1. Structural Biology and Molecular Biophysics

Ligand binding remodels protein side chain conformational heterogeneity

  1. Stephanie A Wankowicz
  2. Saulo H de Oliveira
  3. Daniel W Hogan
  4. Henry van den Bedem
  5. James S Fraser  Is a corresponding author
  1. University of California, San Francisco, United States
  2. Atomwise, Inc, United States
https://doi.org/10.7554/eLife.74114
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  1. Stephanie A Wankowicz
  2. Saulo H de Oliveira
  3. Daniel W Hogan
  4. Henry van den Bedem
  5. James S Fraser
(2022)
Ligand binding remodels protein side chain conformational heterogeneity
eLife 11:e74114.
https://doi.org/10.7554/eLife.74114
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Abstract

While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decrease and relative hydrophobicity increases. Across a series of 13 inhibitor bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from NMR studies suggesting that residual side chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

Data availability

Refined models are available here: https://zenodo.org/record/5533006#.YVJr2Z5KgUsCode can be found in the following repositories:-Dataset selection: https://github.com/stephaniewankowicz/PDB_selection_pipeline-Refinement/qFit pipeline: https://github.com/stephaniewankowicz/refinement_qFit-Analysis/Figures: https://github.com/fraser-lab/Apo_Holo_Analysis-qFit: https://github.com/ExcitedStates/qfit-3.0.

The following data sets were generated

Article and author information

Author details

  1. Stephanie A Wankowicz

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  2. Saulo H de Oliveira

    Atomwise, Inc, San Francisco, United States
    Competing interests
    Saulo H de Oliveira, is an employee of Atomwise Inc..

  3. Daniel W Hogan

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    No competing interests declared.

  4. Henry van den Bedem

    Atomwise, Inc, San Francisco, United States
    Competing interests
    Henry van den Bedem, is an employee of Atomwise Inc..

  5. James S Fraser

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    For correspondence
    jfraser@fraserlab.com
    Competing interests
    James S Fraser, has equity, has received consulting fees, and has sponsored research agreements with Relay Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5080-2859

Funding

National Science Foundation (GRFP 2034836)

  • Stephanie A Wankowicz

National Institutes of Health (GM123159)

  • James S Fraser

National Institutes of Health (GM124149)

  • James S Fraser

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

Reviewing Editor

  1. Axel T Brunger, Stanford University School of Medicine, Howard Hughes Medical Institute, United States

Publication history

  1. Preprint posted: September 21, 2021 (view preprint)
  2. Received: September 22, 2021
  3. Accepted: March 18, 2022
  4. Accepted Manuscript published: March 21, 2022 (version 1)
  5. Version of Record published: May 9, 2022 (version 2)

Copyright

© 2022, Wankowicz 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. Stephanie A Wankowicz
  2. Saulo H de Oliveira
  3. Daniel W Hogan
  4. Henry van den Bedem
  5. James S Fraser
(2022)
Ligand binding remodels protein side chain conformational heterogeneity
eLife 11:e74114.
https://doi.org/10.7554/eLife.74114

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