1
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Patkar SS, Wang B, Mosquera AM, Kiick KL. Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials. Chemistry 2024; 30:e202400582. [PMID: 38501912 DOI: 10.1002/chem.202400582] [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: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/20/2024]
Abstract
The unique biophysical and biochemical properties of intrinsically disordered proteins (IDPs) and their recombinant derivatives, intrinsically disordered protein polymers (IDPPs) offer opportunities for producing multistimuli-responsive materials; their sequence-encoded disorder and tendency for phase separation facilitate the development of multifunctional materials. This review highlights the strategies for enhancing the structural diversity of elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs), and their self-assembled structures via genetic fusion to ordered motifs such as helical or beta sheet domains. In particular, this review describes approaches that harness the synergistic interplay between order-promoting and thermoresponsive building blocks to design hybrid biomaterials, resulting in well-structured, stimuli-responsive supramolecular materials ordered on the nanoscale.
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Affiliation(s)
- Sai S Patkar
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Eli Lilly and Company, 450 Kendall Street, Cambridge, MA, 02142, United States
| | - Bin Wang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Ana Maria Mosquera
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716, United States
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware, 19716, United States
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2
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Viegas RG, Martins IBS, Leite VBP. Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles. J Chem Inf Model 2024; 64:4149-4157. [PMID: 38713459 DOI: 10.1021/acs.jcim.4c00080] [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: 05/08/2024]
Abstract
A substantial portion of various organisms' proteomes comprises intrinsically disordered proteins (IDPs) that lack a defined three-dimensional structure. These IDPs exhibit a diverse array of conformations, displaying remarkable spatiotemporal heterogeneity and exceptional conformational flexibility. Characterizing the structure or structural ensemble of IDPs presents significant conceptual and methodological challenges owing to the absence of a well-defined native structure. While databases such as the Protein Ensemble Database (PED) provide IDP ensembles obtained through a combination of experimental data and molecular modeling, the absence of reaction coordinates poses challenges in comprehensively understanding pertinent aspects of the system. In this study, we leverage the energy landscape visualization method (JCTC, 6482, 2019) to scrutinize four IDP ensembles sourced from PED. ELViM, a methodology that circumvents the need for a priori reaction coordinates, aids in analyzing the ensembles. The specific IDP ensembles investigated are as follows: two fragments of nucleoporin (NUL: 884-993 and NUS: 1313-1390), yeast sic 1 N-terminal (1-90), and the N-terminal SH3 domain of Drk (1-59). Utilizing ELViM enables the comprehensive validation of ensembles, facilitating the detection of potential inconsistencies in the sampling process. Additionally, it allows for identifying and characterizing the most prevalent conformations within an ensemble. Moreover, ELViM facilitates the comparative analysis of ensembles obtained under diverse conditions, thereby providing a powerful tool for investigating the functional mechanisms of IDPs.
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Affiliation(s)
- Rafael G Viegas
- Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, São Paulo 15.808-305, Brazil
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Ingrid B S Martins
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo 15054-000, Brazil
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3
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Duffy EE, Assad EG, Kalish BT, Greenberg ME. Small but mighty: the rise of microprotein biology in neuroscience. Front Mol Neurosci 2024; 17:1386219. [PMID: 38807924 PMCID: PMC11130481 DOI: 10.3389/fnmol.2024.1386219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological functions. While traditional efforts to understand the molecular basis of brain function have focused on well-characterized proteins, recent advances in high-throughput translatome profiling have revealed a staggering number of proteins translated from non-canonical open reading frames (ncORFs) such as 5' and 3' untranslated regions of annotated proteins, out-of-frame internal ORFs, and previously annotated non-coding RNAs. Of note, microproteins < 100 amino acids (AA) that are translated from such ncORFs have often been neglected due to computational and biochemical challenges. Thousands of putative microproteins have been identified in cell lines and tissues including the brain, with some serving critical biological functions. In this perspective, we highlight the recent discovery of microproteins in the brain and describe several hypotheses that have emerged concerning microprotein function in the developing and mature nervous system.
