectroscopy ; double electron electron resonance ; FRET ; ensemble model ; intrinsic disorder ; structural biology ; site-directed spin labelling ; molecular force fields
    Subject code 530
    Language English
    Publisher MDPI
    Publishing country ch
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: MMM: Integrative ensemble modeling and ensemble analysis.

    Jeschke, Gunnar

    Protein science : a publication of the Protein Society

    2020  Volume 30, Issue 1, Page(s) 125–135

    Abstract: Proteins and their complexes can be heterogeneously disordered. In ensemble modeling of such systems with restraints from several experimental techniques the following problems arise: (a) integration of diverse restraints obtained on different samples ... ...

    Abstract Proteins and their complexes can be heterogeneously disordered. In ensemble modeling of such systems with restraints from several experimental techniques the following problems arise: (a) integration of diverse restraints obtained on different samples under different conditions; (b) estimation of a realistic ensemble width; (c) sufficient sampling of conformational space; (d) representation of the ensemble by an interpretable number of conformers; (e) recognition of weak order with site resolution. Here, I introduce several tools that address these problems, focusing on utilization of distance distribution information for estimating ensemble width. The RigiFlex approach integrates such information with high-resolution structures of ordered domains and small-angle scattering data. The EnsembleFit module provides moderately sized ensembles by fitting conformer populations and discarding conformers with low population. EnsembleFit balances the loss in fit quality upon combining restraint subsets from different techniques. Pair correlation analysis for residues and local compaction analysis help in feature detection. The RigiFlex pipeline is tested on data simulated from the structure 70 kDa protein-RNA complex RsmE/RsmZ. It recovers this structure with ensemble width and difference from ground truth both being on the order of 4.2 Å. EnsembleFit reduces the ensemble of the proliferating-cell-nuclear-antigen-associated factor p15
    MeSH term(s) DNA-Binding Proteins/chemistry ; Escherichia coli O157/chemistry ; Escherichia coli Proteins/chemistry ; Humans ; Methyltransferases/chemistry ; Models, Molecular ; Protein Conformation
    Chemical Substances DNA-Binding Proteins ; Escherichia coli Proteins ; PCLAF protein, human ; PaaA2 protein, E coli ; Methyltransferases (EC 2.1.1.-) ; RsmE protein, E coli (EC 2.1.1.-)
    Language English
    Publishing date 2020-10-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.3965
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3407: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 1: Show issues

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  7. Article ; Online: MMM

    Jeschke, Gunnar

    Protein Science, 30 (1)

    Integrative ensemble modeling and ensemble analysis

    2021  

    Abstract: Proteins and their complexes can be heterogeneously disordered. In ensemble modeling of such systems with restraints from several experimental techniques the following problems arise: (a) integration of diverse restraints obtained on different samples ... ...

    Abstract Proteins and their complexes can be heterogeneously disordered. In ensemble modeling of such systems with restraints from several experimental techniques the following problems arise: (a) integration of diverse restraints obtained on different samples under different conditions; (b) estimation of a realistic ensemble width; (c) sufficient sampling of conformational space; (d) representation of the ensemble by an interpretable number of conformers; (e) recognition of weak order with site resolution. Here, I introduce several tools that address these problems, focusing on utilization of distance distribution information for estimating ensemble width. The RigiFlex approach integrates such information with high-resolution structures of ordered domains and small-angle scattering data. The EnsembleFit module provides moderately sized ensembles by fitting conformer populations and discarding conformers with low population. EnsembleFit balances the loss in fit quality upon combining restraint subsets from different techniques. Pair correlation analysis for residues and local compaction analysis help in feature detection. The RigiFlex pipeline is tested on data simulated from the structure 70 kDa protein-RNA complex RsmE/RsmZ. It recovers this structure with ensemble width and difference from ground truth both being on the order of 4.2 angstrom. EnsembleFit reduces the ensemble of the proliferating-cell-nuclear-antigen-associated factor p15(PAF)from 4,939 to 75 conformers while maintaining good fit quality of restraints. Local compaction analysis for the PaaA2 antitoxin fromE. coliO157 revealed correlations between compactness and enhanced residual dipolar couplings in the original NMR restraint set.

