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Kolonko-Adamska M, Zawadzka-Kazimierczuk A, Bartosińska-Marzec P, Koźmiński W, Popowicz G, Krężel A, Ożyhar A, Greb-Markiewicz B. Interaction patterns of methoprene-tolerant and germ cell-expressed Drosophila JH receptors suggest significant differences in their functioning. Front Mol Biosci 2023; 10:1215550. [PMID: 37654797 PMCID: PMC10465699 DOI: 10.3389/fmolb.2023.1215550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Methoprene-tolerant (Met) and germ cell-expressed (Gce) proteins were shown to be juvenile hormone (JH) receptors of Drosophila melanogaster with partially redundant functions. We raised the question of where the functional differentiation of paralogs comes from. Therefore, we tested Met and Gce interaction patterns with selected partners. In this study, we showed the ability of Gce and its C-terminus (GceC) to interact with 14-3-3 in the absence of JH. In contrast, Met or Met C-terminus (MetC) interactions with 14-3-3 were not observed. We also performed a detailed structural analysis of Met/Gce interactions with the nuclear receptor fushi tarazu factor-1 (Ftz-F1) ligand-binding domain. We showed that GceC comprising an Ftz-F1-binding site and full-length protein interacts with Ftz-F1. In contrast to Gce, only MetC (not full-length Met) can interact with Ftz-F1 in the absence of JH. We propose that the described differences result from the distinct tertiary structure and accessibility of binding sites in the full-length Met/Gce. Moreover, we hypothesize that each interacting partner can force disordered MetC and GceC to change the structure in a partner-specific manner. The observed interactions seem to determine the subcellular localization of Met/Gce by forcing their translocation between the nucleus and the cytoplasm, which may affect the activity of the proteins. The presented differences between Met and Gce can be crucial for their functional differentiation during D. melanogaster development and indicate Gce as a more universal and more active paralog. It is consistent with the theory indicating gce as an ancestor gene.
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Affiliation(s)
- M. Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - A. Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - P. Bartosińska-Marzec
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - W. Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - G. Popowicz
- Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - A. Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - A. Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - B. Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
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Kolonko M, Bystranowska D, Taube M, Kozak M, Bostock M, Popowicz G, Ożyhar A, Greb-Markiewicz B. The intrinsically disordered region of GCE protein adopts a more fixed structure by interacting with the LBD of the nuclear receptor FTZ-F1. Cell Commun Signal 2020; 18:180. [PMID: 33153474 PMCID: PMC7643343 DOI: 10.1186/s12964-020-00662-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022] Open
Abstract
The Drosophila melanogaster Germ cell-expressed protein (GCE) is a paralog of the juvenile hormone (JH) receptor - Methoprene tolerant protein (MET). Both proteins mediate JH function, preventing precocious differentiation during D. melanogaster development. Despite that GCE and MET are often referred to as equivalent JH receptors, their functions are not fully redundant and show tissue specificity. Both proteins belong to the family of bHLH-PAS transcription factors. The similarity of their primary structure is limited to defined bHLH and PAS domains, while their long C-terminal fragments (GCEC, METC) show significant differences and are expected to determine differences in GCE and MET protein activities. In this paper we present the structural characterization of GCEC as a coil-like intrinsically disordered protein (IDP) with highly elongated and asymmetric conformation. In comparison to previously characterized METC, GCEC is less compacted, contains more molecular recognition elements (MoREs) and exhibits a higher propensity for induced folding. The NMR shifts perturbation experiment and pull-down assay clearly demonstrated that the GCEC fragment is sufficient to form an interaction interface with the ligand binding domain (LBD) of the nuclear receptor Fushi Tarazu factor-1 (FTZ-F1). Significantly, these interactions can force GCEC to adopt more fixed structure that can modulate the activity, structure and functions of the full-length receptor. The discussed relation of protein functionality with the structural data of inherently disordered GCEC fragment is a novel look at this protein and contributes to a better understanding of the molecular basis of the functions of the C-terminal fragments of the bHLH-PAS family. Video abstract.