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Affiliation(s)
- Erin E. Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Elena G. Assad
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Brian T. Kalish
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada
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4
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Wallner ES, Mair A, Handler D, McWhite C, Xu SL, Dolan L, Bergmann DC. Spatially resolved proteomics of the Arabidopsis stomatal lineage identifies polarity complexes for cell divisions and stomatal pores. Dev Cell 2024; 59:1096-1109.e5. [PMID: 38518768 DOI: 10.1016/j.devcel.2024.03.001] [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: 12/14/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/24/2024]
Abstract
Cell polarity is used to guide asymmetric divisions and create morphologically diverse cells. We find that two oppositely oriented cortical polarity domains present during the asymmetric divisions in the Arabidopsis stomatal lineage are reconfigured into polar domains marking ventral (pore-forming) and outward-facing domains of maturing stomatal guard cells. Proteins that define these opposing polarity domains were used as baits in miniTurboID-based proximity labeling. Among differentially enriched proteins, we find kinases, putative microtubule-interacting proteins, and polar SOSEKIs with their effector ANGUSTIFOLIA. Using AI-facilitated protein structure prediction models, we identify potential protein-protein interaction interfaces among them. Functional and localization analyses of the polarity protein OPL2 and its putative interaction partners suggest a positive interaction with mitotic microtubules and a role in cytokinesis. This combination of proteomics and structural modeling with live-cell imaging provides insights into how polarity is rewired in different cell types and cell-cycle stages.
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Affiliation(s)
- Eva-Sophie Wallner
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Gregor Mendel Institute, Dr. Bohr-Gasse 3, 1030 Wien, Austria; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
| | - Andrea Mair
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | | | - Claire McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Shou-Ling Xu
- Carnegie Institution for Science, Stanford, CA 94305, USA; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Liam Dolan
- Gregor Mendel Institute, Dr. Bohr-Gasse 3, 1030 Wien, Austria
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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5
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Sülzen H, Volkov AN, Geens R, Zahedifard F, Stijlemans B, Zoltner M, Magez S, Sterckx YGJ, Zoll S. Beyond the VSG layer: Exploring the role of intrinsic disorder in the invariant surface glycoproteins of African trypanosomes. PLoS Pathog 2024; 20:e1012186. [PMID: 38648216 PMCID: PMC11065263 DOI: 10.1371/journal.ppat.1012186] [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: 12/18/2023] [Revised: 05/02/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
In the bloodstream of mammalian hosts, African trypanosomes face the challenge of protecting their invariant surface receptors from immune detection. This crucial role is fulfilled by a dense, glycosylated protein layer composed of variant surface glycoproteins (VSGs), which undergo antigenic variation and provide a physical barrier that shields the underlying invariant surface glycoproteins (ISGs). The protective shield's limited permeability comes at the cost of restricted access to the extracellular host environment, raising questions regarding the specific function of the ISG repertoire. In this study, we employ an integrative structural biology approach to show that intrinsically disordered membrane-proximal regions are a common feature of members of the ISG super-family, conferring the ability to switch between compact and elongated conformers. While the folded, membrane-distal ectodomain is buried within the VSG layer for compact conformers, their elongated counterparts would enable the extension beyond it. This dynamic behavior enables ISGs to maintain a low immunogenic footprint while still allowing them to engage with the host environment when necessary. Our findings add further evidence to a dynamic molecular organization of trypanosome surface antigens wherein intrinsic disorder underpins the characteristics of a highly flexible ISG proteome to circumvent the constraints imposed by the VSG coat.
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Affiliation(s)
- Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rob Geens
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Farnaz Zahedifard
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Benoit Stijlemans
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Stefan Magez
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Incheon, South Korea
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Center of Excellence, Department of Pharmaceutical Sciences, Universiteit of Antwerp, Wilrijk, Belgium
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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6
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Guo XY, Yi L, Yang J, An HW, Yang ZX, Wang H. Self-assembly of peptide nanomaterials at biointerfaces: molecular design and biomedical applications. Chem Commun (Camb) 2024; 60:2009-2021. [PMID: 38275083 DOI: 10.1039/d3cc05811e] [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: 01/27/2024]
Abstract
Self-assembly is an important strategy for constructing ordered structures and complex functions in nature. Based on this, people can imitate nature and artificially construct functional materials with novel structures through the supermolecular self-assembly pathway of biological interfaces. Among the many assembly units, peptide molecular self-assembly has received widespread attention in recent years. In this review, we introduce the interactions (hydrophobic interaction, hydrogen bond, and electrostatic interaction) between peptide nanomaterials and biological interfaces, summarizing the latest advancements in multifunctional self-assembling peptide materials. We systematically demonstrate the assembly mechanisms of peptides at biological interfaces, such as proteins and cell membranes, while highlighting their application potential and challenges in fields like drug delivery, antibacterial strategies, and cancer therapy.
