Phosphorylation-Regulated Conformational Diversity and Topological Dynamics of an Intrinsically Disordered Nuclear Receptor

The Journal of Physical Chemistry B, vol. 129, pp. 7719–7730

Abstract

Site-specific phosphorylation of disordered proteins is often considered a marker of protein activity, yet it remains unclear how phosphorylation alters the conformational dynamics of disordered protein chains, such as those in the nuclear receptor superfamily. In the case of the disordered human glucocorticoid receptor N-terminal domain (GR NTD), a negatively charged region known as core activation function 1 (AF1c) features three phosphorylation sites, regulating its function and intracellular localization. Deletion of this sequence dramatically reduces the GR transcriptional activation ability in cell experiments. By developing a circuit topology-based fold analysis approach, combined with atomistic simulations, we reveal that site-specific phosphorylation facilitates the formation of nonlocal contacts, leading to the emergence of disordered compact topologies with significant entanglement, which are distinct from solvent-exposed topologies. While we observe that the topological buildup of solvent-exposed states is similar across different phosphovariants, it depends on the exact phosphorylation site for the disordered topologically compact states. This study thus reveals the complex regulatory role of the GR phosphorylation and introduces a unique analysis framework that can be broadly applied to studying the topological dynamics of disordered proteins.

Authors 5

1. Vasily Akulov Aachen Leiden Institute of Physics (LION) Medical Systems Biophysics and Bioengineering Division of Systems Pharmacology and Pharmacy Leiden Academic Centre for Drug Research Centre for Interdisciplinary Genome Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Centre for Interdisciplinary Genome Research, Faculty of Science

   Leiden Institute of Physics

   Leiden University

   Medical Systems Biophysics and Bioengineering, Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research

   Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, 2333 CC Leiden, The Netherlands

   Leiden Institute of Physics, Leiden University, 2300 RA Leiden, The Netherlands

   Medical Systems Biophysics and Bioengineering, Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

2. Alba Jiménez Panizo

   Institut de Biomedicina de la Universitat de Barcelona · Universitat de Barcelona

   Affiliation as printed

   Department of Biochemistry and Molecular Biomedicine

   Institute of Biomedicine (IBUB) of the University of Barcelona (UB)

   Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08014 Barcelona, Spain

3. Eva Estébanez‐Perpiñá

   Institut de Biomedicina de la Universitat de Barcelona · Universitat de Barcelona

   Affiliation as printed

   Department of Biochemistry and Molecular Biomedicine

   Institute of Biomedicine (IBUB) of the University of Barcelona (UB)

   Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), 08014 Barcelona, Spain

4. John van Noort Aachen Leiden Institute of Physics (LION) Centre for Interdisciplinary Genome Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Centre for Interdisciplinary Genome Research, Faculty of Science

   Leiden Institute of Physics

   Leiden University

   Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, 2333 CC Leiden, The Netherlands

   Leiden Institute of Physics, Leiden University, 2300 RA Leiden, The Netherlands

5. Alireza Mashaghi corresponding Aachen Medical Systems Biophysics and Bioengineering Division of Systems Pharmacology and Pharmacy Leiden Academic Centre for Drug Research Centre for Interdisciplinary Genome Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Centre for Interdisciplinary Genome Research, Faculty of Science

   Leiden University

   Medical Systems Biophysics and Bioengineering, Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research

   Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, 2333 CC Leiden, The Netherlands

   Medical Systems Biophysics and Bioengineering, Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands