101
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Avery C, Patterson J, Grear T, Frater T, Jacobs DJ. Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:1246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein-ligand binding, including allosteric effects, protein-protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
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Affiliation(s)
- Chris Avery
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - John Patterson
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Tyler Grear
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Theodore Frater
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Donald J. Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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102
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Daulat AM, Wagner MS, Audebert S, Kowalczewska M, Ariey-Bonnet J, Finetti P, Bertucci F, Camoin L, Borg JP. The serine/threonine kinase MINK1 directly regulates the function of promigratory proteins. J Cell Sci 2022; 135:276338. [PMID: 35971817 DOI: 10.1242/jcs.259347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 08/08/2022] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the developmental Wnt/planar cell polarity pathway is observed in many cancers and is associated with cancer development. We recently showed that PRICKLE1, a core Wnt/PCP component, is a poor-prognosis marker in triple negative breast cancer (TNBC). PRICKLE1 is phosphorylated by the serine/threonine kinase MINK1 and contributes to TNBC cell motility and invasiveness. However, the identity of MINK1 substrates and the role of MINK1 enzymatic activity in this process remain to be addressed. We performed a phosphoproteomic strategy and identified MINK1 substrates including LL5β. LL5β anchors microtubules at the cell cortex through its association with CLASPs to trigger focal adhesion disassembly. LL5β is phosphorylated by MINK1 promoting its interaction with CLASPs. Using a kinase inhibitor, we demonstrate that the enzymatic activity of MINK1 is involved in the protein complex assembly and localization, and cell migration. Analysis of gene expression data show that the concomitant up-regulation of PRICKLE1 and LL5β mRNA levels encoding MINK1 substrates is associated with a poor metastasis-free survival in TNBC patients. Altogether, our results suggest that MINK1 may represent a potential target in TNBC.
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Affiliation(s)
- Avais M Daulat
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, Cell signaling and Cancer', Marseille, France
| | - Mônica S Wagner
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, Cell signaling and Cancer', Marseille, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Malgorzata Kowalczewska
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, Cell signaling and Cancer', Marseille, France
| | - Jeremy Ariey-Bonnet
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Biologie Structurale et Chimie-Biologie Intégrée, Marseille, France
| | - Pascal Finetti
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Predictive Oncology', Marseille, France
| | - François Bertucci
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Predictive Oncology', Marseille, France
| | - Luc Camoin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Jean-Paul Borg
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, Cell signaling and Cancer', Marseille, France.,Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France.,Institut universitaire de France, France
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103
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The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing. PLoS Pathog 2022; 18:e1010750. [PMID: 35930610 PMCID: PMC9384988 DOI: 10.1371/journal.ppat.1010750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB. Exopolysaccharides are an important component of the extracellular matrix of bacterial and fungal biofilms and provide protection against the host immune response and antibiotics. In Gram-negative bacteria, these polymers are synthesized in the inner membrane and translocated across the periplasm before being secreted across the outer membrane. The periplasm presents both a challenge as an additional environment to cross and an opportunity to chemically alter the polymer prior to secretion to render it more effective. This study focuses on a periplasmic alpha-helical repeat domain whose wide-spread homologues are involved in the export of many chemically distinct exopolysaccharides. We found that in E. coli this superhelical TPR domain acts as a scaffold that can bind the polymer PNAG and alter the enzymatic activity of PgaB, thus providing a means to affect the deacetylation level and chain length of the secreted polymer. Scaffold proteins are known as binding hubs within cellular pathways that often have a central regulatory function and facilitate evolution due to their repetitive modular building blocks. Our study sheds light on the principles of polysaccharide modification and export, which we hope will promote the development of applications against bacterial infections.
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104
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Bychkova VE, Dolgikh DA, Balobanov VA, Finkelstein AV. The Molten Globule State of a Globular Protein in a Cell Is More or Less Frequent Case Rather than an Exception. Molecules 2022; 27:molecules27144361. [PMID: 35889244 PMCID: PMC9319461 DOI: 10.3390/molecules27144361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/01/2023] Open
Abstract
Quite a long time ago, Oleg B. Ptitsyn put forward a hypothesis about the possible functional significance of the molten globule (MG) state for the functioning of proteins. MG is an intermediate between the unfolded and the native state of a protein. Its experimental detection and investigation in a cell are extremely difficult. In the last decades, intensive studies have demonstrated that the MG-like state of some globular proteins arises from either their modifications or interactions with protein partners or other cell components. This review summarizes such reports. In many cases, MG was evidenced to be functionally important. Thus, the MG state is quite common for functional cellular proteins. This supports Ptitsyn’s hypothesis that some globular proteins may switch between two active states, rigid (N) and soft (MG), to work in solution or interact with partners.
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Affiliation(s)
- Valentina E. Bychkova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117871 Moscow, Russia;
| | - Vitalii A. Balobanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
- Correspondence:
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; (V.E.B.); (A.V.F.)
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105
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Ramasamy P, Vandermarliere E, Vranken WF, Martens L. Panoramic Perspective on Human Phosphosites. J Proteome Res 2022; 21:1894-1915. [PMID: 35793420 DOI: 10.1021/acs.jproteome.2c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is the most common reversible post-translational modification of proteins and is key in the regulation of many cellular processes. Due to this importance, phosphorylation is extensively studied, resulting in the availability of a large amount of mass spectrometry-based phospho-proteomics data. Here, we leverage the information in these large-scale phospho-proteomics data sets, as contained in Scop3P, to analyze and characterize proteome-wide protein phosphorylation sites (P-sites). First, we set out to differentiate correctly observed P-sites from false-positive sites using five complementary site properties. We then describe the context of these P-sites in terms of the protein structure, solvent accessibility, structural transitions and disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P-sites. Moreover, we assess the structural dynamics of P-sites in their phosphorylated and unphosphorylated states. As a result, we show how large-scale reprocessing of available proteomics experiments can enable a more reliable view on proteome-wide P-sites. Furthermore, adding the structural context of proteins around P-sites helps uncover possible conformational switches upon phosphorylation. Moreover, by placing sites in different biophysical contexts, we show the differential preference in protein dynamics at phosphorylated sites when compared to the nonphosphorylated counterparts.
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Affiliation(s)
- Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | | | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Centre for Structural Biology, VIB, 1050 Brussels, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
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106
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Bukhari I, Khan MR, Hussain MA, Thorne RF, Yu Y, Zhang B, Zheng P, Mi Y. PINTology: A short history of the lncRNA LINC-PINT in different diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1705. [PMID: 35019222 DOI: 10.1002/wrna.1705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
LINC-PINT is a p53-induced long intergenic noncoding transcript that plays a crucial role in many diseases, especially cancer. This long noncoding RNA (lncRNA) gene produces in total 102 (LNCipedia) alternatively spliced variants (LINC-PINT:1 to LINC-PINT:102). The functions of known variants include RNA transcripts, host transcripts for circular RNA (circRNA) generation and as sources for the translation of short peptides. In most human tumors, LINC-PINT is down-regulated where it serves as a tumor suppressor. However, the diversity of its functions in other maladies signifies its general clinical importance. Current LINC-PINT molecular functions include RNA-protein interactions, miRNA sponging and epigenetic modulation with these mechanisms operating in different cellular contexts to exert effects on biological processes ranging from DNA damage responses, cell cycle and growth arrest, senescence, cell migration and invasion, and apoptosis. Genetic polymorphisms in LINC-PINT have also been functionally associated with cancer and other pathologies including the autoimmune diseases pemphigus foliaceus and arthritis. Hence, LINC-PINT shows great potential as a clinical biomarker, especially for the diagnosis and prognosis of cancer. In this review, we explore the current knowledge highlighting the distinctive molecular functions of LINC-PINT in specific cancers and other disease states. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Ihtisham Bukhari
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Muhammad Riaz Khan
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l'Estrie - Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada.,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mohammed Amir Hussain
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, China.,School of Environmental & Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Yong Yu
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Bingyong Zhang
- Department of Gastroenterology, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Pengyuan Zheng
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Mi
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Gastroenterology, Fifth Affiliated hospital of Zhengzhou University, Zhengzhou, China
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107
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Gyenis L, Menyhart D, Cruise ES, Jurcic K, Roffey SE, Chai DB, Trifoi F, Fess SR, Desormeaux PJ, Núñez de Villavicencio Díaz T, Rabalski AJ, Zukowski SA, Turowec JP, Pittock P, Lajoie G, Litchfield DW. Chemical Genetic Validation of CSNK2 Substrates Using an Inhibitor-Resistant Mutant in Combination with Triple SILAC Quantitative Phosphoproteomics. Front Mol Biosci 2022; 9:909711. [PMID: 35755813 PMCID: PMC9225150 DOI: 10.3389/fmolb.2022.909711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Casein Kinase 2 (CSNK2) is an extremely pleiotropic, ubiquitously expressed protein kinase involved in the regulation of numerous key biological processes. Mapping the CSNK2-dependent phosphoproteome is necessary for better characterization of its fundamental role in cellular signalling. While ATP-competitive inhibitors have enabled the identification of many putative kinase substrates, compounds targeting the highly conserved ATP-binding pocket often exhibit off-target effects limiting their utility for definitive kinase-substrate assignment. To overcome this limitation, we devised a strategy combining chemical genetics and quantitative phosphoproteomics to identify and validate CSNK2 substrates. We engineered U2OS cells expressing exogenous wild type CSNK2A1 (WT) or a triple mutant (TM, V66A/H160D/I174A) with substitutions at residues important for inhibitor binding. These cells were treated with CX-4945, a clinical-stage inhibitor of CSNK2, and analyzed using large-scale triple SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture) quantitative phosphoproteomics. In contrast to wild-type CSNK2A1, CSNK2A1-TM retained activity in the presence of CX-4945 enabling identification and validation of several CSNK2 substrates on the basis of their increased phosphorylation in cells expressing CSNK2A1-TM. Based on high conservation within the kinase family, we expect that this strategy can be broadly adapted for identification of other kinase-substrate relationships.
