1
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024; 64:6041-6052. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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2
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Hurali DT, Banerjee M, Ballal A. Unravelling the involvement of protein disorder in cyanobacterial stress responses. Int J Biol Macromol 2024; 277:133934. [PMID: 39025183 DOI: 10.1016/j.ijbiomac.2024.133934] [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: 05/10/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
This study has explored the involvement of Intrinsically Disordered Proteins (IDPs) in cyanobacterial stress response. IDPs possess distinct physicochemical properties, which allow them to execute diverse functions. Anabaena PCC 7120, the model photosynthetic, nitrogen-fixing cyanobacterium encodes 688 proteins (11 % of the total proteome) with at least one intrinsically disordered region (IDR). Of these, 130 proteins that showed >30 % overall disorder were designated as IDPs. Physico-chemical analysis, showed these IDPs to adopt shapes ranging from 'globular' to 'tadpole-like'. Upon exposure to NaCl, 41 IDP-encoding genes were found to be differentially expressed. Surprisingly, most of these were induced, indicating the importance of IDP-accumulation in overcoming salt stress. Subsequently, six IDPs were identified to be induced by multiple stresses (salt, ammonium and selenite). Interestingly, the presence of these 6-multiple stress-induced IDPs was conserved in filamentous cyanobacteria. Utilizing the experimental proteomic data of Anabaena, these 6 IDPs were found to interact with many proteins involved in diverse pathways, underscoring their physiological importance as protein hubs. This study lays the framework for IDP-related research in Anabaena by (a) identifying, as well as physiochemically characterizing, all the disordered proteins and (b) uncovering a subset of IDPs that are likely to be critical in adaptation to environmental stresses.
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Affiliation(s)
- Deepak T Hurali
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
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3
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Naudi-Fabra S, Elena-Real CA, Vedel IM, Tengo M, Motzny K, Jiang PL, Schmieder P, Liu F, Milles S. An extended interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis. Nat Commun 2024; 15:5884. [PMID: 39003270 PMCID: PMC11246429 DOI: 10.1038/s41467-024-50212-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024] Open
Abstract
The early phases of clathrin mediated endocytosis are organized through a highly complex interaction network mediated by clathrin associated sorting proteins (CLASPs) that comprise long intrinsically disordered regions (IDRs). AP180 is a CLASP exclusively expressed in neurons and comprises a long IDR of around 600 residues, whose function remains partially elusive. Using NMR spectroscopy, we discovered an extended and strong interaction site within AP180 with the major adaptor protein AP2, and describe its binding dynamics at atomic resolution. We find that the 70 residue-long site determines the overall interaction between AP180 and AP2 in a dynamic equilibrium between its bound and unbound states, while weaker binding sites contribute to the overall affinity at much higher concentrations of AP2. Our data suggest that this particular interaction site might play a central role in recruitment of adaptors to the clathrin coated pit, whereas more transient and promiscuous interactions allow reshaping of the interaction network until cargo uptake inside a coated vesicle.
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Affiliation(s)
- Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Carlos A Elena-Real
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Maud Tengo
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Kathrin Motzny
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Pin-Lian Jiang
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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4
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Goradia N, Werner S, Mullapudi E, Greimeier S, Bergmann L, Lang A, Mertens H, Węglarz A, Sander S, Chojnowski G, Wikman H, Ohlenschläger O, von Amsberg G, Pantel K, Wilmanns M. Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2. Nat Commun 2024; 15:5241. [PMID: 38898011 PMCID: PMC11187106 DOI: 10.1038/s41467-024-49488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
While the elucidation of regulatory mechanisms of folded proteins is facilitated due to their amenability to high-resolution structural characterization, investigation of these mechanisms in disordered proteins is more challenging due to their structural heterogeneity, which can be captured by a variety of biophysical approaches. Here, we used the transcriptional master corepressor CtBP, which binds the putative metastasis suppressor RAI2 through repetitive SLiMs, as a model system. Using cryo-electron microscopy embedded in an integrative structural biology approach, we show that RAI2 unexpectedly induces CtBP polymerization through filaments of stacked tetrameric CtBP layers. These filaments lead to RAI2-mediated CtBP nuclear foci and relieve its corepressor function in RAI2-expressing cancer cells. The impact of RAI2-mediated CtBP loss-of-function is illustrated by the analysis of a diverse cohort of prostate cancer patients, which reveals a substantial decrease in RAI2 in advanced treatment-resistant cancer subtypes. As RAI2-like SLiM motifs are found in a wide range of organisms, including pathogenic viruses, our findings serve as a paradigm for diverse functional effects through multivalent interaction-mediated polymerization by disordered proteins in healthy and diseased conditions.
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Affiliation(s)
- Nishit Goradia
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Stefan Werner
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Mildred Scheel Cancer Career Center HaTriCS4, Martinistrasse 52, 20246, Hamburg, Germany
| | - Edukondalu Mullapudi
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sarah Greimeier
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Lina Bergmann
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Andras Lang
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Haydyn Mertens
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aleksandra Węglarz
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Simon Sander
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Grzegorz Chojnowski
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany
| | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstraße 11, 07745, Jena, Germany
| | - Gunhild von Amsberg
- Martini Clinic, Martinistrasse 52, 20246, Hamburg, Germany
- Department of Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Department of Tumor Biology, University Cancer Center Hamburg, Martinistrasse 52, 20246, Hamburg, Germany.
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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5
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Peng R, Rochon K, Stagg SM, Mears JA. The Structure of the Drp1 Lattice on Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588123. [PMID: 38617273 PMCID: PMC11014616 DOI: 10.1101/2024.04.04.588123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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6
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Mahapatra A, Newberry RW. Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity. Protein Sci 2024; 33:e4951. [PMID: 38511533 PMCID: PMC10955625 DOI: 10.1002/pro.4951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/22/2024]
Abstract
The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of α-syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%; this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in α-syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different α-syn variants, we demonstrate that fibrillation of α-syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of α-syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.
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7
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Du S, Hu X, Liu X, Zhan P. Revolutionizing viral disease treatment: Phase separation and lysosome/exosome targeting as new areas and new paradigms for antiviral drug research. Drug Discov Today 2024; 29:103888. [PMID: 38244674 DOI: 10.1016/j.drudis.2024.103888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/26/2023] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
With the advancement of globalization, our world is becoming increasingly interconnected. However, this interconnection means that once an infectious disease emerges, it can rapidly spread worldwide. Specifically, viral diseases pose a growing threat to human health. The COVID-19 pandemic has underscored the pressing need for expedited drug development to combat emerging viral diseases. Traditional drug discovery methods primarily rely on random screening and structure-based optimization, and new approaches are required to address more complex scenarios in drug discovery. Emerging antiviral strategies include phase separation and lysosome/exosome targeting. The widespread implementation of these innovative drug design strategies will contribute towards tackling existing viral infections and future outbreaks.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China; China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 250012 Jinan, Shandong, PR China.
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8
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Wang W, Li D, Xu Q, Cheng J, Yu Z, Li G, Qiao S, Pan J, Wang H, Shi J, Zheng T, Sui G. G-quadruplexes promote the motility in MAZ phase-separated condensates to activate CCND1 expression and contribute to hepatocarcinogenesis. Nat Commun 2024; 15:1045. [PMID: 38316778 PMCID: PMC10844655 DOI: 10.1038/s41467-024-45353-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
G-quadruplexes (G4s) can recruit transcription factors to activate gene expression, but detailed mechanisms remain enigmatic. Here, we demonstrate that G4s in the CCND1 promoter propel the motility in MAZ phase-separated condensates and subsequently activate CCND1 transcription. Zinc finger (ZF) 2 of MAZ is a responsible for G4 binding, while ZF3-5, but not a highly disordered region, is critical for MAZ condensation. MAZ nuclear puncta overlaps with signals of G4s and various coactivators including BRD4, MED1, CDK9 and active RNA polymerase II, as well as gene activation histone markers. MAZ mutants lacking either G4 binding or phase separation ability did not form nuclear puncta, and showed deficiencies in promoting hepatocellular carcinoma cell proliferation and xenograft tumor formation. Overall, we unveiled that G4s recruit MAZ to the CCND1 promoter and facilitate the motility in MAZ condensates that compartmentalize coactivators to activate CCND1 expression and subsequently exacerbate hepatocarcinogenesis.
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Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Qingqing Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiasong Pan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, Harbin, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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9
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Sipko EL, Chappell GF, Berlow RB. Multivalency emerges as a common feature of intrinsically disordered protein interactions. Curr Opin Struct Biol 2024; 84:102742. [PMID: 38096754 DOI: 10.1016/j.sbi.2023.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Intrinsically disordered proteins (IDPs) use their unique molecular properties and conformational plasticity to interact with cellular partners in a wide variety of biological contexts. Multivalency is an important feature of IDPs that allows for utilization of an expanded toolkit for interactions with other macromolecules and confers additional complexity to molecular recognition processes. Recent studies have offered insights into how multivalent interactions of IDPs enable responsive and sensitive regulation in the context of transcription and cellular signaling. Multivalency is also widely recognized as an important feature of IDP interactions that mediate formation of biomolecular condensates. We highlight recent examples of multivalent interactions of IDPs across diverse contexts to illustrate the breadth of biological processes that utilize multivalency in molecular interactions.
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Affiliation(s)
- Emily L Sipko
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett F Chappell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca B Berlow
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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10
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Seth S, Stine B, Bhattacharya A. Fine structures of intrinsically disordered proteins. J Chem Phys 2024; 160:014902. [PMID: 38165099 DOI: 10.1063/5.0176306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024] Open
Abstract
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional screened Coulomb interaction for the charged amino acid beads. Our simulation studies of two different hydropathy scales (HPS1, HPS2) [Dignon et al., PLoS Comput. Biol. 14, e1005941 (2018); Tesei et al. Proc. Natl. Acad. Sci. U. S. A. 118, e2111696118 (2021)] and the comparison with the existing experimental data indicate an optimal interaction parameter ϵ = 0.1 and 0.2 kcal/mol for the HPS1 and HPS2 hydropathy scales. We use these best-fit parameters to investigate both the universal aspects as well as the fine structures of the individual IDPs by introducing additional characteristics. (i) First, we investigate the polymer-specific scaling relations of the IDPs in comparison to the universal scaling relations [Bair et al., J. Chem. Phys. 158, 204902 (2023)] for the homopolymers. By studying the scaled end-to-end distances ⟨RN2⟩/(2Lℓp) and the scaled transverse fluctuations l̃⊥2=⟨l⊥2⟩/L, we demonstrate that IDPs are broadly characterized with a Flory exponent of ν ≃ 0.56 with the conclusion that conformations of the IDPs interpolate between Gaussian and self-avoiding random walk chains. Then, we introduce (ii) Wilson charge index (W) that captures the essential features of charge interactions and distribution in the sequence space and (iii) a skewness index (S) that captures the finer shape variation of the gyration radii distributions as a function of the net charge per residue and charge asymmetry parameter. Finally, our study of the (iv) variation of ⟨Rg⟩ as a function of salt concentration provides another important metric to bring out finer characteristics of the IDPs, which may carry relevant information for the origin of life.
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Brandon Stine
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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11
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An Y, Webb MA, Jacobs WM. Active learning of the thermodynamics-dynamics trade-off in protein condensates. SCIENCE ADVANCES 2024; 10:eadj2448. [PMID: 38181073 PMCID: PMC10775998 DOI: 10.1126/sciadv.adj2448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
Phase-separated biomolecular condensates exhibit a wide range of dynamic properties, which depend on the sequences of the constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing the thermodynamic properties that govern phase separation. Using coarse-grained simulations of intrinsically disordered proteins, we show that the dynamics and thermodynamics of homopolymer condensates are strongly correlated, with increased condensate stability being coincident with low mobilities and high viscosities. We then apply an "active learning" strategy to identify heteropolymer sequences that break this correlation. This data-driven approach and accompanying analysis reveal how heterogeneous amino acid compositions and nonuniform sequence patterning map to a range of independently tunable dynamic and thermodynamic properties of biomolecular condensates. Our results highlight key molecular determinants governing the physical properties of biomolecular condensates and establish design rules for the development of stimuli-responsive biomaterials.
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Affiliation(s)
- Yaxin An
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - William M. Jacobs
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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12
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Pérez-Jover I, Rochon K, Hu D, Mahajan M, Madan Mohan P, Santos-Pérez I, Ormaetxea Gisasola J, Martinez Galvez JM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nat Commun 2024; 15:52. [PMID: 38168038 PMCID: PMC10761769 DOI: 10.1038/s41467-023-44413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mukesh Mahajan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Isaac Santos-Pérez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology, Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anna V Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain.
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain.
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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13
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Mahapatra A, Newberry RW. Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551831. [PMID: 37577712 PMCID: PMC10418173 DOI: 10.1101/2023.08.03.551831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of α-syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%; this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in α-syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different α-syn variants, we demonstrate that fibrillation of α-syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of α-syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.