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Affiliation(s)
- Xin-Yuan Guo
- College of Chemistry, Huazhong Agricultural University, Shizishan 1, Hongshan District, Wuhan, 430070, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Li Yi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Jia Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Hong-Wei An
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
| | - Zi-Xin Yang
- College of Chemistry, Huazhong Agricultural University, Shizishan 1, Hongshan District, Wuhan, 430070, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China.
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7
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García-Morales A, Pulido NO, Balleza D. Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:77-90. [PMID: 37777680 DOI: 10.1007/s00249-023-01682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/20/2023] [Indexed: 10/02/2023]
Abstract
How a protein propagates the conformational changes throughout its structure remains largely unknown. In thermosensitive TRP channels, this allosteric communication is triggered by ligand interaction or in response to temperature changes. Because dynamic allostery suggests a dynamic role of disordered regions, in this work we set out to thoroughly evaluate these regions in six thermosensitive TRP channels. Thus, by contrasting the intrinsic flexibility of the transmembrane region as a function of the degree of disorder in those proteins, we discovered several residues that do not show a direct correlation in both parameters. This kind of structural discrepancy revealed residues that are either reported to be dynamic, functionally relevant or are involved in signal propagation and probably part of allosteric networks. These discrepant, potentially dynamic regions are not exclusive of TRP channels, as this same correlation was found in the Kv Shaker channel.
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Affiliation(s)
- Abigail García-Morales
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Calz. Miguel Angel de Quevedo 2779 Col Formando Hogar, 91897, Veracruz, Ver, Mexico
| | - Nancy O Pulido
- Escuela de Ingeniería y Ciencias, Instituto Tecnológico y de Estudios Superiores de Monterrey, Cuernavaca, Mexico
| | - Daniel Balleza
- Unidad de Investigación y Desarrollo en Alimentos, Instituto Tecnológico de Veracruz, Tecnológico Nacional de México, Calz. Miguel Angel de Quevedo 2779 Col Formando Hogar, 91897, Veracruz, Ver, Mexico.
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8
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Sethi V, Cohen-Gerassi D, Meir S, Ney M, Shmidov Y, Koren G, Adler-Abramovich L, Chilkoti A, Beck R. Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time. Sci Rep 2023; 13:21688. [PMID: 38066072 PMCID: PMC10709347 DOI: 10.1038/s41598-023-48483-w] [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: 08/29/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins.
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Affiliation(s)
- Vaishali Sethi
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Dana Cohen-Gerassi
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Sagi Meir
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Gil Koren
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Lihi Adler-Abramovich
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Roy Beck
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel.
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9
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Fenton M, Gregory E, Daughdrill G. Protein disorder and autoinhibition: The role of multivalency and effective concentration. Curr Opin Struct Biol 2023; 83:102705. [PMID: 37778184 PMCID: PMC10841074 DOI: 10.1016/j.sbi.2023.102705] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Regulation of protein binding through autoinhibition commonly occurs via interactions involving intrinsically disordered regions (IDRs). These intramolecular interactions can directly or allosterically inhibit intermolecular protein or DNA binding, regulate enzymatic activity, and control the assembly of large macromolecular complexes. Autoinhibitory interactions mediated by protein disorder are inherently transient, making their identification and characterization challenging. In this review, we explore the structural and functional diversity of disorder-mediated autoinhibition for a variety of biological mechanisms, with a focus on the role of multivalency and effective concentration. We also discuss the evolution of disordered motifs that participate in autoinhibition using examples where sequence conservation varies from high to low. In some cases, identifiable motifs that are essential for autoinhibition remain intact within a rapidly evolving sequence, over long evolutionary distances. Finally, we examine the potential of AlphaFold2 to predict autoinhibitory intramolecular interactions involving IDRs.