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Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michał Taube
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland
| | - Maciej Kozak
- Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, 61-614, Poznan, Poland.,National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland
| | - Mark Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Grzegorz Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry,
- Wroclaw University of Science and Technology
- , Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
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Clark PL, Plaxco KW, Sosnick TR. Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different. J Mol Biol 2020; 432:2882-2889. [PMID: 32044346 DOI: 10.1016/j.jmb.2020.01.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/30/2022]
Abstract
The argument that the hydrophobic effect is the primary effect driving the folding of globular proteins is nearly universally accepted (including by the authors). But does this view also imply that water is a "poor" solvent for the unfolded states of these same proteins? Here we argue that the answer is "no," that is, folding to a well-packed, extensively hydrogen-bonded native structure differs fundamentally from the nonspecific chain collapse that defines a poor solvent. Thus, the observation that a protein folds in water does not necessitate that water is a poor solvent for its unfolded state. Indeed, chain-solvent interactions that are marginally more favorable than nonspecific intrachain interactions are beneficial to protein function because they destabilize deleterious misfolded conformations and inter-chain interactions.
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Affiliation(s)
- Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
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Kolonko M, Greb-Markiewicz B. bHLH-PAS Proteins: Their Structure and Intrinsic Disorder. Int J Mol Sci 2019; 20:ijms20153653. [PMID: 31357385 PMCID: PMC6695611 DOI: 10.3390/ijms20153653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present the current state of knowledge, based on NMR and X-ray analysis, concerning the structural properties of bHLH–PAS proteins. It is worth noting that all determined structures comprise only selected domains (bHLH and/or PAS). At the same time, substantial parts of proteins, comprising their long C-termini, have not been structurally characterized to date. Interestingly, these regions appear to be intrinsically disordered (IDRs) and are still a challenge to research. We aim to emphasize the significance of IDRs for the flexibility and function of bHLH–PAS proteins. Finally, we propose modern NMR methods for the structural characterization of the IDRs of bHLH–PAS proteins.
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Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proc Natl Acad Sci U S A 2019; 116:8889-8894. [PMID: 30992378 DOI: 10.1073/pnas.1813038116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. We use two independent approaches to further explore this controversy. First, using SAXS we show that fluorophores employed in FRET can contribute to the observed discrepancy. Specifically, we find that addition of Alexa-488 to a normally expanded IDP causes contraction by an additional 15%, a value in reasonable accord with the contraction reported in FRET-based studies. Second, using our simulations and analysis procedure to accurately extract both the radius of gyration (Rg) and end-to-end distance (Ree) from SAXS profiles, we tested the recent suggestion that FRET and SAXS results can be reconciled if the Rg and Ree are "uncoupled" (i.e., no longer simply proportional), in contrast to the case for random walk homopolymers. We find, however, that even for unfolded proteins, these two measures of unfolded state dimensions remain proportional. Together, these results suggest that improved analysis procedures and a correction for significant, fluorophore-driven interactions are sufficient to reconcile prior SAXS and FRET studies, thus providing a unified picture of the nature of unfolded polypeptide chains in the absence of denaturant.
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Riback JA, Bowman MA, Zmyslowski A, Knoverek CR, Jumper J, Kaye EB, Freed KF, Clark PL, Sosnick TR. Response to Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”. Science 2018; 361:361/6405/eaar7949. [PMID: 30166460 DOI: 10.1126/science.aar7949] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022]
Abstract
Best et al. claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al. comment. A plausible origin is fluorophore interactions in FRET experiments.
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Affiliation(s)
- Joshua A Riback
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Micayla A Bowman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Adam Zmyslowski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Catherine R Knoverek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - John Jumper
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Emily B Kaye
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Karl F Freed
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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