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14
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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15
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Kumar A, Madhurima K, Naganathan AN, Vallurupalli P, Sekhar A. Probing excited state 1Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch. Methods 2023; 218:198-209. [PMID: 37607621 PMCID: PMC7615522 DOI: 10.1016/j.ymeth.2023.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
Over 40% of eukaryotic proteomes and 15% of bacterial proteomes are predicted to be intrinsically disordered based on their amino acid sequence. Intrinsically disordered proteins (IDPs) exist as heterogeneous ensembles of interconverting conformations and pose a challenge to the structure-function paradigm by apparently functioning without possessing stable structural elements. IDPs play a prominent role in biological processes involving extensive intermolecular interaction networks and their inherently dynamic nature facilitates their promiscuous interaction with multiple structurally diverse partner molecules. NMR spectroscopy has made pivotal contributions to our understanding of IDPs because of its unique ability to characterize heterogeneity at atomic resolution. NMR methods such as Chemical Exchange Saturation Transfer (CEST) and relaxation dispersion have enabled the detection of 'invisible' excited states in biomolecules which are transiently and sparsely populated, yet central for function. Here, we develop a 1Hα CEST pulse sequence which overcomes the resonance overlap problem in the 1Hα-13Cα plane of IDPs by taking advantage of the superior resolution in the 1H-15N correlation spectrum. In this sequence, magnetization is transferred after 1H CEST using a triple resonance coherence transfer pathway from 1Hα (i) to 1HN(i + 1) during which the 15N(t1) and 1HN(t2) are frequency labelled. This approach is integrated with spin state-selective CEST for eliminating spurious dips in CEST profiles resulting from dipolar cross-relaxation. We apply this sequence to determine the excited state 1Hα chemical shifts of the intrinsically disordered DNA binding domain (CytRN) of the bacterial cytidine repressor (CytR), which transiently acquires a functional globally folded conformation. The structure of the excited state, calculated using 1Hα chemical shifts in conjunction with other excited state NMR restraints, is a three-helix bundle incorporating a helix-turn-helix motif that is vital for binding DNA.
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Affiliation(s)
- Ajith Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Pramodh Vallurupalli
- Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500046, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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16
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Camacho-Zarco AR, Yu L, Krischuns T, Dedeoglu S, Maurin D, Bouvignies G, Crépin T, Ruigrok RWH, Cusack S, Naffakh N, Blackledge M. Multivalent Dynamic Colocalization of Avian Influenza Polymerase and Nucleoprotein by Intrinsically Disordered ANP32A Reveals the Molecular Basis of Human Adaptation. J Am Chem Soc 2023; 145:20985-21001. [PMID: 37707433 PMCID: PMC10540212 DOI: 10.1021/jacs.3c06965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Indexed: 09/15/2023]
Abstract
Adaptation of avian influenza RNA polymerase (FluPol) to human cells requires mutations on the 627-NLS domains of the PB2 subunit. The E627K adaptive mutation compensates a 33-amino-acid deletion in the acidic intrinsically disordered domain of the host transcription regulator ANP32A, a deletion that restricts FluPol activity in mammalian cells. The function of ANP32A in the replication transcription complex and in particular its role in host restriction remains poorly understood. Here we characterize ternary complexes formed between ANP32A, FluPol, and the viral nucleoprotein, NP, supporting the putative role of ANP32A in shuttling NP to the replicase complex. We demonstrate that while FluPol and NP can simultaneously bind distinct linear motifs on avian ANP32A, the deletion in the shorter human ANP32A blocks this mode of colocalization. NMR reveals that NP and human-adapted FluPol, containing the E627 K mutation, simultaneously bind the identical extended linear motif on human ANP32A in an electrostatically driven, highly dynamic and multivalent ternary complex. This study reveals a probable molecular mechanism underlying host adaptation, whereby E627K, which enhances the basic surface of the 627 domain, is selected to confer the necessary multivalent properties to allow ANP32A to colocalize NP and FluPol in human cells.
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Affiliation(s)
- Aldo R. Camacho-Zarco
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Lefan Yu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Tim Krischuns
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Selin Dedeoglu
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Damien Maurin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire
des Biomolécules, Département de Chimie, École
Normale Supérieur, UPMC Université Paris 06, CNRS, PSL Research University, 24 rue Lhomond, 75005 Paris, France
| | - Thibaut Crépin
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Rob W. H. Ruigrok
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
| | - Stephan Cusack
- European
Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Nadia Naffakh
- Institut
Pasteur, Université Paris Cité,
CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, 75015 Paris, France
| | - Martin Blackledge
- Institut
de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS
UMR5075, 71 Avenue des
Martyrs, 38000 Grenoble, France
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17
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Pérez-Jover I, Rochon K, Hu D, Mohan PM, Santos-Perez I, Gisasola JO, Galvez JMM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1-catalyzed mitochondrial fission through a conserved disordered C-terminal Short Linear Motif. RESEARCH SQUARE 2023:rs.3.rs-3161608. [PMID: 37503116 PMCID: PMC10371074 DOI: 10.21203/rs.3.rs-3161608/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial fission, but the regulatory mechanisms remain ambiguous. Here we found that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, leading to the fission of model membranes in vitro. In vivo, the availability of the native CT-SLiM is a requirement for productive mitochondrial fission, as both non-native extension and deletion of the CT-SLiM severely impair its progression. Thus, contrary to prevailing models, Drp1-catalyzed mitochondrial fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Isaac Santos-Perez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jason A. Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anna V. Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- Instituto Biofisika, University of the Basque Country, 48940 Leioa, Spain
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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18
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Han X, Hu Z, Surya W, Ma Q, Zhou F, Nordenskiöld L, Torres J, Lu L, Miao Y. The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization. Cell Rep 2023; 42:112594. [PMID: 37269287 DOI: 10.1016/j.celrep.2023.112594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/21/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Coronins play critical roles in actin network formation. The diverse functions of coronins are regulated by the structured N-terminal β propeller and the C-terminal coiled coil (CC). However, less is known about a middle "unique region" (UR), which is an intrinsically disordered region (IDR). The UR/IDR is an evolutionarily conserved signature in the coronin family. By integrating biochemical and cell biology experiments, coarse-grained simulations, and protein engineering, we find that the IDR optimizes the biochemical activities of coronins in vivo and in vitro. The budding yeast coronin IDR plays essential roles in regulating Crn1 activity by fine-tuning CC oligomerization and maintaining Crn1 as a tetramer. The IDR-guided optimization of Crn1 oligomerization is critical for F-actin cross-linking and regulation of Arp2/3-mediated actin polymerization. The final oligomerization status and homogeneity of Crn1 are contributed by three examined factors: helix packing, the energy landscape of the CC, and the length and molecular grammar of the IDR.
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Affiliation(s)
- Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zixin Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Feng Zhou
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore 636921, Singapore.