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Affiliation(s)
- Malissa Fenton
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Emily Gregory
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Gary Daughdrill
- Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
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10
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Wallner ES, Dolan L, Bergmann DC. Arabidopsis stomatal lineage cells establish bipolarity and segregate differential signaling capacity to regulate stem cell potential. Dev Cell 2023; 58:1643-1656.e5. [PMID: 37607546 DOI: 10.1016/j.devcel.2023.07.024] [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: 02/14/2023] [Revised: 04/04/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
Cell polarity combined with asymmetric cell divisions (ACDs) generates cellular diversity. In the Arabidopsis stomatal lineage, a single cortical polarity domain marked by BASL orients ACDs and is segregated to the larger daughter to enforce cell fate. We discovered a second, oppositely positioned polarity domain defined by OCTOPUS-LIKE (OPL) proteins, which forms prior to ACD and is segregated to the smaller (meristemoid) daughter. Genetic and misexpression analyses show that OPLs promote meristemoid-amplifying divisions and delay stomatal fate progression. Polarity mediates OPL segregation into meristemoids but is not required for OPL function. OPL localization and activity are largely independent of other stomatal polarity genes and of the brassinosteroid signaling components associated with OPLs in other contexts. While OPLs are unique to seed plants, ectopic expression in the liverwort Marchantia suppressed epidermal fate progression, suggesting that OPLs engage ancient and broadly conserved pathways to regulate cell division and cell fate.
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Affiliation(s)
- Eva-Sophie Wallner
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Gregor Mendel Institute, Dr.-Bohr-Gasse 3, 1030 Wien, Austria; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
| | - Liam Dolan
- Gregor Mendel Institute, Dr.-Bohr-Gasse 3, 1030 Wien, Austria
| | - Dominique C Bergmann
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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11
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Shimada MK. Splicing Modulators Are Involved in Human Polyglutamine Diversification via Protein Complexes Shuttling between Nucleus and Cytoplasm. Int J Mol Sci 2023; 24:ijms24119622. [PMID: 37298574 DOI: 10.3390/ijms24119622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Length polymorphisms of polyglutamine (polyQs) in triplet-repeat-disease-causing genes have diversified during primate evolution despite them conferring a risk of human-specific diseases. To explain the evolutionary process of this diversification, there is a need to focus on mechanisms by which rapid evolutionary changes can occur, such as alternative splicing. Proteins that can bind polyQs are known to act as splicing factors and may provide clues about the rapid evolutionary process. PolyQs are also characterized by the formation of intrinsically disordered (ID) regions, so I hypothesized that polyQs are involved in the transportation of various molecules between the nucleus and cytoplasm to regulate mechanisms characteristic of humans such as neural development. To determine target molecules for empirical research to understand the evolutionary change, I explored protein-protein interactions (PPIs) involving the relevant proteins. This study identified pathways related to polyQ binding as hub proteins scattered across various regulatory systems, including regulation via PQBP1, VCP, or CREBBP. Nine ID hub proteins with both nuclear and cytoplasmic localization were found. Functional annotations suggested that ID proteins containing polyQs are involved in regulating transcription and ubiquitination by flexibly changing PPI formation. These findings explain the relationships among splicing complex, polyQ length variations, and modifications in neural development.
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Affiliation(s)
- Makoto K Shimada
- Center for Medical Science, Fujita Health University, Toyoake 470-1192, Japan
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12
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Aparicio Chacón MV, Van Dingenen J, Goormachtig S. Characterization of Arbuscular Mycorrhizal Effector Proteins. Int J Mol Sci 2023; 24:ijms24119125. [PMID: 37298075 DOI: 10.3390/ijms24119125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.
