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Romero-Pérez PS, Moran HM, Horani A, Truong A, Manriquez-Sandoval E, Ramirez JF, Martinez A, Gollub E, Hunter K, Lotthammer JM, Emenecker RJ, Boothby TC, Holehouse AS, Fried SD, Sukenik S. Protein surface chemistry encodes an adaptive resistance to desiccation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.604841. [PMID: 39131385 PMCID: PMC11312438 DOI: 10.1101/2024.07.28.604841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Cellular desiccation - the loss of nearly all water from the cell - is a recurring stress in an increasing number of ecosystems that can drive proteome-wide protein unfolding and aggregation. For cells to survive this stress, at least some of the proteome must disaggregate and resume function upon rehydration. The molecular determinants that underlie the ability of proteins to do this remain largely unknown. Here, we apply quantitative and structural proteomic mass spectrometry to desiccated and rehydrated yeast extracts to show that some proteins possess an innate capacity to survive extreme water loss. Structural analysis correlates the ability of proteins to resist desiccation with their surface chemistry. Remarkably, highly resistant proteins are responsible for the production of the cell's building blocks - amino acids, metabolites, and sugars. Conversely, those proteins that are most desiccation-sensitive are involved in ribosome biogenesis and other energy consuming processes. As a result, the rehydrated proteome is preferentially enriched with metabolite and small molecule producers and depleted of some of the cell's heaviest consumers. We propose this functional bias enables cells to kickstart their metabolism and promote cell survival following desiccation and rehydration.
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Affiliation(s)
| | - Haley M. Moran
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Azeem Horani
- Quantitative and Systems Biology Program, University of California Merced, Merced, CA 95343, USA
| | - Alexander Truong
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Edgar Manriquez-Sandoval
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Alec Martinez
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Edith Gollub
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Kara Hunter
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Shahar Sukenik
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
- Quantitative and Systems Biology Program, University of California Merced, Merced, CA 95343, USA
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Usher ET, Fossat MJ, Holehouse AS. Phosphorylation of disordered proteins tunes local and global intramolecular interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598315. [PMID: 38915510 PMCID: PMC11195077 DOI: 10.1101/2024.06.10.598315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.
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Affiliation(s)
- Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
| | - Martin J. Fossat
- Department of Biological Physics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO, USA
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Ginell GM, Emenecker RJ, Lotthammer JM, Usher ET, Holehouse AS. Direct prediction of intermolecular interactions driven by disordered regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597104. [PMID: 38895487 PMCID: PMC11185574 DOI: 10.1101/2024.06.03.597104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for a wide variety of cellular functions, many of which involve interactions with partner proteins. Molecular recognition is typically considered through the lens of sequence-specific binding events. However, a growing body of work has shown that IDRs often interact with partners in a manner that does not depend on the precise order of the amino acid order, instead driven by complementary chemical interactions leading to disordered bound-state complexes. Despite this emerging paradigm, we lack tools to describe, quantify, predict, and interpret these types of structurally heterogeneous interactions from the underlying amino acid sequences. Here, we repurpose the chemical physics developed originally for molecular simulations to develop an approach for predicting intermolecular interactions between IDRs and partner proteins. Our approach enables the direct prediction of phase diagrams, the identification of chemically-specific interaction hotspots on IDRs, and a route to develop and test mechanistic hypotheses regarding IDR function in the context of molecular recognition. We use our approach to examine a range of systems and questions to highlight its versatility and applicability.
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Affiliation(s)
- Garrett M. Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Ryan. J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Emery T. Usher
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
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Lotthammer JM, Ginell GM, Griffith D, Emenecker RJ, Holehouse AS. Direct prediction of intrinsically disordered protein conformational properties from sequence. Nat Methods 2024; 21:465-476. [PMID: 38297184 PMCID: PMC10927563 DOI: 10.1038/s41592-023-02159-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024]
Abstract
Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence-ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.
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Affiliation(s)
- Jeffrey M Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Garrett M Ginell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA.
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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