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19
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Li S, Wang Y, Lai L. Small molecules in regulating protein phase separation. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1075-1083. [PMID: 37294104 PMCID: PMC10415206 DOI: 10.3724/abbs.2023106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/15/2023] [Indexed: 06/10/2023] Open
Abstract
Biomolecular condensates formed by phase separation are involved in many cellular processes. Dysfunctional or abnormal condensates are closely associated with neurodegenerative diseases, cancer and other diseases. Small molecules can effectively regulate protein phase separation by modulating the formation, dissociation, size and material properties of condensates. Discovery of small molecules to regulate protein phase separation provides chemical probes for deciphering the underlying mechanism and potential novel treatments for condensate-related diseases. Here we review the advances of small molecule regulation of phase separation. The discovery, chemical structures of recently found small molecule phase separation regulators and how they modulate biological condensates are summarized and discussed. Possible strategies to accelerate the discovery of more liquid-liquid phase separation (LLPS)-regulating small molecules are proposed.
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Affiliation(s)
- Siyang Li
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
| | - Yanyan Wang
- BNLMSPeking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Luhua Lai
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- BNLMSPeking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
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20
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Saurabh S, Nadendla K, Purohit SS, Sivakumar PM, Cetinel S. Fuzzy Drug Targets: Disordered Proteins in the Drug-Discovery Realm. ACS OMEGA 2023; 8:9729-9747. [PMID: 36969402 PMCID: PMC10034788 DOI: 10.1021/acsomega.2c07708] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) form a large part of the eukaryotic proteome. Contrary to the structure-function paradigm, the disordered proteins perform a myriad of functions in vivo. Consequently, they are involved in various disease pathways and are plausible drug targets. Unlike folded proteins, that have a defined structure and well carved out drug-binding pockets that can guide lead molecule selection, the disordered proteins require alternative drug-development methodologies that are based on an acceptable picture of their conformational ensemble. In this review, we discuss various experimental and computational techniques that contribute toward understanding IDP "structure" and describe representative pursuances toward IDP-targeting drug development. We also discuss ideas on developing rational drug design protocols targeting IDPs.
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Affiliation(s)
- Suman Saurabh
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Karthik Nadendla
- Center
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Lensfield
Road, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Shubh Sanket Purohit
- Department
of Clinical Haematology, Sahyadri Superspeciality
Hospital, Pune, Maharashtra 411038, India
| | - Ponnurengam Malliappan Sivakumar
- Institute
of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- School
of Medicine and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
| | - Sibel Cetinel
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
- Faculty of
Engineering and Natural Sciences, Molecular Biology, Genetics and
Bioengineering Program, Sabanci University, Istanbul 34956, Turkey
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21
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Batista M, Donker EIM, Bon C, Guillien M, Caisso A, Mourey Funding L, Marie François Funding J, Maveyraud L, Zerbib D. The conserved yeast protein Knr4 involved in cell wall integrity is a multi-domain intrinsically disordered protein. J Mol Biol 2023; 435:168048. [PMID: 36933821 DOI: 10.1016/j.jmb.2023.168048] [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: 10/26/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Knr4/Smi1 proteins are specific to the fungal kingdom and their deletion in the model yeast Saccharomyces cerevisiae and the human pathogen Candida albicans results in hypersensitivity to specific antifungal agents and a wide range of parietal stresses. In S. cerevisiae, Knr4 is located at the crossroads of several signalling pathways, including the conserved cell wall integrity and calcineurin pathways. Knr4 interacts genetically and physically with several protein members of those pathways. Its sequence suggests that it contains large intrinsically disordered regions. Here, a combination of small-angle X-ray scattering (SAXS) and crystallographic analysis led to a comprehensive structural view of Knr4. This experimental work unambiguously showed that Knr4 comprises two large intrinsically disordered regions flanking a central globular domain whose structure has been established. The structured domain is itself interrupted by a disordered loop. Using the CRISPR/Cas9 genome editing technique, strains expressing KNR4 genes deleted from different domains were constructed. The N-terminal domain and the loop are essential for optimal resistance to cell wall-binding stressors. The C-terminal disordered domain, on the other hand, acts as a negative regulator of this function of Knr4. The identification of molecular recognition features, the possible presence of secondary structure in these disordered domains and the functional importance of the disordered domains revealed here designate these domains as putative interacting spots with partners in either pathway. Targeting these interacting regions is a promising route to the discovery of inhibitory molecules that could increase the susceptibility of pathogens to the antifungals currently in clinical use.
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Affiliation(s)
- Manon Batista
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Ellen I M Donker
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Myriam Guillien
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Adriana Caisso
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France
| | - Lionel Mourey Funding
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France.
| | - Didier Zerbib
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France.
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22
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Decle-Carrasco S, Rodríguez-Piña AL, Rodríguez-Zapata LC, Castano E. Current research on viral proteins that interact with fibrillarin. Mol Biol Rep 2023; 50:4631-4643. [PMID: 36928641 PMCID: PMC10018631 DOI: 10.1007/s11033-023-08343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
The nucleolus is a multifunctional nuclear domain primarily dedicated to ribosome biogenesis. Certain viruses developed strategies to manipulate host nucleolar proteins to facilitate their replication by modulating ribosomal RNA (rRNA) processing. This association interferes with nucleolar functions resulting in overactivation or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and affecting stress response. The nucleolar protein fibrillarin (FBL) is an important target of some plant and animal viruses. FBL is an essential and highly conserved S-adenosyl methionine (SAM) dependent methyltransferase, capable of rRNA degradation by its intrinsically disordered region (IDR), the glycine/arginine-rich (GAR) domain. It forms a ribonucleoprotein complex that directs 2'-O-methylations in more than 100 sites of pre-rRNAs. It is involved in multiple cellular processes, including initiation of transcription, oncogenesis, and apoptosis, among others. The interaction with animal viruses, including human viruses, triggered its redistribution to the nucleoplasm and cytoplasm, interfering with its role in pre-rRNA processing. Viral-encoded proteins with IDRs as nucleocapsids, matrix, Tat protein, and even a viral snoRNA, can associate with FBL, forcing the nucleolar protein to undergo atypical functions. Here we review the molecular mechanisms employed by animal and human viruses to usurp FBL functions and the effect on cellular processes, particularly in ribosome biogenesis.
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Affiliation(s)
- Stefano Decle-Carrasco
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Alma Laura Rodríguez-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas. Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, México.