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Affiliation(s)
- María V Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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13
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Belhart K, Sisti F, Gestal MC, Fernández J. Bordetella bronchiseptica diguanylate cyclase BdcB inhibits the type three secretion system and impacts the immune response. Sci Rep 2023; 13:7157. [PMID: 37130958 PMCID: PMC10154355 DOI: 10.1038/s41598-023-34106-x] [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: 12/17/2022] [Accepted: 04/24/2023] [Indexed: 05/04/2023] Open
Abstract
Bordetella bronchiseptica is a gram-negative bacterium that causes respiratory diseases in different animals, including mice, making B. bronchiseptica the gold-standard model to investigate host-pathogen interaction at the molecular level. B. bronchiseptica utilizes many different mechanisms to precisely regulate the expression of virulence factors. Cyclic di-GMP is a second messenger synthesized by diguanylate cyclases and degraded by phosphodiesterases that regulates the expression of multiple virulence factors including biofilm formation. As in other bacteria, we have previously shown that c-di-GMP regulates motility and biofilm formation in B. bronchiseptica. This work describes the diguanylate cyclase BdcB (Bordetella diguanylate cyclase B) as an active diguanylate cyclase that promotes biofilm formation and inhibits motility in B. bronchiseptica. The absence of BdcB increased macrophage cytotoxicity in vitro and induced a greater production of TNF-α, IL-6, and IL-10 by macrophages. Our study reveals that BdcB regulates the expression of components of T3SS, an important virulence factor of B. bronchiseptica. The Bb∆bdcB mutant presented increased expression of T3SS-mediated toxins such as bteA, responsible for cytotoxicity. Our in vivo results revealed that albeit the absence of bdcB did not affect the ability of B. bronchiseptica to infect and colonize the respiratory tract of mice, mice infected with Bb∆bdcB presented a significantly higher pro-inflammatory response than those infected with wild type B. bronchiseptica.
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Affiliation(s)
- Keila Belhart
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Federico Sisti
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mónica C Gestal
- Department of Microbiology and Immunology, Louisiana State University (LSU) Health Sciences Center at Shreveport, Shreveport, LA, USA.
| | - Julieta Fernández
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina.
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14
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Daoui O, Mali SN, Elkhattabi K, Elkhattabi S, Chtita S. Repositioning Cannabinoids and Terpenes as Novel EGFR-TKIs Candidates for Targeted Therapy Against Cancer: A virtual screening model using CADD and biophysical simulations. Heliyon 2023; 9:e15545. [PMID: 37128337 PMCID: PMC10148140 DOI: 10.1016/j.heliyon.2023.e15545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
This study examines the potential of Cannabis sativa L. plants to be repurposed as therapeutic agents for cancer treatment through designing of hybrid Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). A set of 50 phytochemicals was taken from Cannabinoids and Terpenes and subjected for screening using Semi-flexible and Flexible Molecular Docking methods, MM-GBSA free binding energy computations, and pharmacokinetic/pharmacodynamic (ADME-Tox) predictions. Nine promising phytochemicals, Cannabidiolic acid (CBDA), Cannabidiol (CBD), Tetrahydrocannabivarin (THCV), Dronabinol (Δ-9-THC), Delta-8-Tetrahydrocannabinol (Δ-8-THC), Cannabicyclol (CBL), Delta9-tetrahydrocannabinolic acid (THCA), Beta-Caryophyllene (BCP), and Gamma-Elemene (γ-Ele) were identified as potential EGFR-TKIs natural product candidates for cancer therapy. To further validate these findings, a set of Molecular Dynamics simulations were conducted over a 200 ns trajectory. This hybrid early drug discovery screening strategy has the potential to yield a new generation of EGFR-TKIs based on natural cannabis products, suitable for cancer therapy. In addition, the application of this computational strategy in the virtual screening of both natural and synthetic chemical libraries could support the discovery of a wide range of lead drug agents to address numerous diseases.
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Affiliation(s)
- Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, P.O. Box 72, Fez, Morocco
- Corresponding author.
