Ligand binding remodels protein side chain conformational heterogeneity

Abstract
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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

(2021) Ligand binding remodels protein side chain conformational heterogeneity
Zenodo,.

https://zenodo.org/record/5533006#.YVJr2Z5KgUs

Article and author information

Author details

Stephanie A Wankowicz

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Saulo H de Oliveira

Atomwise, Inc, San Francisco, United States

Competing interests
Saulo H de Oliveira, is an employee of Atomwise Inc..
Daniel W Hogan

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States

Competing interests
No competing interests declared.
Henry van den Bedem

Atomwise, Inc, San Francisco, United States

Competing interests
Henry van den Bedem, is an employee of Atomwise Inc..
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..

"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.

Copyright

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.