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23
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Aptamer Affinity to P53 DBD: A Molecular Dynamics Study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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24
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Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology. Biomolecules 2023; 13:biom13010124. [PMID: 36671509 PMCID: PMC9856150 DOI: 10.3390/biom13010124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late 1990s when a few groups, working independently, convinced the community that these 'weird' proteins could have important functions. Over the past two decades, it has become clear that IDPs play critical roles in a multitude of biological phenomena with prominent examples including coordination in signaling hubs, enabling gene regulation, and regulating ion channels, just to name a few. One contributing factor that delayed appreciation of IDP functional significance is the experimental difficulty in characterizing their dynamic conformations. The combined application of multiple methods, termed integrative structural biology, has emerged as an essential approach to understanding IDP phenomena. Here, we review some of the recent applications of the integrative structural biology philosophy to study IDPs.
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25
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Tolkatchev D, Smith GE, Kostyukova AS. Nuclear Magnetic Resonance-Guided Structural Analysis of Moderate-Affinity Protein Complexes with Intrinsically Disordered Polypeptides. Methods Mol Biol 2023; 2652:405-437. [PMID: 37093489 PMCID: PMC11273159 DOI: 10.1007/978-1-0716-3147-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Binding affinity of an individual binding site of an intrinsically disordered protein for its folded partner may be moderate. In such cases, a straightforward determination of the structure of the binding interface is difficult. We offer a hybrid protocol combining NMR chemical shift information, NMR spectral data on amino acid residue sequence substitution effects, residual dipolar coupling, and molecular dynamics simulation that allowed us to determine the structure of a complex between the intrinsically disordered tropomyosin-binding site of leiomodin and a coiled-coil peptide modeling the N-terminal fragment of tropomyosin. The protocol can be used for other moderate-affinity complexes composed of an intrinsically disordered peptide bound to a structured protein partner.
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Affiliation(s)
- Dmitri Tolkatchev
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.
| | - Garry E Smith
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Alla S Kostyukova
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
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26
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Luo Y, Xiang S, Feng J. Protein Phase Separation: New Insights into Carcinogenesis. Cancers (Basel) 2022; 14:cancers14235971. [PMID: 36497453 PMCID: PMC9740862 DOI: 10.3390/cancers14235971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Phase separation is now acknowledged as an essential biologic mechanism wherein distinct activated molecules assemble into a different phase from the surrounding constituents of a cell. Condensates formed by phase separation play an essential role in the life activities of various organisms under normal physiological conditions, including the advanced structure and regulation of chromatin, autophagic degradation of incorrectly folded or unneeded proteins, and regulation of the actin cytoskeleton. During malignant transformation, abnormally altered condensate assemblies are often associated with the abnormal activation of oncogenes or inactivation of tumor suppressors, resulting in the promotion of the carcinogenic process. Thus, understanding the role of phase separation in various biological evolutionary processes will provide new ideas for the development of drugs targeting specific condensates, which is expected to be an effective cancer therapy strategy. However, the relationship between phase separation and cancer has not been fully elucidated. In this review, we mainly summarize the main processes and characteristics of phase separation and the main methods for detecting phase separation. In addition, we summarize the cancer proteins and signaling pathways involved in phase separation and discuss their promising future applications in addressing the unmet clinical therapeutic needs of people with cancer. Finally, we explain the means of targeted phase separation and cancer treatment.
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27
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Patil A. Enrichment patterns of intrinsic disorder in proteins. Biophys Rev 2022; 14:1487-1493. [PMID: 36659984 PMCID: PMC9842814 DOI: 10.1007/s12551-022-01016-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022] Open
Abstract
Intrinsically disordered regions in proteins have been shown to be important in protein function. However, not all proteins contain the same amount of intrinsic disorder. The variation in the levels of intrinsic disorder in different types of proteins has been extensively studied over the last two decades. It is now known that the levels of intrinsic disorder vary in proteins across organisms, functions, diseases, and cellular locations. This review consolidates the known trends in the abundance of intrinsic disorder identified in groups of proteins across varying conditions and functions. It also presents new data towards the understanding of intrinsic disorder in cell type-specific proteins. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01016-7.
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Affiliation(s)
- Ashwini Patil
- Combinatics Inc., 2-2-6 Sugano, Ichikawa-Shi, Chiba, 272-0824 Japan
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28
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Sun C, Feng Y, Fan G. IDPsBind: a repository of binding sites for intrinsically disordered proteins complexes with known 3D structures. BMC Mol Cell Biol 2022; 23:33. [PMID: 35883018 PMCID: PMC9327236 DOI: 10.1186/s12860-022-00434-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Intrinsically disordered proteins (IDPs) lack a stable three-dimensional structure under physiological conditions but play crucial roles in many biological processes. Intrinsically disordered proteins perform various biological functions by interacting with other ligands.
Results
Here, we present a database, IDPsBind, which displays interacting sites between IDPs and interacting ligands by using the distance threshold method in known 3D structure IDPs complexes from the PDB database. IDPsBind contains 9626 IDPs complexes and 880 intrinsically disordered proteins verified by experiments. The current release of the IDPsBind database is defined as version 1.0. IDPsBind is freely accessible at http://www.s-bioinformatics.cn/idpsbind/home/.
Conclusions
IDPsBind provides more comprehensive interaction sites for IDPs complexes of known 3D structures. It can not only help the subsequent studies of the interaction mechanism of intrinsically disordered proteins but also provides a suitable background for developing the algorithms for predicting the interaction sites of intrinsically disordered proteins.
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29
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NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates. Essays Biochem 2022; 66:863-873. [PMID: 36416859 PMCID: PMC9760423 DOI: 10.1042/ebc20220056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022]
Abstract
The spatial and temporal organization of interactions between proteins underlie the regulation of most cellular processes. The requirement for such interactions to be specific predisposes a view that protein-protein interactions are relatively static and are formed through the stable complementarity of the interacting partners. A growing body of reports indicate, however, that many interactions lead to fuzzy complexes with an ensemble of conformations in dynamic exchange accounting for the observed binding. Here, we discuss how NMR has facilitated the characterization of these discrete, dynamic complexes and how such characterization has aided the understanding of dynamic, condensed phases of phase-separating proteins with exchanging multivalent interactions.
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30
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Jara KA, Loening NM, Reardon PN, Yu Z, Woonnimani P, Brooks C, Vesely CH, Barbar EJ. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein. eLife 2022; 11:e80217. [PMID: 36416224 PMCID: PMC9771362 DOI: 10.7554/elife.80217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulates IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued, and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrates that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.
