1. Structural Biology and Molecular Biophysics
  2. Chromosomes and Gene Expression
Download icon

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

  1. Ramasubramanian Sundaramoorthy
  2. Amanda L Hughes
  3. Vijender Singh
  4. Nicola Wiechens
  5. Daniel P Ryan
  6. Hassane El-Mkami
  7. Maxim Petoukhov
  8. Dmitri I svergun
  9. Barbara Treutlein
  10. Salina Quack
  11. Monika Fischer
  12. Jens Michaelis
  13. Bettina Böttcher
  14. David G Norman
  15. Tom Owen-Hughes  Is a corresponding author
  1. University of Dundee, United Kingdom
  2. The Australian National University, Australia
  3. University of St Andrews, United Kingdom
  4. European Molecular Biology Laboratory, Germany
  5. Max Planck Institute for Evolutionary Anthropolgy, Germany
  6. Ulm University, Germany
  7. Universitat Würzburg, Germany
Research Article
  • Cited 39
  • Views 2,745
  • Annotations
Cite this article as: eLife 2017;6:e22510 doi: 10.7554/eLife.22510

Abstract

The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.

Data availability

The following data sets were generated
    1. Ramasubramanian Sundaramoorthy
    (2016) Chd1-nuc-engaged
    Publicly available at the Electron Microscopy Data Bank (accession no. EMDB-3502).
    http://www.ebi.ac.uk/pdbe/entry/emdb/EMDB-3502
    1. Vijender Singh
    (2016) Chd1 Nuc Seq
    Publicly available at the EMBL European Archive (accession no: PRJEB15701).
    http://www.ebi.ac.uk/ena/data/view/PRJEB15701
    1. Ramasubramanian Sundaramoorthy
    (2016) Chd1-nuc apo
    Publicly available at the Electron Microscopy Data Bank (accession no. EMDB-3517).
    http://www.ebi.ac.uk/pdbe/entry/emdb/EMDB-3517
    1. Ramasubramanian Sundaramoorthy
    (2016) SAXS
    Publicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBU7).
    https://www.sasbdb.org/data/SASDBU7
    1. Ramasubramanian Sundaramoorthy
    (2016) SAXS
    Publicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBV7).
    https://www.sasbdb.org/data/SASDBV7
    1. Ramasubramanian Sundaramoorthy
    (2016) SAXS
    Publicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBW7).
    https://www.sasbdb.org/data/SASDBW7
    1. Ramasubramanian Sundaramoorthy
    (2016) SAXS
    Publicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBX7).
    https://www.sasbdb.org/data/SASDBX7
    1. Ramasubramanian Sundaramoorthy
    (2016) SAXS
    Publicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBY7).
    https://www.sasbdb.org/data/SASDBY7

Article and author information

Author details

  1. Ramasubramanian Sundaramoorthy

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  2. Amanda L Hughes

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  3. Vijender Singh

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  4. Nicola Wiechens

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  5. Daniel P Ryan

    Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9842-2620

  6. Hassane El-Mkami

    School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  7. Maxim Petoukhov

    Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
    Competing interests
    The authors declare that no competing interests exist.

  8. Dmitri I svergun

    Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
    Competing interests
    The authors declare that no competing interests exist.

  9. Barbara Treutlein

    Max Planck Institute for Evolutionary Anthropolgy, Ulm, Germany
    Competing interests
    The authors declare that no competing interests exist.

  10. Salina Quack

    Institute for Biophysics, Ulm University, Ulm, Germany
    Competing interests
    The authors declare that no competing interests exist.

  11. Monika Fischer

    Institute for Biophysics, Ulm University, Ulm, Germany
    Competing interests
    The authors declare that no competing interests exist.

  12. Jens Michaelis

    Institute for Biophysics, Ulm University, Ulm, Germany
    Competing interests
    The authors declare that no competing interests exist.

  13. Bettina Böttcher

    Lehrstuhl für Biochemie, Universitat Würzburg, Würzburg, Germany
    Competing interests
    The authors declare that no competing interests exist.

  14. David G Norman

    Nucelic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7658-7720

  15. Tom Owen-Hughes

    Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
    For correspondence
    t.a.owenhughes@dundee.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0618-8185

Funding

Wellcome (95062)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Vijender Singh
  • Nicola Wiechens
  • Tom Owen-Hughes

Wellcome (097945/B/11/Z)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Vijender Singh
  • Nicola Wiechens
  • Tom Owen-Hughes

Wellcome (099149/Z/12/Z)

  • Ramasubramanian Sundaramoorthy
  • Hassane El-Mkami
  • David G Norman
  • Tom Owen-Hughes

Wellcome (97945)

  • Ramasubramanian Sundaramoorthy
  • Amanda L Hughes
  • Nicola Wiechens
  • Daniel P Ryan
  • David G Norman
  • Tom Owen-Hughes