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Affiliation(s)
- Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Edward S Cruise
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Scott E Roffey
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Darren B Chai
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Flaviu Trifoi
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Sam R Fess
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paul J Desormeaux
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Adam J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Stephanie A Zukowski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jacob P Turowec
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paula Pittock
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
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108
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Abstract
Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.
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109
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Shen H, Shi H, Feng B, Ding C, Yu S. A versatile biomimetic multienzyme cascade nanoplatform based on boronic acid-modified metal-organic framework for colorimetric biosensing. J Mater Chem B 2022; 10:3444-3451. [PMID: 35394481 DOI: 10.1039/d2tb00158f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combination of bio- and chemo-catalysts for sequential cascades has received considerable attention in analytical fields because of the regulable catalytic efficiency and selectivity under various physiological conditions. In this paper, a versatile multienzyme cascade nanoplatform with excellent activity for biosensing is demonstrated by combining metal-organic framework (MOF)-based nanozyme with natural enzymes. A boronic acid-modified MOF, MIL-100(Fe)-BA, was obtained via a microwave-assisted metal-ligand-fragment co-assembly strategy. On the one hand, MIL-100(Fe)-BA could serve as a nanozyme with dual oxidase/peroxidase bioactivity to detect glutathione and ascorbic acid with a detection limit of 0.12 μM and 0.09 μM, respectively. On the other hand, the hierarchically porous MIL-100(Fe)-BA possesses adequate recognition sites for immobilizing enzymes with acceptable protein leakage, enabling it to act like a scaffold for the fixation of a single enzyme (sarcosine oxidase) or bi-enzymes (acetylcholinesterase/choline oxidase) and guide a multienzyme cascade reaction system with high efficiency. The cascade nanoplatform has merits of both artificial nanozymes and natural enzymes, providing satisfactory sarcosine/acetylcholine sensing ability with detection limits of 0.26 μM and 1.18 μM. The developed catalytic system not only expands the application of nanozymes in tandem enzymatic bio-catalysis, but provides a facile and efficient multienzyme cascade nanoplatform for biosensing and other applications.
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Affiliation(s)
- Hao Shen
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Haimei Shi
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bin Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuanfan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shaoning Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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110
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Dreyer CA, VanderVorst K, Carraway KL. Vangl as a Master Scaffold for Wnt/Planar Cell Polarity Signaling in Development and Disease. Front Cell Dev Biol 2022; 10:887100. [PMID: 35646914 PMCID: PMC9130715 DOI: 10.3389/fcell.2022.887100] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 01/04/2023] Open
Abstract
The establishment of polarity within tissues and dynamic cellular morphogenetic events are features common to both developing and adult tissues, and breakdown of these programs is associated with diverse human diseases. Wnt/Planar cell polarity (Wnt/PCP) signaling, a branch of non-canonical Wnt signaling, is critical to the establishment and maintenance of polarity in epithelial tissues as well as cell motility events critical to proper embryonic development. In epithelial tissues, Wnt/PCP-mediated planar polarity relies upon the asymmetric distribution of core proteins to establish polarity, but the requirement for this distribution in Wnt/PCP-mediated cell motility remains unclear. However, in both polarized tissues and migratory cells, the Wnt/PCP-specific transmembrane protein Vangl is required and appears to serve as a scaffold upon which the core pathway components as well as positive and negative regulators of Wnt/PCP signaling assemble. The current literature suggests that the multiple interaction domains of Vangl allow for the binding of diverse signaling partners for the establishment of context- and tissue-specific complexes. In this review we discuss the role of Vangl as a master scaffold for Wnt/PCP signaling in epithelial tissue polarity and cellular motility events in developing and adult tissues, and address how these programs are dysregulated in human disease.
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Affiliation(s)
| | | | - Kermit L. Carraway
- Department of Biochemistry and Molecular Medicine and the UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, Sacramento, CA, United States
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111
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George B, Haque A, Sahu V, Joldoshova A, Singh Y, Quinones JE, George SK, Amin HM. Enhancing Antigen Retrieval to Unmask Signaling Phosphoproteins in Formalin-fixed Archival Tissues. Appl Immunohistochem Mol Morphol 2022; 30:333-339. [PMID: 35510772 PMCID: PMC9096965 DOI: 10.1097/pai.0000000000001022] [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: 08/10/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
The introduction of targeted therapy has revolutionized cancer treatment. Nonetheless, for this approach to succeed, it is crucial to identify the targets, particularly when activated, in tumor tissues. Phosphorylation is a posttranslational modification that causes activation of numerous oncogenic protein kinases and transcription regulators. Hence, phosphoproteins is a class of biomarkers that has therapeutic and prognostic implications directly relevant to cancer patients' management. Despite the progress in histopathology methodology, analysis of the expression of phosphoproteins in tumor tissues still represents a challenge owing to preanalytical and analytical factors that include antigen retrieval strategies. In this study, we tested the hypothesis that optimizing antigen retrieval methods will improve phosphoproteins unmasking and enhance their immunohistochemical staining signal. We screened 4 antigen retrieval methods by using antibodies specific for 3 oncogenic phosphoproteins to stain human lymphoma tumors that were developed in severe combined immunodeficiency mice and subsequently fixed in formalin for 2 years. Then, we used antibodies specific for 15 survival phosphoproteins to compare the most effective method identified from our screening experiment to the antigen retrieval method that is most commonly utilized. Using the antigen retrieval buffer Tris-EDTA at pH 9.0 and heating for 45 minutes at 97°C unmasked and significantly enhanced the staining of 9 of the 15 phosphoproteins (P<0.0001). Our antigen retrieval approach is cost effective and feasible for clinical and research settings. We anticipate that combining this approach with the newly proposed methods to improve tissue fixation will further improve unmasking of phosphoproteins in human and animal tissues.
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Affiliation(s)
- Bhawana George
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abedul Haque
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vishal Sahu
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Albina Joldoshova
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yashandeep Singh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Janet E. Quinones
- Pathology/Histology Laboratories, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Suraj Konnath George
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hesham M. Amin
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
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112
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Shi T, Zeng J, Zhou J, Yu Y, Lu H. Correlation Between Improved Mating Efficiency and Weakened Scaffold-Kinase Interaction in the Mating Pheromone Response Pathway Revealed by Interspecies Complementation. Front Microbiol 2022; 13:865829. [PMID: 35495719 PMCID: PMC9048679 DOI: 10.3389/fmicb.2022.865829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Scaffold protein Ste5 and associated kinases, including Ste11, Ste7, and Fus3, are core components of the mating pheromone pathway, which is required to induce a mating response. Orthologs of these proteins are widely present in fungi, but to which extent one protein can be replaced by its ortholog is less well understood. Here, interspecies complementation was carried out to evaluate the functional homology of Ste5 and associated kinases in Kluyveromyces lactis, K. marxianus, and Saccharomyces cerevisiae. These three species occupy important positions in the evolution of hemiascomycetes. Results indicated that Ste5 and associated kinases in K. lactis and K. marxianus could be functionally replaced by their orthologs to different extents. However, the extent of sequence identity, either between full-length proteins or between domains, did not necessarily indicate the extent of functional replaceability. For example, Ste5, the most unconserved protein in sequence, achieved the highest average functional replaceability. Notably, swapping Ste5 between K. lactis and K. marxianus significantly promoted mating in both species and the weakened interaction between the Ste5 and Ste7 might contribute to this phenotype. Consistently, chimeric Ste5 displaying a higher affinity for Ste7 decreased the mating efficiency, while chimeric Ste5 displaying a lower affinity for Ste7 improved the mating efficiency. Furthermore, the length of a negatively charged segment in the Ste7-binding domain of Ste5 was negatively correlated with the mating efficiency in K. lactis and K. marxianus. Extending the length of the segment in KlSte5 improved its interaction with Ste7 and that might contribute to the reduced mating efficiency. Our study suggested a novel role of Ste5-Ste7 interaction in the negative regulation of the pheromone pathway. Meanwhile, Ste5 mutants displaying improved mating efficiency facilitated the breeding and selection of Kluyveromyces strains for industrial applications.
