Fuzzy supertertiary interactions within PSD-95 enable ligand binding

  1. George L Hamilton
  2. Nabanita Saikia
  3. Sujit Basak
  4. Franceine S Welcome
  5. Fang Wu
  6. Jakub Kubiak
  7. Changcheng Zhang
  8. Yan Hao
  9. Claus AM Seidel
  10. Feng Ding  Is a corresponding author
  11. Hugo Sanabria  Is a corresponding author
  12. Mark E Bowen  Is a corresponding author
  1. Clemson University, United States
  2. Stony Brook University, United States
  3. Heinrich-Heine-University Düsseldorf, Germany
  4. Heinrich Heine University Düsseldorf, Germany

Abstract

The scaffold protein PSD-95 links postsynaptic receptors to sites of presynaptic neurotransmitter release. Flexible linkers between folded domains in PSD-95 enable a dynamic supertertiary structure. Interdomain interactions within the PSG supramodule, formed by PDZ3, SH3 and Guanylate Kinase domains, regulate PSD-95 activity. Here we combined Discrete Molecular Dynamics and single molecule FRET to characterize the PSG supramodule, with time resolution spanning picoseconds to seconds. We used a FRET network to measure distances in full-length PSD-95 and model the conformational ensemble. We found that PDZ3 samples two conformational basins, which we confirmed with disulfide mapping. To understand effects on activity, we measured binding of the synaptic adhesion protein neuroligin. We found that PSD-95 bound neuroligin well at physiological pH while truncated PDZ3 bound poorly. Our hybrid structural models reveal how the supertertiary context of PDZ3 enables recognition of this critical synaptic ligand.

Data availability

Datasets of FRET values from smTIRF have been uploaded as Figure 4-Source Data 1. The MATLAB scripts used to analyze smTIRF data have been uploaded as Source Code 1. Datasets from Confocal Microscopy with Multiparameter Fluorescence Detection (Raw, MFD Bursts, TCSPC, PDA, and FCS), along with structures used in generating simulated distances and DMD screening, are available at Zenodo (DOI: 10.5281/zenodo.6983428). Datasets from Discrete Molecular Dynamics are available at https://dlab.clemson.edu/research/PSD95-PSG/.

Article and author information

Author details

  1. George L Hamilton

    Department of Physics and Astronomy, Clemson University, Clemson, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Nabanita Saikia

    Department of Physics and Astronomy, Clemson University, Clemson, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sujit Basak

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Franceine S Welcome

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Fang Wu

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Jakub Kubiak

    Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Changcheng Zhang

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Yan Hao

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Claus AM Seidel

    Institute for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5171-149X
  10. Feng Ding

    Department of Physics and Astronomy, Clemson University, Clemson, United States
    For correspondence
    fding@clemson.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1850-6336
  11. Hugo Sanabria

    Department of Physics and Astronomy, Clemson University, Clemson, United States
    For correspondence
    hsanabr@clemson.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7068-6827
  12. Mark E Bowen

    Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
    For correspondence
    mark.bowen@stonybrook.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9525-6986

Funding

National Institute of Mental Health (MH081923)

  • Mark E Bowen

National Institute of General Medical Sciences (GM130451)

  • Hugo Sanabria

National Institute of General Medical Sciences (GM119691)

  • Feng Ding

National Science Foundation (MCB1749778)

  • Hugo Sanabria

National Science Foundation (CBET1553945)

  • Feng Ding

European Research Council (671208)

  • George L Hamilton
  • Claus AM Seidel
  • Hugo Sanabria

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

Reviewing Editor

  1. Mary B Kennedy, California Institute of Technology, United States

Publication history

  1. Received: January 21, 2022
  2. Accepted: September 6, 2022
  3. Accepted Manuscript published: September 7, 2022 (version 1)

Copyright

© 2022, Hamilton 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.

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  1. George L Hamilton
  2. Nabanita Saikia
  3. Sujit Basak
  4. Franceine S Welcome
  5. Fang Wu
  6. Jakub Kubiak
  7. Changcheng Zhang
  8. Yan Hao
  9. Claus AM Seidel
  10. Feng Ding
  11. Hugo Sanabria
  12. Mark E Bowen
(2022)
Fuzzy supertertiary interactions within PSD-95 enable ligand binding
eLife 11:e77242.
https://doi.org/10.7554/eLife.77242
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