European Molecular Biology Organization (ALTF 380-2015)

  • Amanda L Hughes

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Timothy Formosa, University of Utah, United States

Publication history

  1. Received: November 9, 2016
  2. Accepted: March 15, 2017
  3. Accepted Manuscript published: March 23, 2017 (version 1)
  4. Version of Record published: April 13, 2017 (version 2)

Copyright

© 2017, Sundaramoorthy et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,745
    Page views
  • 741
    Downloads
  • 39
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, Crossref, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Categories and tags

Research organism

Further reading

    1. Structural Biology and Molecular Biophysics

    Tracking the movement of discrete gating charges in a voltage-gated potassium channel

    Michael F Priest et al.
    Research Article Updated

    Positively charged amino acids respond to membrane potential changes to drive voltage sensor movement in voltage-gated ion channels, but determining the displacements of voltage sensor gating charges has proven difficult. We optically tracked the movement of the two most extracellular charged residues (R1 and R2) in the Shaker potassium channel voltage sensor using a fluorescent positively charged bimane derivative (qBBr) that is strongly quenched by tryptophan. By individually mutating residues to tryptophan within the putative pathway of gating charges, we observed that the charge motion during activation is a rotation and a tilted translation that differs between R1 and R2. Tryptophan-induced quenching of qBBr also indicates that a crucial residue of the hydrophobic plug is linked to the Cole–Moore shift through its interaction with R1. Finally, we show that this approach extends to additional voltage-sensing membrane proteins using the Ciona intestinalis voltage-sensitive phosphatase (CiVSP).

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor

    Yongjian Huang et al.
    Research Article

    The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that couples the binding of extracellular ligands, such as EGF and transforming growth factor-α (TGF-α), to the initiation of intracellular signaling pathways. EGFR binds to EGF and TGF-α with similar affinity, but generates different signals from these ligands. To address the mechanistic basis of this phenomenon, we have carried out cryo-EM analyses of human EGFR bound to EGF and TGF-α. We show that the extracellular module adopts an ensemble of dimeric conformations when bound to either EGF or TGF-α. The two extreme states of this ensemble represent distinct ligand-bound quaternary structures in which the membrane-proximal tips of the extracellular module are either juxtaposed or separated. EGF and TGF-α differ in their ability to maintain the conformation with the membrane-proximal tips of the extracellular module separated, and this conformation is stabilized preferentially by an oncogenic EGFR mutation. Close proximity of the transmembrane helices at the junction with the extracellular module has been associated previously with increased EGFR activity. Our results show how EGFR can couple the binding of different ligands to differential modulation of this proximity, thereby suggesting a molecular mechanism for the generation of ligand-sensitive differential outputs in this receptor family.

    1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics

    Neutrophil-mediated oxidative stress and albumin structural damage predict COVID-19-associated mortality

    Mohamed A Badawy et al.
    Research Article

    Human serum albumin (HSA) is the frontline antioxidant protein in blood with established anti-inflammatory and anticoagulation functions. Here we report that COVID-19-induced oxidative stress inflicts structural damages to HSA and is linked with mortality outcome in critically ill patients. We recruited 39 patients who were followed up for a median of 12.5 days (1-35 days), among them 23 had died. Analyzing blood samples from patients and healthy individuals (n=11), we provide evidence that neutrophils are major sources of oxidative stress in blood and that hydrogen peroxide is highly accumulated in plasmas of non-survivors. We then analyzed electron paramagnetic resonance (EPR) spectra of spin labelled fatty acids (SLFA) bound with HSA in whole blood of control, survivor, and non-survivor subjects (n=10-11). Non-survivor' HSA showed dramatically reduced protein packing order parameter, faster SLFA correlational rotational time, and smaller S/W ratio (strong-binding/weak-binding sites within HSA), all reflecting remarkably fluid protein microenvironments. Following loading/unloading of 16-DSA we show that transport function of HSA maybe impaired in severe patients. Stratified at the means, Kaplan–Meier survival analysis indicated that lower values of S/W ratio and accumulated H2O2 in plasma significantly predicted in-hospital mortality (S/W≤0.15, 81.8% (18/22) vs. S/W>0.15, 18.2% (4/22), p=0.023; plasma [H2O2]>8.6 mM, 65.2% (15/23) vs. 34.8% (8/23), p=0.043). When we combined these two parameters as the ratio ((S/W)/[H2O2]) to derive a risk score, the resultant risk score lower than the mean (< 0.019) predicted mortality with high fidelity (95.5% (21/22) vs. 4.5% (1/22), logrank c2 = 12.1, p=4.9x10-4). The derived parameters may provide a surrogate marker to assess new candidates for COVID-19 treatments targeting HSA replacements and/or oxidative stress.