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Affiliation(s)
- Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Junyuan Zeng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- *Correspondence: Yao Yu,
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- Hong Lu,
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113
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Chen X, Wang Y, Dai X, Ding L, Chen J, Yao G, Liu X, Luo S, Shi J, Wang L, Nechushtai R, Pikarsky E, Willner I, Fan C, Li J. Single-Stranded DNA-Encoded Gold Nanoparticle Clusters as Programmable Enzyme Equivalents. J Am Chem Soc 2022; 144:6311-6320. [PMID: 35353520 DOI: 10.1021/jacs.1c13116] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Nanozymes have emerged as a class of novel catalytic nanomaterials that show great potential to substitute natural enzymes in various applications. Nevertheless, spatial organization of multiple subunits in a nanozyme to rationally engineer its catalytic properties remains to be a grand challenge. Here, we report a DNA-based approach to encode the organization of gold nanoparticle clusters (GNCs) for the construction of programmable enzyme equivalents (PEEs). We find that single-stranded (ss-) DNA scaffolds can self-fold into nanostructures with prescribed poly-adenine (polyA) loops and double-stranded stems and that the polyA loops serve as specific sites for seed-free nucleation and growth of GNCs with well-defined particle numbers and interparticle spaces. A spectrum of GNCs, ranging from oligomers with discrete particle numbers (2-4) to polymer-like chains, are in situ synthesized in this manner. The polymeric GNCs with multiple spatially organized nanoparticles as subunits show programmable peroxidase-like catalytic activity that can be tuned by the scaffold size and the inter-polyA spacer length. This study thus opens new routes to the rational design of nanozymes for various biological and biomedical applications.
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Affiliation(s)
- Xiaoliang Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, University of Chinese Academy of Sciences, Beijing 100049, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xinpei Dai
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjiang Ding
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielin Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangbao Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shihua Luo
- Department of Traumatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200025, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200127, China
| | - Rachel Nechushtai
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Pikarsky
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, University of Chinese Academy of Sciences, Beijing 100049, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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114
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Liu L, Hong F, Liu H, Zhou X, Jiang S, Šulc P, Jiang JH, Yan H. A localized DNA finite-state machine with temporal resolution. SCIENCE ADVANCES 2022; 8:eabm9530. [PMID: 35333578 PMCID: PMC8956261 DOI: 10.1126/sciadv.abm9530] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/02/2022] [Indexed: 05/21/2023]
Abstract
The identity and timing of environmental stimulus play a pivotal role in living organisms in programming their signaling networks and developing specific phenotypes. The ability to unveil history-dependent signals will advance our understanding of temporally regulated biological processes. Here, we have developed a two-input, five-state DNA finite-state machine (FSM) to sense and record the temporally ordered inputs. The spatial organization of the processing units on DNA origami enables facile modulation of the energy landscape of DNA strand displacement reactions, allowing precise control of the reactions along predefined paths for different input orders. The use of spatial constraints brings about a simple, modular design for the FSM with a minimum set of orthogonal components and confers minimized leaky reactions and fast kinetics. The FSM demonstrates the capability of sensing the temporal orders of two microRNAs, highlighting its potential for temporally resolved biosensing and smart therapeutics.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Fan Hong
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xu Zhou
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Corresponding author. (H.Y.); (J.-H.J.)
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author. (H.Y.); (J.-H.J.)
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115
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Afza F, Singh N, Shriya S, Bisoyi P, Kashyap AK, Jain BP. Genome wide identification and analysis of WD40 domain containing proteins in Danio rerio. GENE REPORTS 2022; 26:101426. [DOI: 10.1016/j.genrep.2021.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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116
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Yerramilli VS, Ross AH, Scarlata S, Gericke A. IQGAP1 scaffolding links phosphoinositide kinases to cytoskeletal reorganization. Biophys J 2022; 121:793-807. [PMID: 35077666 PMCID: PMC8943696 DOI: 10.1016/j.bpj.2022.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/24/2021] [Accepted: 01/21/2022] [Indexed: 11/02/2022] Open
Abstract
IQGAP1 is a multidomain scaffold protein that coordinates the direction and impact of multiple signaling pathways by scaffolding its various binding partners. However, the spatial and temporal resolution of IQGAP1 scaffolding remains unclear. Here, we use fluorescence imaging and correlation methods that allow for real-time live-cell changes in IQGAP1 localization and complex formation during signaling. We find that IQGAP1 and PIPKIγ interact on both the plasma membrane and in cytosol. Epidermal growth factor (EGF) stimulation, which can initiate cytoskeletal changes, drives the movement of the cytosolic pool toward the plasma membrane to promote cytoskeletal changes. We also observe that a significant population of cytosolic IQGAP1-PIPKIγ complexes localize to early endosomes, and in some instances form aggregated clusters which become highly mobile upon EGF stimulation. Our imaging studies show that PIPKIγ and PI3K bind simultaneously to IQGAP1, which may accelerate conversion of PI4P to PI(3,4,5)P3 that is required for cytoskeletal changes. Additionally, we find that IQGAP1 is responsible for PIPKIγ association with two proteins associated with cytoskeletal changes, talin and Cdc42, during EGF stimulation. These results directly show that IQGAP1 provides a physical link between phosphoinositides (through PIPKIγ), focal adhesion formation (through talin), and cytoskeletal reorganization (through Cdc42) upon EGF stimulation. Taken together, our results support the importance of IQGAP1 in regulating cell migration by linking phosphoinositide lipid signaling with cytoskeletal reorganization.
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Affiliation(s)
- V. Siddartha Yerramilli
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Alonzo H. Ross
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Suzanne Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Arne Gericke
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts.
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117
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Kahn J, Xiong Y, Huang J, Gang O. Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold. JACS AU 2022; 2:357-366. [PMID: 35252986 PMCID: PMC8889550 DOI: 10.1021/jacsau.1c00387] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 05/31/2023]
Abstract
DNA nanotechnology has increasingly been used as a platform to scaffold enzymes based on its unmatched ability to structure enzymes in a desired format. The capability to organize enzymes has taken many forms from more traditional 2D pairings on individual scaffolds to recent works introducing enzyme organizations in 3D lattices. As the ability to define nanoscale structure has grown, it is critical to fully deconstruct the impact of enzyme organization at the single-scaffold level. Here, we present an open, three-dimensional (3D) DNA wireframe octahedron which is used to create a library of spatially arranged organizations of glucose oxidase and horseradish peroxidase. We explore the contribution of enzyme spacing, arrangement, and location on the 3D scaffold to cascade activity. The experiments provide insight into enzyme scaffold design, including the insignificance of scaffold sequence makeup on activity, an increase in activity at small enzyme spacings of <10 nm, and activity changes that arise from discontinuities in scaffold architecture. Most notably, the experiments allow us to determine that enzyme colocalization itself on the DNA scaffold dominates over any specific enzyme arrangement.
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Affiliation(s)
- Jason
S. Kahn
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Yan Xiong
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - James Huang
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York New York 10027, United States
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118
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LaCroix R, Lin B, Kang TY, Levchenko A. Complex effects of kinase localization revealed by compartment-specific regulation of protein kinase A activity. eLife 2022; 11:e66869. [PMID: 35199643 PMCID: PMC8871369 DOI: 10.7554/elife.66869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
Kinase activity in signaling networks frequently depends on regulatory subunits that can both inhibit activity by interacting with the catalytic subunits and target the kinase to distinct molecular partners and subcellular compartments. Here, using a new synthetic molecular interaction system, we show that translocation of a regulatory subunit of the protein kinase A (PKA-R) to the plasma membrane has a paradoxical effect on the membrane kinase activity. It can both enhance it at lower translocation levels, even in the absence of signaling inputs, and inhibit it at higher translocation levels, suggesting its role as a linker that can both couple and decouple signaling processes in a concentration-dependent manner. We further demonstrate that superposition of gradients of PKA-R abundance across single cells can control the directionality of cell migration, reversing it at high enough input levels. Thus, complex in vivo patterns of PKA-R localization can drive complex phenotypes, including cell migration.