| | - Suraj N. Mali
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, India, 835215
| | - Kaouakeb Elkhattabi
- Department of Fundamental Sciences, Faculty of Dental Medicine, Mohammed V University in Rabat, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, P.O. Box 72, Fez, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, P.O. Box 7955, Casablanca, Morocco
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15
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Chuang CK, Chen SF, Su YH, Chen WH, Lin WM, Wang IC, Shyue SK. The Role of SCL Isoforms in Embryonic Hematopoiesis. Int J Mol Sci 2023; 24:ijms24076427. [PMID: 37047400 PMCID: PMC10094407 DOI: 10.3390/ijms24076427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/16/2023] [Accepted: 03/26/2023] [Indexed: 04/01/2023] Open
Abstract
Three waves of hematopoiesis occur in the mouse embryo. The primitive hematopoiesis appears as blood islands in the extra embryonic yolk sac at E7.5. The extra embryonic pro-definitive hematopoiesis launches in late E8 and the embryonic definitive one turns on at E10.5 indicated by the emergence of hemogenic endothelial cells on the inner wall of the extra embryonic arteries and the embryonic aorta. To study the roles of SCL protein isoforms in murine hematopoiesis, the SCL-large (SCL-L) isoform was selectively destroyed with the remaining SCL-small (SCL-S) isoform intact. It was demonstrated that SCL-S was specifically expressed in the hemogenic endothelial cells (HECs) and SCL-L was only detected in the dispersed cells after budding from HECs. The SCLΔ/Δ homozygous mutant embryos only survived to E10.5 with normal extra embryonic vessels and red blood cells. In wild-type mouse embryos, a layer of neatly aligned CD34+ and CD43+ cells appeared on the endothelial wall of the aorta of the E10.5 fetus. However, the cells at the same site expressed CD31 rather than CD34 and/or CD43 in the E10.5 SCLΔ/Δ embryo, indicating that only the endothelial lineage was developed. These results reveal that the SCL-S is sufficient to sustain the primitive hematopoiesis and SCL-L is necessary to launch the definitive hematopoiesis.
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16
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Kamran DES, Hussain M, Mirza T. Investigating In Situ Expression of c-MYC and Candidate Ubiquitin-Specific Proteases in DLBCL and Assessment for Peptidyl Disruptor Molecule against c-MYC-USP37 Complex. Molecules 2023; 28:molecules28062441. [PMID: 36985413 PMCID: PMC10058055 DOI: 10.3390/molecules28062441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Diffuse Large B-Cell Lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma (NHL). Elevated expression of c-MYC in DLBCL is associated with poor prognosis of the disease. In different cancers, c-MYC has been found regulated by different ubiquitin-specific proteases (USPs), but to date, the role of USPs in c-MYC regulation has not been investigated in DLBCL. In this study, in situ co expression of c-MYC and three candidates USPs, USP28, USP36 and USP37, have been investigated in both the ABC and GCB subtypes of DLBCL. This shows that USP37 expression is positively correlated with the c-MYC expression in the ABC subtype of DLBCL. Structurally, both c-MYC and USP37 has shown large proportion of intrinsically disordered regions, minimizing their chances for full structure crystallization. Peptide array and docking simulations has shown that N-terminal region of c-MYC interacts directly with residues within and in proximity of catalytically active C19 domain of the USP37. Given the structural properties of the interaction sites in the c-MYC-USP37 complex, a peptidyl inhibitor has been designed. Molecular docking has shown that the peptide fits well in the targeted site of c-MYC, masking most of its residues involved in the binding with USP37. The findings could further be exploited to develop therapeutic interventions against the ABC subtype of DLBCL.