    ISSN:1469-896X

    ISSN:0961-8368
    Keywords Distance distributions ; Docking ; Ensemble modeling ; Integrative structural biology ; Protein complexes ; RNA ; Site-directed spin labeling
    Subject code 612
    Language English
    Publisher Wiley
    Publishing country ch
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Quo vadis EPR?

    Jeschke, Gunnar

    Journal of magnetic resonance (San Diego, Calif. : 1997)

    2019  Volume 306, Page(s) 36–41

    Abstract: Complexity of paramagnetic catalysts and materials increases, and the same applies to systems targeted by integrative structural biology. Hence, EPR spectroscopists must find ways to enhance information content of their data. I argue that a third major ... ...

    Abstract Complexity of paramagnetic catalysts and materials increases, and the same applies to systems targeted by integrative structural biology. Hence, EPR spectroscopists must find ways to enhance information content of their data. I argue that a third major wave of method development in EPR spectroscopy, which is triggered by recent advances in digital electronics and computing, can achieve this. Transfer of NMR methods to EPR will go on, but part of the new EPR methodology will depend on completely new concepts.
    Language English
    Publishing date 2019-07-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1469665-4
    ISSN 1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
    ISSN (online) 1096-0856 ; 1557-8968
    ISSN 1090-7807 ; 0022-2364
    DOI 10.1016/j.jmr.2019.07.008
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  9. Book ; Online: Ensemble model of dispersed hnRNP A1

    Jeschke, Gunnar

    2020  

    Abstract: Based on the NMR structure of UP1 (PDB 2LYV), the glycine-rich domain (188-320) was modelled using 19 distance distribution restraints. The ensemble model was validated by jack-knife resampling. ... MMMx (github.com/gjeschke/MMMx) ...

    Abstract Based on the NMR structure of UP1 (PDB 2LYV), the glycine-rich domain (188-320) was modelled using 19 distance distribution restraints. The ensemble model was validated by jack-knife resampling.

    MMMx (github.com/gjeschke/MMMx)
    Keywords ensemble model ; distance distributions ; RNA-binding protein ; Intrinsically disordered domains ; EPR spectroscopy ; DEER spectroscopy ; info:eu-repo/classification/ddc/570 ; Life sciences
    Language English
    Publishing date 2020-12-01
    Publisher ETH Zurich
    Publishing country ch
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Integrative ensemble modeling of proteins and their complexes with distance distribution restraints.

    Jeschke, Gunnar / Esteban-Hofer, Laura

    Methods in enzymology

    2022  Volume 666, Page(s) 145–169

    Abstract: Many proteins and protein complexes exhibit regions that are intrinsically disordered. Whereas an arsenal of techniques exists to characterize structured proteins or protein regions, characterization of the vast conformational space occupied by ... ...

    Abstract Many proteins and protein complexes exhibit regions that are intrinsically disordered. Whereas an arsenal of techniques exists to characterize structured proteins or protein regions, characterization of the vast conformational space occupied by intrinsically disordered regions remains a challenging task due the ensemble-averaging nature of many techniques that provide mean value restraints. More representative information can be gained in the form of distribution restraints, such as EPR-derived distance distributions. Previously we developed the ensemble modeling tool MMM, where we partition the macromolecule into structured and unstructured domains and utilize an integrative structural approach with a focus on EPR-derived distance restraints. Here we present the successor program of MMM: MMMx. All the modeling functionality was ported to MMMx and is now accessed by a uniform script format, allowing to combine the different modules at will to modeling pipelines. During the conception of MMMx many of the tools were improved or updated. We discuss the general functionality of MMMx and its modules, and illustrate some of the modeling tools by application examples.
    MeSH term(s) Models, Molecular ; Protein Conformation ; Protein Domains ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2022-03-25
    Publishing country United States
    Document type Journal Article
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2022.02.010
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