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Affiliation(s)
- Rebecca LaCroix
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale Systems Biology Institute, Yale UniversityWest HavenUnited States
| | - Benjamin Lin
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale Systems Biology Institute, Yale UniversityWest HavenUnited States
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU Langone HealthNew YorkUnited States
| | - Tae-Yun Kang
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale Systems Biology Institute, Yale UniversityWest HavenUnited States
| | - Andre Levchenko
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Yale Systems Biology Institute, Yale UniversityWest HavenUnited States
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119
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Guo J, Amini S, Lei Q, Ping Y, Agola JO, Wang L, Zhou L, Cao J, Franco S, Noureddine A, Miserez A, Zhu W, Brinker CJ. Robust and Long-Term Cellular Protein and Enzymatic Activity Preservation in Biomineralized Mammalian Cells. ACS NANO 2022; 16:2164-2175. [PMID: 35143166 DOI: 10.1021/acsnano.1c08103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Preservation of evolved biological structure and function in robust engineering materials is of interest for storage of biological samples before diagnosis and development of vaccines, sensors, and enzymatic reactors and has the potential to avoid cryopreservation and its associated cold-chain issues. Here, we demonstrate that "freezing cells in amorphous silica" is a powerful technique for long-term preservation of whole mammalian cell proteomic structure and function at room temperature. Biomimetic silicification employs the crowded protein microenvironment of mammalian cells as a catalytic framework to proximally transform monomeric silicic acid into silicates forming a nanoscopic silica shell over all biomolecular interfaces. Silicification followed by dehydration preserves and passivates proteomic information within a nanoscale thin silica coating that exhibits size selective permeability (<3.6 nm), preventing protein leaching and protease degradation of cellular contents, while providing access of small molecular constituents for cellular enzymatic reaction. Exposure of dehydrated silicified cells to mild etchant or prolonged hydrolysis removes the silica, completely rerevealing biomolecular components and restoring their accessibility and functionality.
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Affiliation(s)
- Jimin Guo
- Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Internal Medicine, Molecular Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Shahrouz Amini
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Qi Lei
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Jacob Ongudi Agola
- Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Lu Wang
- Department of Biochemistry and Molecular Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Liang Zhou
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Jiangfan Cao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Stefan Franco
- Department of Internal Medicine, Molecular Medicine, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Achraf Noureddine
- Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ali Miserez
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - C Jeffrey Brinker
- Center for Micro-Engineered Materials and the Department of Chemical and Biological Engineering, The University of New Mexico, Albuquerque, New Mexico 87131, United States
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120
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Jameson N, Gavagan M, Zalatan JG. A kinetic mechanism for systems-level behavior in GTPase signaling. Trends Biochem Sci 2022; 47:459-460. [DOI: 10.1016/j.tibs.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
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121
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Hierarchically encapsulating enzymes with multi-shelled metal-organic frameworks for tandem biocatalytic reactions. Nat Commun 2022; 13:305. [PMID: 35027566 PMCID: PMC8758787 DOI: 10.1038/s41467-022-27983-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 12/10/2021] [Indexed: 01/25/2023] Open
Abstract
Biocatalytic transformations in living organisms, such as multi-enzyme catalytic cascades, proceed in different cellular membrane-compartmentalized organelles with high efficiency. Nevertheless, it remains challenging to mimicking biocatalytic cascade processes in natural systems. Herein, we demonstrate that multi-shelled metal-organic frameworks (MOFs) can be used as a hierarchical scaffold to spatially organize enzymes on nanoscale to enhance cascade catalytic efficiency. Encapsulating multi-enzymes with multi-shelled MOFs by epitaxial shell-by-shell overgrowth leads to 5.8~13.5-fold enhancements in catalytic efficiencies compared with free enzymes in solution. Importantly, multi-shelled MOFs can act as a multi-spatial-compartmental nanoreactor that allows physically compartmentalize multiple enzymes in a single MOF nanoparticle for operating incompatible tandem biocatalytic reaction in one pot. Additionally, we use nanoscale Fourier transform infrared (nano-FTIR) spectroscopy to resolve nanoscale heterogeneity of vibrational activity associated to enzymes encapsulated in multi-shelled MOFs. Furthermore, multi-shelled MOFs enable facile control of multi-enzyme positions according to specific tandem reaction routes, in which close positioning of enzyme-1-loaded and enzyme-2-loaded shells along the inner-to-outer shells could effectively facilitate mass transportation to promote efficient tandem biocatalytic reaction. This work is anticipated to shed new light on designing efficient multi-enzyme catalytic cascades to encourage applications in many chemical and pharmaceutical industrial processes. Mimicking multi-enzyme catalytic cascades in natural systems with spatial organization in confined structures is gaining increasing attention in the emerging field of systems chemistry. Here, the authors demonstrate that multi-shelled metal-organic frameworks can be used as a hierarchical scaffold to spatially organize enzymes on nanoscale to enhance cascade catalytic efficiency.
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122
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Swamy H, Glading AJ. Is Location Everything? Regulation of the Endothelial CCM Signaling Complex. Front Cardiovasc Med 2022; 9:954780. [PMID: 35898265 PMCID: PMC9309484 DOI: 10.3389/fcvm.2022.954780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Recent advances have steadily increased the number of proteins and pathways known to be involved in the development of cerebral cavernous malformation (CCM). Our ability to synthesize this information into a cohesive and accurate signaling model is limited, however, by significant gaps in our knowledge of how the core CCM proteins, whose loss of function drives development of CCM, are regulated. Here, we review what is known about the regulation of the three core CCM proteins, the scaffolds KRIT1, CCM2, and CCM3, with an emphasis on binding interactions and subcellular location, which frequently control scaffolding protein function. We highlight recent work that challenges the current model of CCM complex signaling and provide recommendations for future studies needed to address the large number of outstanding questions.
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Affiliation(s)
- Harsha Swamy
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States
| | - Angela J Glading
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States
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123
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Yang X, Tan Z, Sun H, Tong Y, Huang X, Ren J, Wang C, Shen W. Fabrication of Hierarchical Nanoreactor based on COFs for Cascade Enzyme Catalysis. Chem Commun (Camb) 2022; 58:3933-3936. [DOI: 10.1039/d2cc00269h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hierarchical nanoreactor based on covalent organic frameworks (COFs) was fabricated using polystyrene spheres (PSs) as template. When applied in cascade catalysis, the nanoreactor improved significantly the catalytic activity of...
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124
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Lee A, Mason ML, Lin T, Kumar SB, Kowdley D, Leung JH, Muhanna D, Sun Y, Ortega-Anaya J, Yu L, Fitzgerald J, DeVries AC, Nelson RJ, Weil ZM, Jiménez-Flores R, Parquette JR, Ziouzenkova O. Amino Acid Nanofibers Improve Glycemia and Confer Cognitive Therapeutic Efficacy to Bound Insulin. Pharmaceutics 2021; 14:pharmaceutics14010081. [PMID: 35056977 PMCID: PMC8778970 DOI: 10.3390/pharmaceutics14010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 12/04/2022] Open
Abstract
Diabetes poses a high risk for debilitating complications in neural tissues, regulating glucose uptake through insulin-dependent and predominantly insulin-independent pathways. Supramolecular nanostructures provide a flexible strategy for combinatorial regulation of glycemia. Here, we compare the effects of free insulin to insulin bound to positively charged nanofibers comprised of self-assembling amino acid compounds (AACs) with an antioxidant-modified side chain moiety (AAC2) in both in vitro and in vivo models of type 1 diabetes. Free AAC2, free human insulin (hINS) and AAC2-bound-human insulin (AAC2-hINS) were tested in streptozotocin (STZ)-induced mouse model of type 1 diabetes. AAC2-hINS acted as a complex and exhibited different properties compared to free AAC2 or hINS. Mice treated with the AAC2-hINS complex were devoid of hypoglycemic episodes, had improved levels of insulin in circulation and in the brain, and increased expression of neurotransmitter taurine transporter, Slc6a6. Consequently, treatment with AAC2-hINS markedly advanced both physical and cognitive performance in mice with STZ-induced and genetic type 1 diabetes compared to treatments with free AAC2 or hINS. This study demonstrates that the flexible nanofiber AAC2 can serve as a therapeutic platform for the combinatorial treatment of diabetes and its complications.
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Affiliation(s)
- Aejin Lee
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
| | - McKensie L. Mason
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (M.L.M.); (T.L.); (Y.S.); (J.R.P.)
| | - Tao Lin
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (M.L.M.); (T.L.); (Y.S.); (J.R.P.)
| | - Shashi Bhushan Kumar
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
| | - Devan Kowdley
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
| | - Jacob H. Leung
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
| | - Danah Muhanna
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
| | - Yuan Sun
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (M.L.M.); (T.L.); (Y.S.); (J.R.P.)
| | - Joana Ortega-Anaya
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (J.O.-A.); (R.J.-F.)
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA;
| | - Julie Fitzgerald
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA; (J.F.); (A.C.D.); (Z.M.W.)
| | - A. Courtney DeVries
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA; (J.F.); (A.C.D.); (Z.M.W.)
- Department of Neuroscience, West Virginia University, Morgantown, WV 26506, USA
| | - Randy J. Nelson
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26506, USA;
| | - Zachary M. Weil
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA; (J.F.); (A.C.D.); (Z.M.W.)
| | - Rafael Jiménez-Flores
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (J.O.-A.); (R.J.-F.)
| | - Jon R. Parquette
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; (M.L.M.); (T.L.); (Y.S.); (J.R.P.)
| | - Ouliana Ziouzenkova
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA; (A.L.); (S.B.K.); (D.K.); (J.H.L.); (D.M.)