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Affiliation(s)
- Durr E Sameen Kamran
- Department of Pathology, Dow Ishrat-ul-Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi 75330, Pakistan
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan
| | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi 75330, Pakistan
| | - Talat Mirza
- Department of Research, Ziauddin University, Karachi 75000, Pakistan
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17
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Brender JR, Ramamoorthy A, Gursky O, Bhunia A. Intrinsic disorder and structural biology: Searching where the light isn't. Biophys Chem 2023; 292:106912. [PMID: 36335754 DOI: 10.1016/j.bpc.2022.106912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffrey R Brender
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Olga Gursky
- Boston University School of Medicine, Department of Physiology & Biophysics, W302, 700 Albany St, Boston, MA 02118, USA
| | - Anirban Bhunia
- Biomolecular NMR and Drug Design Laboratory, Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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18
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Mapping the protein binding site of the (pro)renin receptor using in silico 3D structural analysis. Hypertens Res 2022; 46:959-971. [PMID: 36481966 PMCID: PMC10073018 DOI: 10.1038/s41440-022-01094-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
AbstractWe have previously reported that monoclonal antibodies against the (pro)renin receptor [(P)RR] can reduce the Wnt/β-catenin-dependent development of pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer. Antibodies against two (P)RR regions (residues 47–60 and 200–213) located in the extracellular domain (ECD) reduced the proliferation of human PDAC cells in vitro. Although these regions probably participate in the activation of Wnt/β-catenin signaling, their functional significance remains unclear. Moreover, the (P)RR ECD is predicted to possess an intrinsically disordered region (IDR), which allows multiple protein interactions because of its conformational flexibility. In this study, we investigated the significance of the two regions and the IDR by in silico 3D structural analysis using the AlphaFold2 program and evolutionary sequence conservation profile. The model showed that ECD adopted a folded domain (residues 17–269) and had an IDR (residues 270–296). The two regions mapped onto the structural model formed a continuous surface patch comprising evolutionarily conserved hydrophobic residues. The homodimeric structure predicted by AlphaFold2 showed that full-length (P)RR comprising the ECD, single-span transmembrane, and cytoplasmic domains formed a twofold symmetric dimer via the ECD, which explains the experimentally proven homodimerization. The dimer model possessed two hand-shaped grooves with residues 47–60 and 200–213 in their palms and the IDR as their fingers. Based on these findings, we propose that the IDR-containing hydrophobic grooves act as a binding site for (P)RR and perform multiple functions, including Wnt signaling activation.
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19
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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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20
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Lázár T, Tantos A, Tompa P, Schad E. Intrinsic protein disorder uncouples affinity from binding specificity. Protein Sci 2022; 31:e4455. [PMID: 36305763 PMCID: PMC9601785 DOI: 10.1002/pro.4455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is "uncoupling" specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence-supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the Kd for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well-characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, Kd ) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.
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Affiliation(s)
- Tamas Lázár
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Agnes Tantos
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium,Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
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21
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Yoo JH, Kahne SC, Darwin KH. A conserved loop sequence of the proteasome system depupylase Dop regulates substrate selectivity in Mycobacterium tuberculosis. J Biol Chem 2022; 298:102478. [PMID: 36100038 PMCID: PMC9556782 DOI: 10.1016/j.jbc.2022.102478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/12/2023] Open
Abstract
Mycobacteria use a proteasome system that is similar to a eukaryotic proteasome but do not use ubiquitin to target proteins for degradation. Instead, mycobacteria encode a prokaryotic ubiquitin-like protein (Pup) that posttranslationally modifies proteins to mark them for proteolysis. Pupylation occurs on lysines of targeted proteins and is catalyzed by the ligase PafA. Like ubiquitylation, pupylation can be reversed by the depupylase Dop, which shares high structural similarity with PafA. Unique to Dop near its active site is a disordered loop of approximately 40 amino acids that is highly conserved among diverse dop-containing bacterial genera. To understand the function of this domain, we deleted discrete sequences from the Dop loop and assessed pupylation in mutant strains of Mycobacterium tuberculosis. We determined that various Dop loop mutations resulted in altered pupylome profiles, in particular when mutant dop alleles were overexpressed. Taken together, our data suggest these conserved amino acids play a role in substrate selectivity for Dop.
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Affiliation(s)
- Jin Hee Yoo
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Shoshanna C Kahne
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, New York, USA.