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Affiliation(s)
- Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | | | - Patrick N Reardon
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
- Oregon State University NMR FacilityCorvallisUnited States
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Prajna Woonnimani
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Cat H Vesely
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
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31
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Samulevich ML, Shamilov R, Aneskievich BJ. Thermostable Proteins from HaCaT Keratinocytes Identify a Wide Breadth of Intrinsically Disordered Proteins and Candidates for Liquid-Liquid Phase Separation. Int J Mol Sci 2022; 23:ijms232214323. [PMID: 36430801 PMCID: PMC9692912 DOI: 10.3390/ijms232214323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) move through an ensemble of conformations which allows multitudinous roles within a cell. Keratinocytes, the predominant cell type in mammalian epidermis, have had only a few individual proteins assessed for intrinsic disorder and its possible contribution to liquid-liquid phase separation (LLPS), especially in regard to what functions or structures these proteins provide. We took a holistic approach to keratinocyte IDPs starting with enrichment via the isolation of thermostable proteins. The keratinocyte protein involucrin, known for its resistance to heat denaturation, served as a marker. It and other thermostable proteins were identified by liquid chromatography tandem mass spectrometry and subjected to extensive bioinformatic analysis covering gene ontology, intrinsic disorder, and potential for LLPS. Numerous proteins unique to keratinocytes and other proteins with shared expression in multiple cell types were identified to have IDP traits (e.g., compositional bias, nucleic acid binding, and repeat motifs). Among keratinocyte-specific proteins, many that co-assemble with involucrin into the cell-specific structure known as the cornified envelope scored highly for intrinsic disorder and potential for LLPS. This suggests intrinsic disorder and LLPS are previously unrecognized traits for assembly of the cornified envelope, echoing the contribution of intrinsic disorder and LLPS to more widely encountered features such as stress granules and PML bodies.
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Affiliation(s)
- Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269-3092, USA
- Correspondence: ; Tel.: +1-860-486-3053; Fax: +1-860-486-5792
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32
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Mohanty P, Kapoor U, Sundaravadivelu Devarajan D, Phan TM, Rizuan A, Mittal J. Principles Governing the Phase Separation of Multidomain Proteins. Biochemistry 2022; 61:2443-2455. [PMID: 35802394 PMCID: PMC9669140 DOI: 10.1021/acs.biochem.2c00210] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A variety of membraneless organelles, often termed "biological condensates", play an important role in the regulation of cellular processes such as gene transcription, translation, and protein quality control. On the basis of experimental and theoretical investigations, liquid-liquid phase separation (LLPS) has been proposed as a possible mechanism for the origin of biological condensates. LLPS requires multivalent macromolecules that template the formation of long-range, intermolecular interaction networks and results in the formation of condensates with defined composition and material properties. Multivalent interactions driving LLPS exhibit a wide range of modes from highly stereospecific to nonspecific and involve both folded and disordered regions. Multidomain proteins serve as suitable macromolecules for promoting phase separation and achieving disparate functions due to their potential for multivalent interactions and regulation. Here, we aim to highlight the influence of the domain architecture and interdomain interactions on the phase separation of multidomain protein condensates. First, the general principles underlying these interactions are illustrated on the basis of examples of multidomain proteins that are predominantly associated with nucleic acid binding and protein quality control and contain both folded and disordered regions. Next, the examples showcase how LLPS properties of folded and disordered regions can be leveraged to engineer multidomain constructs that form condensates with the desired assembly and functional properties. Finally, we highlight the need for improvements in coarse-grained computational models that can provide molecular-level insights into multidomain protein condensates in conjunction with experimental efforts.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Utkarsh Kapoor
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | | | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
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33
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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34
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van Tartwijk FW, Kaminski CF. Protein Condensation, Cellular Organization, and Spatiotemporal Regulation of Cytoplasmic Properties. Adv Biol (Weinh) 2022; 6:e2101328. [PMID: 35796197 DOI: 10.1002/adbi.202101328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/15/2022] [Indexed: 01/28/2023]
Abstract
The cytoplasm is an aqueous, highly crowded solution of active macromolecules. Its properties influence the behavior of proteins, including their folding, motion, and interactions. In particular, proteins in the cytoplasm can interact to form phase-separated assemblies, so-called biomolecular condensates. The interplay between cytoplasmic properties and protein condensation is critical in a number of functional contexts and is the subject of this review. The authors first describe how cytoplasmic properties can affect protein behavior, in particular condensate formation, and then describe the functional implications of this interplay in three cellular contexts, which exemplify how protein self-organization can be adapted to support certain physiological phenotypes. The authors then describe the formation of RNA-protein condensates in highly polarized cells such as neurons, where condensates play a critical role in the regulation of local protein synthesis, and describe how different stressors trigger extensive reorganization of the cytoplasm, both through signaling pathways and through direct stress-induced changes in cytoplasmic properties. Finally, the authors describe changes in protein behavior and cytoplasmic properties that may occur in extremophiles, in particular organisms that have adapted to inhabit environments of extreme temperature, and discuss the implications and functional importance of these changes.
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Affiliation(s)
- Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
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35
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Choi J, Kim R, Koh J. Quantitative Frameworks for Multivalent Macromolecular Interactions in Biological Linear Lattice Systems. Mol Cells 2022; 45:444-453. [PMID: 35754369 PMCID: PMC9260134 DOI: 10.14348/molcells.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.
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Affiliation(s)
- Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ryeonghyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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36
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Mignon J, Mottet D, Leyder T, Uversky VN, Perpète EA, Michaux C. Structural characterisation of amyloidogenic intrinsically disordered zinc finger protein isoforms DPF3b and DPF3a. Int J Biol Macromol 2022; 218:57-71. [PMID: 35863661 DOI: 10.1016/j.ijbiomac.2022.07.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 11/05/2022]
Abstract
Double PHD fingers 3 (DPF3) is a zinc finger protein, found in the BAF chromatin remodelling complex, and is involved in the regulation of gene expression. Two DPF3 isoforms have been identified, respectively named DPF3b and DPF3a. Very limited structural information is available for these isoforms, and their specific functionality still remains poorly studied. In a previous work, we have demonstrated the first evidence of DPF3a being a disordered protein sensitive to amyloid fibrillation. Intrinsically disordered proteins (IDPs) lack a defined tertiary structure, existing as a dynamic conformational ensemble, allowing them to act as hubs in protein-protein interaction networks. In the present study, we have more thoroughly characterised DPF3a in vitro behaviour, as well as unravelled and compared the structural properties of the DPF3b isoform, using an array of predictors and biophysical techniques. Predictions, spectroscopy, and dynamic light scattering have revealed a high content in disorder: prevalence of random coil, aromatic residues partially to fully exposed to the solvent, and large hydrodynamic diameters. DPF3a appears to be more disordered than DPF3b, and exhibits more expanded conformations. Furthermore, we have shown that they both time-dependently aggregate into amyloid fibrils, as revealed by typical circular dichroism, deep-blue autofluorescence, and amyloid-dye binding assay fingerprints. Although spectroscopic and microscopic analyses have unveiled that they share a similar aggregation pathway, DPF3a fibrillates at a faster rate, likely through reordering of its C-terminal domain.