- Correspondence: ; Tel.: +1-614-292-5034
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125
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Jensen KL, Noes-Holt G, Sørensen AT, Madsen KL. A Novel Peripheral Action of PICK1 Inhibition in Inflammatory Pain. Front Cell Neurosci 2021; 15:750902. [PMID: 34975407 PMCID: PMC8714954 DOI: 10.3389/fncel.2021.750902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic pain is a major healthcare problem that impacts one in five adults across the globe. Current treatment is compromised by dose-limiting side effects including drowsiness, apathy, fatigue, loss of ability to function socially and professionally as well as a high abuse liability. Most of these side effects result from broad suppression of excitatory neurotransmission. Chronic pain states are associated with specific changes in the efficacy of synaptic transmission in the pain pathways leading to amplification of non-noxious stimuli and spontaneous pain. Consequently, a reversal of these specific changes may pave the way for the development of efficacious pain treatment with fewer side effects. We have recently described a high-affinity, bivalent peptide TAT-P4-(C5)2, enabling efficient targeting of the neuronal scaffold protein, PICK1, a key protein in mediating chronic pain sensitization. In the present study, we demonstrate that in an inflammatory pain model, the peptide does not only relieve mechanical allodynia by targeting PICK1 involved in central sensitization, but also by peripheral actions in the inflamed paw. Further, we assess the effects of the peptide on novelty-induced locomotor activity, abuse liability, and memory performance without identifying significant side effects.
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Affiliation(s)
- Kathrine Louise Jensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kenneth Lindegaard Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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126
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Jeung HC, Puentes R, Aleshin A, Indarte M, Correa RG, Bankston LA, Layng FIAL, Ahmed Z, Wistuba I, Yao Y, Duenas DG, Zhang S, Meuillet EJ, Marassi F, Liddington RC, Kirkpatrick L, Powis G. PLEKHA7 signaling is necessary for the growth of mutant KRAS driven colorectal cancer. Exp Cell Res 2021; 409:112930. [PMID: 34800542 DOI: 10.1016/j.yexcr.2021.112930] [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: 08/06/2021] [Revised: 10/26/2021] [Accepted: 11/14/2021] [Indexed: 10/19/2022]
Abstract
Plekha7 (Pleckstrin homology [PH] domain containing, family A member 7) regulates the assembly of proteins of the cytoplasmic apical zonula adherens junction (AJ), thus ensuring cell-cell adhesion and tight-junction barrier integrity. Little is known of Plekha7 function in cancer. In colorectal cancer (CRC) Plekha7 expression is elevated compared to adjacent normal tissue levels, increasing with clinical stage. Plekha7 was present at plasma membrane AJ with wild-type KRas (wt-KRas) but was dispersed in cells expressing mutant KRas (mut-KRas). Fluorescence lifetime imaging microscopy (FLIM) indicated a direct Plekha7 interaction with wt-KRas but scantily with mut-KRas. Inhibiting Plekha7 specifically decreased mut-KRas cell signaling, proliferation, attachment, migration, and retarded mut-KRAS CRC tumor growth. Binding of diC8-phosphoinositides (PI) to the PH domain of Plekha7 was relatively low affinity. This may be because a D175 amino acid residue plays a "sentry" role preventing PI(3,4)P2 and PI(3,4,5)P3 binding. Molecular or pharmacological inhibition of the Plekha7 PH domain prevented the growth of mut-KRas but not wt-KRas cells. Taken together the studies suggest that Plekha7, in addition to maintaining AJ structure plays a role in mut-KRas signaling and phenotype through interaction of its PH domain with membrane mut-KRas, but not wt-KRas, to increase the efficiency of mut-KRas downstream signaling.
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Affiliation(s)
- Hei-Cheul Jeung
- MD Anderson Cancer Center, Houston, TX, USA; Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-Gu, Seoul, South Korea
| | - Roisin Puentes
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Alexander Aleshin
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | - Ricardo G Correa
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Laurie A Bankston
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Fabiana I A L Layng
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | | | - Yong Yao
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Daniela G Duenas
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | | | - Francesca Marassi
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | - Robert C Liddington
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA
| | | | - Garth Powis
- Sanford Burnham Prebys Medical Discovery Institute Cancer Center, La Jolla, CA, USA; PHusis Therapeutics, La Jolla, CA, USA.
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127
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Ghelani T, Montenegro-Venegas C, Fejtova A, Dresbach T. Nanoscopical Analysis Reveals an Orderly Arrangement of the Presynaptic Scaffold Protein Bassoon at the Golgi-Apparatus. Front Mol Neurosci 2021; 14:744034. [PMID: 34867184 PMCID: PMC8632625 DOI: 10.3389/fnmol.2021.744034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/22/2021] [Indexed: 11/18/2022] Open
Abstract
Bassoon is a core scaffold protein of the presynaptic active zone. In brain synapses, the C-terminus of Bassoon is oriented toward the plasma membrane and its N-terminus is oriented toward synaptic vesicles. At the Golgi-apparatus, Bassoon is thought to assemble active zone precursor structures, but whether it is arranged in an orderly fashion is unknown. Understanding the topology of this large scaffold protein is important for models of active zone biogenesis. Using stimulated emission depletion nanoscopy in cultured hippocampal neurons, we found that an N-terminal intramolecular tag of recombinant Bassoon, but not C-terminal tag, colocalized with markers of the trans-Golgi network (TGN). The N-terminus of Bassoon was located between 48 and 69 nm away from TGN38, while its C-terminus was located between 100 and 115 nm away from TGN38. Sequences within the first 95 amino acids of Bassoon were required for this arrangement. Our results indicate that, at the Golgi-apparatus, Bassoon is oriented with its N-terminus toward and its C-terminus away from the trans Golgi network membrane. Moreover, they suggest that Bassoon is an extended molecule at the trans Golgi network with the distance between amino acids 97 and 3,938, estimated to be between 46 and 52 nm. Our data are consistent with a model, in which the N-terminus of Bassoon binds to the membranes of the trans-Golgi network, while the C-terminus associates with active zone components, thus reflecting the topographic arrangement characteristic of synapses also at the Golgi-apparatus.
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Affiliation(s)
- Tina Ghelani
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
| | - Carolina Montenegro-Venegas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany.,Institute for Pharmacology and Toxicology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Anna Fejtova
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Department of Psychiatry and Psychotherapy, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.,RG Presynaptic Plasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Thomas Dresbach
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
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128
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Changes in ion channel expression and function associated with cardiac arrhythmogenic remodeling by Sorbs2. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166247. [PMID: 34487812 DOI: 10.1016/j.bbadis.2021.166247] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022]
Abstract
The Sorbin and SH3 domain-containing protein 2 (Sorbs2) is an important component of cardiomyocyte sarcomere. It has been recently reported that loss of Sorbs2 is causally associated with arrhythmogenic cardiomyopathy in human. However, the ionic mechanisms leading to cardiac arrhythmogenesis by Sorbs2 deficiency are unknown. In this study, we hypothesized that Sorbs2 plays an important role in regulating cardiac ion channel expression and function. Using electrophysiological and molecular biological approaches, we found that the Sorbs2 knockout (KO) mice progressively developed cardiac structural and electrical remodeling as early as 1 to 2 months of age and died prematurely at 5 to 7 months of age. Electrocardiographic recordings showed that Sorbs2 KO mice had conduction delays, spontaneous ventricular extrasystoles and polymorphic ventricular tachyarrhythmia. Intracellular recordings revealed abnormal action potentials with depolarized resting potential, reduced upstroke velocity, prolonged repolarization, and effective refractory period in the ventricular preparations of Sorbs2 KO mice. Patch clamp experiments demonstrated that Sorbs2 KO mice displayed distinct abnormalities in the expression and function of cardiac ion channels, including those of the voltage-gated Na+ channels, L-type Ca2+ channels, the voltage-gated K+ channels and the inward-rectifier K+ channels. Moreover, Sorbs2 physically interacted with the RNAs and/or proteins of important cardiac ion channels and directly regulated their expression in vitro. Our results indicate that Sorbs2 plays a pivotal role in the regulation of cardiac channel physiology. Loss of Sorbs2 promotes cardiac ion channelopathies and life-threatening arrhythmias.