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22
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Berge-Seidl S, Nielsen NV, Rodriguez Alfonso AA, Etscheid M, Kandanur SPS, Haug BE, Stensland M, Thiede B, Karacan M, Preising N, Wiese S, Ständker L, Declerck PJ, Løset GÅ, Kanse SM. Identification of a Phage Display-Derived Peptide Interacting with the N-Terminal Region of Factor VII Activating Protease (FSAP) Enables Characterization of Zymogen Activation. ACS Chem Biol 2022; 17:2631-2642. [PMID: 36070465 PMCID: PMC9486805 DOI: 10.1021/acschembio.2c00538] [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] [Indexed: 01/19/2023]
Abstract
Factor VII Activating protease (FSAP) has a protective effect in diverse disease conditions as inferred from studies in FSAP-/- mice and humans deficient in FSAP activity due to single-nucleotide polymorphism. The zymogen form of FSAP in plasma is activated by extracellular histones that are released during tissue injury or inflammation or by positively charged surfaces. However, it is not clear whether this activation mechanism is specific and amenable to manipulation. Using a phage display approach, we have identified a Cys-constrained 11 amino acid peptide, NNKC9/41, that activates pro-FSAP in plasma. The synthetic linear peptide has a propensity to cyclize through the terminal Cys groups, of which the antiparallel cyclic dimer, but not the monocyclic peptide, is the active component. Other commonly found zymogens in the plasma, related to the hemostasis system, were not activated. Binding studies with FSAP domain deletion mutants indicate that the N-terminus of FSAP is the key interaction site of this peptide. In a monoclonal antibody screen, we identified MA-FSAP-38C7 that prevented the activation of pro-FSAP by the peptide. This antibody bound to the LESLDP sequence (amino acids 30-35) in an intrinsically disordered stretch in the N-terminus of FSAP. The plasma clotting time was shortened by NNKC9/41, and this was reversed by MA-FSAP-38C7, demonstrating the utility of this peptide. Peptide NNKC9/41 will be useful as a tool to delineate the molecular mechanism of activation of pro-FSAP, elucidate its biological role, and provide a starting point for the pharmacological manipulation of FSAP activity.
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Affiliation(s)
| | - Nis Valentin Nielsen
- Oslo
University Hospital and Medical Faculty, University of Oslo, 0372 Oslo, Norway
| | | | | | | | - Bengt Erik Haug
- Department
of Chemistry and Center for Pharmacy, University
of Bergen, 5007 Bergen, Norway
| | - Maria Stensland
- Oslo
University Hospital and Medical Faculty, University of Oslo, 0372 Oslo, Norway
| | - Bernd Thiede
- Department
of Biosciences, University of Oslo, 0371 Oslo, Norway
| | | | | | | | | | - Paul J. Declerck
- Department
of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Geir Åge Løset
- Department
of Biosciences, University of Oslo, 0371 Oslo, Norway,Nextera
AS, 0349 Oslo, Norway
| | - Sandip M. Kanse
- Oslo
University Hospital and Medical Faculty, University of Oslo, 0372 Oslo, Norway,
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23
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Al-Hazmi GH, Ibrahim AA, Refat MS, Adam FA, Allam A, Shakya S, Alsuhaibani AM. Intermolecular charge-transfer complexes between chlorothiazide antihypertensive drug against iodine sigma and picric acid pi acceptors: DFT and molecular docking interaction study with Covid-19 protease. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Chou-Zheng L, Hatoum-Aslan A. Critical roles for 'housekeeping' nucleases in type III CRISPR-Cas immunity. eLife 2022; 11:81897. [PMID: 36479971 PMCID: PMC9762709 DOI: 10.7554/elife.81897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
CRISPR-Cas systems are a family of adaptive immune systems that use small CRISPR RNAs (crRNAs) and CRISPR-associated (Cas) nucleases to protect prokaryotes from invading plasmids and viruses (i.e., phages). Type III systems launch a multilayered immune response that relies upon both Cas and non-Cas cellular nucleases, and although the functions of Cas components have been well described, the identities and roles of non-Cas participants remain poorly understood. Previously, we showed that the type III-A CRISPR-Cas system in Staphylococcus epidermidis employs two degradosome-associated nucleases, PNPase and RNase J2, to promote crRNA maturation and eliminate invading nucleic acids (Chou-Zheng and Hatoum-Aslan, 2019). Here, we identify RNase R as a third 'housekeeping' nuclease critical for immunity. We show that RNase R works in concert with PNPase to complete crRNA maturation and identify specific interactions with Csm5, a member of the type III effector complex, which facilitate nuclease recruitment/stimulation. Furthermore, we demonstrate that RNase R and PNPase are required to maintain robust anti-plasmid immunity, particularly when targeted transcripts are sparse. Altogether, our findings expand the known repertoire of accessory nucleases required for type III immunity and highlight the remarkable capacity of these systems to interface with diverse cellular pathways to ensure successful defense.
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Affiliation(s)
- Lucy Chou-Zheng
- Microbiology Department, University of Illinois Urbana-ChampaignUrbanaUnited States
| | - Asma Hatoum-Aslan
- Microbiology Department, University of Illinois Urbana-ChampaignUrbanaUnited States
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