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Affiliation(s)
- Julien Mignon
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
| | - Denis Mottet
- University of Liège, GIGA-Molecular Biology of Diseases, Gene Expression and Cancer Laboratory, B34, Avenue de l'Hôpital, 4000 Liège, Belgium.
| | - Tanguy Leyder
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Institute of Life, Earth and Environment (ILEE), University of Namur, Namur, Belgium.
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
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37
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Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:biom12070907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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38
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Regulating FUS Liquid-Liquid Phase Separation via Specific Metal Recognition. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2763-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Quiroga IY, Ahn JH, Wang GG, Phanstiel D. Oncogenic fusion proteins and their role in three-dimensional chromatin structure, phase separation, and cancer. Curr Opin Genet Dev 2022; 74:101901. [PMID: 35427897 PMCID: PMC9156545 DOI: 10.1016/j.gde.2022.101901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/05/2022] [Indexed: 11/27/2022]
Abstract
Three-dimensional (3D) chromatin structure plays a critical role in development, gene regulation, and cellular identity. Alterations to this structure can have profound effects on cellular phenotypes and have been associated with a variety of diseases including multiple types of cancer. One of several forces that help shape 3D chromatin structure is liquid-liquid phase separation, a form of self-association between biomolecules that can sequester regions of chromatin into subnuclear droplets or even membraneless organelles like nucleoli. This review focuses on a class of oncogenic fusion proteins that appear to exert their oncogenic function via phase-separation-driven alterations to 3D chromatin structure. Here, we review what is known about the mechanisms by which these oncogenic fusion proteins phase separate in the nucleus and their role in shaping the 3D chromatin structure. We discuss the potential for this phenomenon to be a more widespread mechanism of oncogenesis.
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Affiliation(s)
- Ivana Y Quiroga
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Douglas Phanstiel
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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40
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Liu J, Zhorabek F, Zhang T, Lam JWY, Tang BZ, Chau Y. Multifaceted Cargo Recruitment and Release from Artificial Membraneless Organelles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201721. [PMID: 35596607 DOI: 10.1002/smll.202201721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Liquid-liquid phase separation (LLPS) drives membraneless organelles (MLOs) formation for organizing biomolecules. Artificial MLOs (AMLOs) have been constructed mostly via the LLPS of engineered proteins capable of regulating limited types of biomolecules. Here, leveraging a minimalist AMLO, driven by LLPS of polymer-oligopeptide hybrids, enrichment, recruitment, and release of multifaceted cargoes are quantitatively shown, including small fluorescent molecules, fluorophore-containing macromolecules, proteins, DNAs, and RNAs. Cargoes show up to 105 -fold enrichment, whilst recruitment and release are triggered by variations of temperature, pH, and/or ionic strength. Also, the first efficacious, rapid, and reversible control of aggregation-induced emission with over 30 folds of modulation of overall fluorescence intensity is achieved, by intensifying the aggregation of luminogens in AMLO. The AMLO is a simple yet versatile platform for potential drug delivery and biosensor applications.
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Affiliation(s)
- Jianhui Liu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Fariza Zhorabek
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Tianfu Zhang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Jacky W Y Lam
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
| | - Ben Zhong Tang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Shenzhen City, Guangdong, 518172, P. R. China
| | - Ying Chau
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, P. R. China
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41
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Maccaroni K, La Torre M, Burla R, Saggio I. Phase Separation in the Nucleus and at the Nuclear Periphery during Post-Mitotic Nuclear Envelope Reformation. Cells 2022; 11:cells11111749. [PMID: 35681444 PMCID: PMC9179440 DOI: 10.3390/cells11111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Membrane-enclosed organelle compartmentalization is not the only way by which cell processes are spatially organized. Phase separation is emerging as a new driver in the organization of membrane-less compartments and biological processes. Liquid–liquid phase separation has been indicated as a new way to control the kinetics of molecular reactions and is based on weak multivalent interactions affecting the stoichiometry of the molecules involved. In the nucleus, liquid–liquid phase separation may represent an ancestral means of controlling genomic activity by forming discrete chromatin regions, regulating transcriptional activity, contributing to the assembly of DNA damage response foci, and controlling the organization of chromosomes. Liquid–liquid phase separation also contributes to chromatin function through its role in the reorganization of the nuclear periphery in the post-mitotic phase. Herein, we describe the basic principles regulating liquid–liquid phase separation, analyze examples of phase separation occurring in the nucleus, and dedicate attention to the implication of liquid–liquid phase separation in the reorganization of the nuclear periphery by the endosomal sorting complexes required for transport (ESCRT) machinery. Although some caution is warranted, current scientific knowledge allows for the hypothesis that many factors and processes in the cell are yet to be discovered which are functionally associated with phase separation.
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Affiliation(s)
- Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
| | - Romina Burla
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
- CNR Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
- CNR Institute of Molecular Biology and Pathology, 00185 Rome, Italy
- Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Correspondence:
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42
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Gao H, Zhao L, Zhong B, Zhang B, Gong Z, Zhao B, Liu Y, Zhao Q, Zhang L, Zhang Y. In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane-Permeable, and Alkynyl-Enrichable Crosslinker. Anal Chem 2022; 94:7551-7558. [PMID: 35575683 DOI: 10.1021/acs.analchem.2c00335] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemical crosslinking coupled with mass spectrometry (CXMS) has emerged as a powerful technique to obtain the dynamic conformations and interaction interfaces of protein complexes. Limited by the poor cell membrane permeability, chemical reactivity, and biocompatibility of crosslinkers, in vivo crosslinking to capture the dynamics of protein complexes with finer temporal resolution and higher coverage is attractive but challenging. In this work, a trifunctional crosslinker bis(succinimidyl) with propargyl tag (BSP), involving compact size, proper amphipathy, and enrichment capacity, was developed to enable better cell membrane permeability and efficient crosslinking in 5 min without obvious cellular interference. Followed by a two-step enrichment method based on click chemistry at the peptide level, 13,098 crosslinked peptides (5068 inter-crosslinked peptides and 8030 intra-crosslinked peptides) were identified under the data threshold of peptide-spectrum matches (PSMs) ≥2 on the basic of the FDR control of 1%, which was the most comprehensive dataset for homo species cells by a non-cleavable crosslinker. Besides, the interactome network comprising 1519 proteins connected by 2913 interaction edges in various intracellular compartments, as well as 80S ribosome structural dynamics, were characterized, showing the great potential of our in vivo crosslinking approach in minutes. All these results demonstrated that our developed BSP could provide a valuable toolkit for the in-depth in vivo analysis of protein-protein interactions (PPIs) and protein architectures with finer temporal resolution.