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129
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Pan J, Zhu M, Shen X, Wu S, Wei W, Li S. Dual-Responsive Bilayer Reactor Capable of Non-Tandem/Tandem Adjustable Catalytic Ability. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-021-02144-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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130
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Chen PW, Gasilina A, Yadav MP, Randazzo PA. Control of cell signaling by Arf GTPases and their regulators: Focus on links to cancer and other GTPase families. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119171. [PMID: 34774605 DOI: 10.1016/j.bbamcr.2021.119171] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/23/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022]
Abstract
The ADP-ribosylation factors (Arfs) comprise a family of regulatory GTP binding proteins. The Arfs regulate membrane trafficking and cytoskeleton remodeling, processes critical for eukaryotes and which have been the focus of most studies on Arfs. A more limited literature describes a role in signaling and in integrating several signaling pathways to bring about specific cell behaviors. Here, we will highlight work describing function of Arf1, Arf6 and several effectors and regulators of Arfs in signaling.
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Affiliation(s)
- Pei-Wen Chen
- Department of Biology, Williams College, Williamstown, MA, United States of America
| | - Anjelika Gasilina
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD, United States of America(1); Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, United States of America
| | - Mukesh P Yadav
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, United States of America
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, United States of America.
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131
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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132
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Lin Y, Wang H, Xu J, Huang Y, Gong W, Wang Q, Huang Z, Xie S, Lin J. High spatio-temporal resolution measurement of A 1 R and A 2A R interactions combined with Iem-spFRET and E-FRET methods. JOURNAL OF BIOPHOTONICS 2021; 14:e202100172. [PMID: 34328277 DOI: 10.1002/jbio.202100172] [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: 06/04/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
A1 R-A2A R heterodimers regulate striatal glutamatergic neurotransmission. However, few researches about kinetics have been reported. Here, we combined Iem-spFRET and E-FRET to investigate the kinetics of A1 R and A2A R interaction. Iem-spFRET obtains the energy transfer efficiency of the whole cell. E-FRET gets energy transfer efficiency with high spatial resolution, whereas, it was prone to biases because background was easily selected due to manual operation. To study the interaction with high spatio-temporal resolution, Iem-spFRET was used to correct the deviation of E-FRET. In this paper, A1 R and A2A R interaction was monitored, and the changes of FRET efficiency of the whole or/and partial cell membrane were described. The results showed that activation of A1 R or A2A R leads to rapid aggregation, inhibition of A1 R or A2A R leads to slow segregation, and the interaction is reversible. These results demonstrated that combination of Iem-spFRET and E-FRET could measure A1 R and A2A R interaction with high spatio-temporal resolution.
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Affiliation(s)
- Yating Lin
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Haoyu Wang
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Jianshu Xu
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Yiming Huang
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Wei Gong
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Qiwen Wang
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Zufang Huang
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Shusen Xie
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Juqiang Lin
- MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
- School of Opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, Fujian, China
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133
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Tang Z, Li X, Tong L, Yang H, Wu J, Zhang X, Song T, Huang S, Zhu F, Chen G, Ouyang G. A Biocatalytic Cascade in an Ultrastable Mesoporous Hydrogen-Bonded Organic Framework for Point-of-Care Biosensing. Angew Chem Int Ed Engl 2021; 60:23608-23613. [PMID: 34459532 DOI: 10.1002/anie.202110351] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/19/2021] [Indexed: 11/08/2022]
Abstract
Herein, we report the first example of using mesoporous hydrogen-bonded organic frameworks (MHOFs) as the protecting scaffold to organize a biocatalytic cascade. The confined microenvironment of MHOFs has robust and large transport channels, allowing the efficient transport of a wide range of biocatalytic substrates. This new MHOF-confined cascade system shows superior activity, extended scope of catalytic substrates, and ultrahigh stability that enables the operation of complex chemical transformations in a porous carrier. In addition, the advantages of MHOF-confined cascades system for point-of-care biosensing are also demonstrated. This study highlights the advantages of HOFs as scaffold for multiple enzyme assemblies, which has huge potential for mimicking complex cellular transformation networks in a controllable manner.
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Affiliation(s)
- Zhuopeng Tang
- Department of Radiology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510150, China
| | - Xinyi Li
- Department of Radiology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510150, China
| | - Linjing Tong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Huangsheng Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiayi Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiliu Zhang
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510120, China
| | - Ting Song
- Department of Radiology, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510150, China
| | - Siming Huang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
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134
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Zhang H, Zhao Y, Liu X, Liu Y, Wang X, Fu Y, Fu S, Zhang J. A novel upregulated LncRNA-AC026150.8 promotes chemo-resistance and predicts poor prognosis in acute myeloid leukemia. Cancer Med 2021; 10:8614-8629. [PMID: 34664783 PMCID: PMC8633226 DOI: 10.1002/cam4.4349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AML is a common hematological malignancy with poor prognosis, the pathogenesis is still unclear. lncRNA takes part in occurrence and development of AML. This research aims to explore new differentially expressed lncRNAs and their effects on AML. METHODS Database-based bioinformatics analysis was performed to screen differentially expressed lncRNA in AML, real-time PCR was used to analyze gene expression. Kaplan-Meier survival analysis was performed to determine prognostic effect of AC026150.8 in AML. The cell drug resistance experiment was performed to test effect of AC026150.8 on chemo-resistance of AML cells. Catrapid online software and RNA pull-down, mass spectrometry, western-blot were used to predict and verify the combination of AC026150.8 and RNA splicing factors. RESULTS AC026150.8 was upregulated in AML patients and related to poor prognosis. High leukocyte counts, FAB classification, MLL-AF9 expression and NPM1 mutations were associated with high AC026150.8 expression. Upregulated of AC026150.8 increased the drug resistance of AML cells. AC026150.8 could be combined with splicing factor PCBP1. CONCLUSIONS For the first time, our study found that the upregulated AC026150.8 in AML is related to poor prognosis, overexpression of AC026150.8 could increase drug resistance of AML cells, and confirmed its scaffolding effect in combination with splicing factors. It is necessary to further study AC026150.8 and its downstream target genes to clarify the mechanism of AC026150.8 in AML.
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Affiliation(s)
- Henan Zhang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Zhao
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuan Liu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yusi Liu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaohui Wang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu Fu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Fu
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jihong Zhang
- Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
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135
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Liu Y, Huang Y, Lu R, Xin F, Liu G. Synthetic biology applications of the yeast mating signal pathway. Trends Biotechnol 2021; 40:620-631. [PMID: 34666896 DOI: 10.1016/j.tibtech.2021.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Cell fusion is a fundamental biological process that is involved in the development of most eukaryotic organisms. During the fusion process in Saccharomyces cerevisiae, cells respond to pheromones to trigger the MAPK (mitogen-activated protein kinase) cascade to initiate mating, followed by polarization, cell-wall remodeling, membrane fusion, and karyogamy. We highlight the applications of the yeast mating signal pathway in promoter engineering for tuning the expression of output genes, as well as in metabolic engineering for decoupling growth and metabolism, biosensors for sensitive detection and signal amplification, genetic circuits for programmable biological functionalities, and artificial consortia for cell-cell communication. Strategies such as exploiting rational engineering of modular circuits and optimizing the reproductive pathway to precisely maneuver physiological events have implications for scientific research and industrial development.
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Affiliation(s)
- Ying Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Yuxin Huang
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Ran Lu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Fengxue Xin
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China
| | - Guannan Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Jiangsu Province, China; Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Jiangsu Province, China.
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136
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Worst EG, Finkler M, Schenkelberger M, Kurt Ö, Helms V, Noireaux V, Ott A. A Methylation-Directed, Synthetic Pap Switch Based on Self-Complementary Regulatory DNA Reconstituted in an All E. coli Cell-Free Expression System. ACS Synth Biol 2021; 10:2725-2739. [PMID: 34550672 DOI: 10.1021/acssynbio.1c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyelonephritis-associated pili (pap) enable migration of the uropathogenic Escherichia coli strain (UPEC) through the urinary tract. UPEC can switch between a stable 'ON phase' where the corresponding pap genes are expressed and a stable 'OFF phase' where their transcription is repressed. Hereditary DNA methylation of either one of two GATC motives within the regulatory region stabilizes the respective phase over many generations. The underlying molecular mechanism is only partly understood. Previous investigations suggest that in vivo phase-variation stability results from cooperative action of the transcriptional regulators Lrp and PapI. Here, we use an E. coli cell-free expression system to study molecular functions of the pap regulatory region based on a specially designed, synthetic construct flanked by two reporter genes encoding fluorescent proteins for simple readout. On the basis of our observations we suggest that besides Lrp, the conformation of the self-complementary regulatory DNA plays a strong role in the regulation of phase-variation. Our work not only contributes to better understand the phase variation mechanism, but it represents a successful start for mimicking stable, hereditary, and strong expression control based on methylation. The conformation of the regulatory DNA corresponds to a Holliday junction. Gene expression must be expected to respond if opposite arms of the junction are drawn outward.
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Affiliation(s)
- Emanuel G. Worst
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Finkler
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Schenkelberger
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Ömer Kurt
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Universität des Saarlandes, Center for Bioinformatics, Saarbrücken, 66041, Germany
| | - Vincent Noireaux
- University of Minnesota, School of Physics and Astronomy, Minneapolis, Minnesota 55455, United States
| | - Albrecht Ott
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
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137
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Tang Z, Li X, Tong L, Yang H, Wu J, Zhang X, Song T, Huang S, Zhu F, Chen G, Ouyang G. A Biocatalytic Cascade in an Ultrastable Mesoporous Hydrogen‐Bonded Organic Framework for Point‐of‐Care Biosensing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zhuopeng Tang
- Department of Radiology the Third Affiliated Hospital of Guangzhou Medical University Guangzhou Medical University Guangzhou 510150 China
| | - Xinyi Li
- Department of Radiology the Third Affiliated Hospital of Guangzhou Medical University Guangzhou Medical University Guangzhou 510150 China
| | - Linjing Tong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Huangsheng Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Jiayi Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Xiliu Zhang
- Guanghua School of Stomatology Hospital of Stomatology Guangdong Provincial Key Laboratory of Stomatology Sun Yat-sen University Guangzhou 510120 China
| | - Ting Song
- Department of Radiology the Third Affiliated Hospital of Guangzhou Medical University Guangzhou Medical University Guangzhou 510150 China
| | - Siming Huang
- School of Pharmaceutical Sciences Guangzhou Medical University Guangzhou 511436 China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-sen University Guangzhou 510275 China
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138
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Zhang JF, Mehta S, Zhang J. Signaling Microdomains in the Spotlight: Visualizing Compartmentalized Signaling Using Genetically Encoded Fluorescent Biosensors. Annu Rev Pharmacol Toxicol 2021; 61:587-608. [PMID: 33411579 DOI: 10.1146/annurev-pharmtox-010617-053137] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How cells muster a network of interlinking signaling pathways to faithfully convert diverse external cues to specific functional outcomes remains a central question in biology. Through their ability to convert dynamic biochemical activities to rapid and precise optical readouts, genetically encoded fluorescent biosensors have become instrumental in unraveling the molecular logic controlling the specificity of intracellular signaling. In this review, we discuss how the use of genetically encoded fluorescent biosensors to visualize dynamic signaling events within their native cellular context is elucidating the different strategies employed by cells to organize signaling activities into discrete compartments, or signaling microdomains, to ensure functional specificity.
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Affiliation(s)
- Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA;
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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139
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Guo Z, Kang S, Wu Q, Wang S, Crickmore N, Zhou X, Bravo A, Soberón M, Zhang Y. The regulation landscape of MAPK signaling cascade for thwarting Bacillus thuringiensis infection in an insect host. PLoS Pathog 2021; 17:e1009917. [PMID: 34495986 PMCID: PMC8452011 DOI: 10.1371/journal.ppat.1009917] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/20/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
Host-pathogen interactions are central components of ecological networks where the MAPK signaling pathways act as central hubs of these complex interactions. We have previously shown that an insect hormone modulated MAPK signaling cascade participates as a general switch to trans-regulate differential expression of diverse midgut genes in the diamondback moth, Plutella xylostella (L.) to cope with the insecticidal action of Cry1Ac toxin, produced by the entomopathogenic bacterium Bacillus thuringiensis (Bt). The relationship between topology and functions of this four-tiered phosphorylation signaling cascade, however, is an uncharted territory. Here, we carried out a genome-wide characterization of all the MAPK orthologs in P. xylostella to define their phylogenetic relationships and to confirm their evolutionary conserved modules. Results from quantitative phosphoproteomic analyses, combined with functional validations studies using specific inhibitors and dsRNAs lead us to establish a MAPK "road map", where p38 and ERK MAPK signaling pathways, in large part, mount a resistance response against Bt toxins through regulating the differential expression of multiple Cry toxin receptors and their non-receptor paralogs in P. xylostella midgut. These data not only advance our understanding of host-pathogen interactions in agricultural pests, but also inform the future development of biopesticides that could suppress Cry resistance phenotypes.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZG); (YZ)
| | - Shi Kang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Alejandra Bravo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Mario Soberón
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZG); (YZ)
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140
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Arosa FA, Esgalhado AJ, Reste-Ferreira D, Cardoso EM. Open MHC Class I Conformers: A Look through the Looking Glass. Int J Mol Sci 2021; 22:ijms22189738. [PMID: 34575902 PMCID: PMC8470049 DOI: 10.3390/ijms22189738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Studies carried out during the last few decades have consistently shown that cell surface MHC class I (MHC-I) molecules are endowed with functions unrelated with antigen presentation. These include cis–trans-interactions with inhibitory and activating KIR and LILR, and cis-interactions with receptors for hormones, growth factors, cytokines, and neurotransmitters. The mounting body of evidence indicates that these non-immunological MHC-I functions impact clinical and biomedical settings, including autoimmune responses, tumor escape, transplantation, and neuronal development. Notably, most of these functions appear to rely on the presence in hematopoietic and non-hematopoietic cells of heavy chains not associated with β2m and the peptide at the plasma membrane; these are known as open MHC-I conformers. Nowadays, open conformers are viewed as functional cis-trans structures capable of establishing physical associations with themselves, with other surface receptors, and being shed into the extracellular milieu. We review past and recent developments, strengthening the view that open conformers are multifunctional structures capable of fine-tuning cell signaling, growth, differentiation, and cell communication.
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Affiliation(s)
- Fernando A Arosa
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
- Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - André J Esgalhado
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Débora Reste-Ferreira
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Elsa M Cardoso
- Health Sciences Research Center (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal
- Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
- Health School, Guarda Polytechnic Institute, 6300-749 Guarda, Portugal
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141
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Ghomlaghi M, Yang G, Shin SY, James DE, Nguyen LK. Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1. PLoS Comput Biol 2021; 17:e1008513. [PMID: 34529665 PMCID: PMC8478217 DOI: 10.1371/journal.pcbi.1008513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 09/28/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022] Open
Abstract
The PI3K/MTOR signalling network regulates a broad array of critical cellular processes, including cell growth, metabolism and autophagy. The mechanistic target of rapamycin (MTOR) kinase functions as a core catalytic subunit in two physically and functionally distinct complexes mTORC1 and mTORC2, which also share other common components including MLST8 (also known as GβL) and DEPTOR. Despite intensive research, how mTORC1 and 2 assembly and activity are coordinated, and how they are functionally linked remain to be fully characterized. This is due in part to the complex network wiring, featuring multiple feedback loops and intricate post-translational modifications. Here, we integrate predictive network modelling, in vitro experiments and -omics data analysis to elucidate the emergent dynamic behaviour of the PI3K/MTOR network. We construct new mechanistic models that encapsulate critical mechanistic details, including mTORC1/2 coordination by MLST8 (de)ubiquitination and the Akt-to-mTORC2 positive feedback loop. Model simulations validated by experimental studies revealed a previously unknown biphasic, threshold-gated dependence of mTORC1 activity on the key mTORC2 subunit SIN1, which is robust against cell-to-cell variation in protein expression. In addition, our integrative analysis demonstrates that ubiquitination of MLST8, which is reversed by OTUD7B, is regulated by IRS1/2. Our results further support the essential role of MLST8 in enabling both mTORC1 and 2's activity and suggest MLST8 as a viable therapeutic target in breast cancer. Overall, our study reports a new mechanistic model of PI3K/MTOR signalling incorporating MLST8-mediated mTORC1/2 formation and unveils a novel regulatory linkage between mTORC1 and mTORC2.
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Affiliation(s)
- Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
- Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Guang Yang
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Sung-Young Shin
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
- Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David E. James
- Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Lan K. Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
- Biomedicine Discovery Institute, Monash University, Melbourne, Australia
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142
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p27 Kip1, an Intrinsically Unstructured Protein with Scaffold Properties. Cells 2021; 10:cells10092254. [PMID: 34571903 PMCID: PMC8465030 DOI: 10.3390/cells10092254] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/27/2022] Open
Abstract
The Cyclin-dependent kinase (CDK) regulator p27Kip1 is a gatekeeper of G1/S transition. It also regulates G2/M progression and cytokinesis completion, via CDK-dependent or -independent mechanisms. Recently, other important p27Kip1 functions have been described, including the regulation of cell motility and migration, the control of cell differentiation program and the activation of apoptosis/autophagy. Several factors modulate p27Kip1 activities, including its level, cellular localization and post-translational modifications. As a matter of fact, the protein is phosphorylated, ubiquitinated, SUMOylated, O-linked N-acetylglicosylated and acetylated on different residues. p27Kip1 belongs to the family of the intrinsically unstructured proteins and thus it is endowed with a large flexibility and numerous interactors, only partially identified. In this review, we look at p27Kip1 properties and ascribe part of its heterogeneous functions to the ability to act as an anchor or scaffold capable to participate in the construction of different platforms for modulating cell response to extracellular signals and allowing adaptation to environmental changes.