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Affiliation(s)
- Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.,University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhou Gong
- CAS Innovation Academy for Precision Measurement Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yi Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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43
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Dai Z, Li G, Chen Q, Yang X. Ser392 phosphorylation modulated a switch between p53 and transcriptional condensates. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194827. [PMID: 35618207 DOI: 10.1016/j.bbagrm.2022.194827] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Human p53 is a transcription factor regulating the transcription of a variety of target genes. Under various stresses, its tumor suppressor function was activated by the phosphorylation of p53. In this study, we found that full-length wild-type p53 could form phase-separated condensates with the aggregation tendency in vitro and in vivo. The LLPS of p53 was regulated by multiple functional domains. Specific DNA could promote the formation of p53 condensates. Fluorescence recovery data after photobleaching revealed that the Ser392 phosphorylation enhanced the fluidity of p53 condensates. Fluorescence analysis suggested that Ser392 phosphorylation increased the p53 concentration in condensates involved in transcription initiation and the stability of p53-mediated transcriptional condensates. The experiments in cells showed that p53 was evenly dispersed in the nucleus, it formed the dynamic condensates under the UV radiation-induced DNA damage, and the Ser392 nonphosphorylatable mutant S392A p53 formed condensates with significantly reduced number and size. These findings revealed that p53 phosphorylation modified its LLPS behavior, and suggested a mechanism that phosphorylation regulated condensate preference.
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Affiliation(s)
- Zhuojun Dai
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong Province 510006, PR China
| | - Guoli Li
- Ministry of Agriculture Key Laboratory of Animal Biochemistry and Nutrition, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450002, PR China
| | - Qunyang Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong Province 510006, PR China
| | - Xiaorong Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong Province 510006, PR China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, PR China.
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44
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Camacho-Zarco AR, Schnapka V, Guseva S, Abyzov A, Adamski W, Milles S, Jensen MR, Zidek L, Salvi N, Blackledge M. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem Rev 2022; 122:9331-9356. [PMID: 35446534 PMCID: PMC9136928 DOI: 10.1021/acs.chemrev.1c01023] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Intrinsically disordered
proteins are ubiquitous throughout all
known proteomes, playing essential roles in all aspects of cellular
and extracellular biochemistry. To understand their function, it is
necessary to determine their structural and dynamic behavior and to
describe the physical chemistry of their interaction trajectories.
Nuclear magnetic resonance is perfectly adapted to this task, providing
ensemble averaged structural and dynamic parameters that report on
each assigned resonance in the molecule, unveiling otherwise inaccessible
insight into the reaction kinetics and thermodynamics that are essential
for function. In this review, we describe recent applications of NMR-based
approaches to understanding the conformational energy landscape, the
nature and time scales of local and long-range dynamics and how they
depend on the environment, even in the cell. Finally, we illustrate
the ability of NMR to uncover the mechanistic basis of functional
disordered molecular assemblies that are important for human health.
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Affiliation(s)
| | - Vincent Schnapka
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Serafima Guseva
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Anton Abyzov
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Wiktor Adamski
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Lukas Zidek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic
| | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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45
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Chakrabarti P, Chakravarty D. Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophys Chem 2022; 283:106769. [DOI: 10.1016/j.bpc.2022.106769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
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46
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Baldina AA, Nikolaev KG, Ivanov AS, Nikitina AA, Rubtsova MY, Vorovitch MF, Ishmukhametov AA, Egorov AM, Skorb EV. Immunochemical biosensor for single virus particle detection based on molecular crowding polyelectrolyte system. J Appl Polym Sci 2022. [DOI: 10.1002/app.52360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna A. Baldina
- Infochemistry Scientific Center ITMO University Saint Petersburg Russia
| | | | - Artemii S. Ivanov
- Infochemistry Scientific Center ITMO University Saint Petersburg Russia
| | - Anna A. Nikitina
- Infochemistry Scientific Center ITMO University Saint Petersburg Russia
| | - Maya Yu. Rubtsova
- Faculty of Chemistry M.V. Lomonosov Moscow State University Moscow Russia
| | - Mikhail F. Vorovitch
- Chumakov Federal Scientific Center for Research and Development of Immune‐and‐Biological Products of Russian Academy of Sciences Federal State Budgetary Scientific Institution (FSBSI "Chumakov FSC R&D IBP RAS") Moscow Russia
- Institute for Translational Medicine and Biotechnology Sechenov First Moscow State Medical University Moscow Russia
| | - Aydar A. Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune‐and‐Biological Products of Russian Academy of Sciences Federal State Budgetary Scientific Institution (FSBSI "Chumakov FSC R&D IBP RAS") Moscow Russia
- Institute for Translational Medicine and Biotechnology Sechenov First Moscow State Medical University Moscow Russia
| | - Alex M. Egorov
- Faculty of Chemistry M.V. Lomonosov Moscow State University Moscow Russia
- Chumakov Federal Scientific Center for Research and Development of Immune‐and‐Biological Products of Russian Academy of Sciences Federal State Budgetary Scientific Institution (FSBSI "Chumakov FSC R&D IBP RAS") Moscow Russia
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47
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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48
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Oláh J, Szénási T, Lehotzky A, Norris V, Ovádi J. Challenges in Discovering Drugs That Target the Protein-Protein Interactions of Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031550. [PMID: 35163473 PMCID: PMC8835748 DOI: 10.3390/ijms23031550] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/17/2022] Open
Abstract
Protein–protein interactions (PPIs) outnumber proteins and are crucial to many fundamental processes; in consequence, PPIs are associated with several pathological conditions including neurodegeneration and modulating them by drugs constitutes a potentially major class of therapy. Classically, however, the discovery of small molecules for use as drugs entails targeting individual proteins rather than targeting PPIs. This is largely because discovering small molecules to modulate PPIs has been seen as extremely challenging. Here, we review the difficulties and limitations of strategies to discover drugs that target PPIs directly or indirectly, taking as examples the disordered proteins involved in neurodegenerative diseases.
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Affiliation(s)
- Judit Oláh
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Tibor Szénási
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Attila Lehotzky
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
| | - Victor Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France;
| | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, 1117 Budapest, Hungary; (J.O.); (T.S.); (A.L.)
- Correspondence:
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49
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Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins. Proc Natl Acad Sci U S A 2022; 119:2117338119. [PMID: 35012986 PMCID: PMC8784115 DOI: 10.1073/pnas.2117338119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.
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50
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Naudi-Fabra S, Blackledge M, Milles S. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins. Biomolecules 2021; 12:biom12010027. [PMID: 35053175 PMCID: PMC8773649 DOI: 10.3390/biom12010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid–liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
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