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143
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Zhang YQ, Feng TT, Cao YF, Zhang XY, Wang T, Huanca Nina MR, Wang LC, Yu HL, Xu JH, Ge J, Bai YP. Confining Enzyme Clusters in Bacteriophage P22 Enhances Cofactor Recycling and Stereoselectivity for Chiral Alcohol Synthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan-Qing Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao-Tao Feng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Yu-Fei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Li-Cheng Wang
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
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144
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Garabedian MV, Wang W, Dabdoub JB, Tong M, Caldwell RM, Benman W, Schuster BS, Deiters A, Good MC. Designer membraneless organelles sequester native factors for control of cell behavior. Nat Chem Biol 2021; 17:998-1007. [PMID: 34341589 PMCID: PMC8387445 DOI: 10.1038/s41589-021-00840-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/24/2021] [Indexed: 02/08/2023]
Abstract
Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to ninety percent of a targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division, and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.
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Affiliation(s)
- Mikael V Garabedian
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Wentao Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorge B Dabdoub
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Tong
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Reese M Caldwell
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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145
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Bennett ZT, Li S, Sumer BD, Gao J. Polyvalent design in the cGAS-STING pathway. Semin Immunol 2021; 56:101580. [PMID: 34920941 PMCID: PMC8792294 DOI: 10.1016/j.smim.2021.101580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023]
Abstract
Polyvalent interactions mediate the formation of higher-order macromolecular assemblies to improve the sensitivity, specificity, and temporal response of biological signals. In host defense, innate immune pathways recognize danger signals to alert host of insult or foreign invasion, while limiting aberrant activation from auto-immunity and cellular senescence. Of recent attention are the unique higher-order assemblies in the cGAS-STING pathway. Natural stimulation of cGAS enzymes by dsDNA induces phase separation and enzymatic activation for switchlike production of cGAMP. Subsequent binding of cGAMP to STING induces oligomerization of STING molecules, offering a scaffold for kinase assembly and signaling transduction. Additionally, the discovery of PC7A, a synthetic polymer which activates STING through a non-canonical biomolecular condensation, illustrates the engineering design of agonists by polyvalency principles. Herein, we discuss a mechanistic and functional comparison of natural and synthetic agonists to advance our understanding in STING signaling and highlight the principles of polyvalency in innate immune activation. The combination of exogenous cGAMP along with synthetic PC7A stimulation of STING offers a synergistic strategy in spatiotemporal orchestration of the immune milieu for a safe and effective immunotherapy against cancer.
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Affiliation(s)
- Zachary T Bennett
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Suxin Li
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Baran D Sumer
- Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jinming Gao
- Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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146
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Merő B, Koprivanacz K, Cserkaszky A, Radnai L, Vas V, Kudlik G, Gógl G, Sok P, Póti ÁL, Szeder B, Nyitray L, Reményi A, Geiszt M, Buday L. Characterization of the Intramolecular Interactions and Regulatory Mechanisms of the Scaffold Protein Tks4. Int J Mol Sci 2021; 22:ijms22158103. [PMID: 34360869 PMCID: PMC8348221 DOI: 10.3390/ijms22158103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
The scaffold protein Tks4 is a member of the p47phox-related organizer superfamily. It plays a key role in cell motility by being essential for the formation of podosomes and invadopodia. In addition, Tks4 is involved in the epidermal growth factor (EGF) signaling pathway, in which EGF induces the translocation of Tks4 from the cytoplasm to the plasma membrane. The evolutionarily-related protein p47phox and Tks4 share many similarities in their N-terminal region: a phosphoinositide-binding PX domain is followed by two SH3 domains (so called “tandem SH3”) and a proline-rich region (PRR). In p47phox, the PRR is followed by a relatively short, disordered C-terminal tail region containing multiple phosphorylation sites. These play a key role in the regulation of the protein. In Tks4, the PRR is followed by a third and a fourth SH3 domain connected by a long (~420 residues) unstructured region. In p47phox, the tandem SH3 domain binds the PRR while the first SH3 domain interacts with the PX domain, thereby preventing its binding to the membrane. Based on the conserved structural features of p47phox and Tks4 and the fact that an intramolecular interaction between the third SH3 and the PX domains of Tks4 has already been reported, we hypothesized that Tks4 is similarly regulated by autoinhibition. In this study, we showed, via fluorescence-based titrations, MST, ITC, and SAXS measurements, that the tandem SH3 domain of Tks4 binds the PRR and that the PX domain interacts with the third SH3 domain. We also investigated a phosphomimicking Thr-to-Glu point mutation in the PRR as a possible regulator of intramolecular interactions. Phosphatidylinositol-3-phosphate (PtdIns(3)P) was identified as the main binding partner of the PX domain via lipid-binding assays. In truncated Tks4 fragments, the presence of the tandem SH3, together with the PRR, reduced PtdIns(3)P binding, while the presence of the third SH3 domain led to complete inhibition.
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Affiliation(s)
- Balázs Merő
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Kitti Koprivanacz
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Anna Cserkaszky
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - László Radnai
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Virag Vas
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Gyöngyi Kudlik
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - Gergő Gógl
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
| | - Péter Sok
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Ádám L. Póti
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Bálint Szeder
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (B.M.); (K.K.); (A.C.); (L.R.); (V.V.); (G.K.); (B.S.)
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
| | - Attila Reményi
- Research Centre for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary; (P.S.); (Á.L.P.); (A.R.)
| | - Miklós Geiszt
- Department of Physiology, Semmelweis University, 1094 Budapest, Hungary;
| | - László Buday
- Department of Biochemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (G.G.); (L.N.)
- Department of Molecular Biology, Semmelweis University Medical School, 1094 Budapest, Hungary
- Correspondence:
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147
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Zieger HL, Choquet D. Nanoscale synapse organization and dysfunction in neurodevelopmental disorders. Neurobiol Dis 2021; 158:105453. [PMID: 34314857 DOI: 10.1016/j.nbd.2021.105453] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Neurodevelopmental disorders such as those linked to intellectual disabilities or autism spectrum disorder are thought to originate in part from genetic defects in synaptic proteins. Single gene mutations linked to synapse dysfunction can broadly be separated in three categories: disorders of transcriptional regulation, disorders of synaptic signaling and disorders of synaptic scaffolding and structures. The recent developments in super-resolution imaging technologies and their application to synapses have unraveled a complex nanoscale organization of synaptic components. On the one hand, part of receptors, adhesion proteins, ion channels, scaffold elements and the pre-synaptic release machinery are partitioned in subsynaptic nanodomains, and the respective organization of these nanodomains has tremendous impact on synaptic function. For example, pre-synaptic neurotransmitter release sites are partly aligned with nanometer precision to postsynaptic receptor clusters. On the other hand, a large fraction of synaptic components is extremely dynamic and constantly exchanges between synaptic domains and extrasynaptic or intracellular compartments. It is largely the combination of the exquisitely precise nanoscale synaptic organization of synaptic components and their high dynamic that allows the rapid and profound regulation of synaptic function during synaptic plasticity processes that underlie adaptability of brain function, learning and memory. It is very tempting to speculate that genetic defects that lead to neurodevelopmental disorders and target synaptic scaffolds and structures mediate their deleterious impact on brain function through perturbing synapse nanoscale dynamic organization. We discuss here how applying super-resolution imaging methods in models of neurodevelopmental disorders could help in addressing this question.
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Affiliation(s)
- Hanna L Zieger
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Daniel Choquet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France; Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000 Bordeaux, France.
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148
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Mishra D, Bepler T, Teague B, Berger B, Broach J, Weiss R. An engineered protein-phosphorylation toggle network with implications for endogenous network discovery. Science 2021; 373:eaav0780. [PMID: 34210851 PMCID: PMC11203391 DOI: 10.1126/science.aav0780] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/29/2021] [Indexed: 12/23/2022]
Abstract
Synthetic biological networks comprising fast, reversible reactions could enable engineering of new cellular behaviors that are not possible with slower regulation. Here, we created a bistable toggle switch in Saccharomyces cerevisiae using a cross-repression topology comprising 11 protein-protein phosphorylation elements. The toggle is ultrasensitive, can be induced to switch states in seconds, and exhibits long-term bistability. Motivated by our toggle's architecture and size, we developed a computational framework to search endogenous protein pathways for other large and similar bistable networks. Our framework helped us to identify and experimentally verify five formerly unreported endogenous networks that exhibit bistability. Building synthetic protein-protein networks will enable bioengineers to design fast sensing and processing systems, allow sophisticated regulation of cellular processes, and aid discovery of endogenous networks with particular functions.
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Affiliation(s)
- Deepak Mishra
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan Bepler
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Brian Teague
- Department of Biology, University of Wisconsin, Stout, WI, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jim Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
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149
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Bao F, Hao P, An S, Yang Y, Liu Y, Hao Q, Ejaz M, Guo XX, Xu TR. Akt scaffold proteins: the key to controlling specificity of Akt signaling. Am J Physiol Cell Physiol 2021; 321:C429-C442. [PMID: 34161152 DOI: 10.1152/ajpcell.00146.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The phosphatidylinositol 3-kinase-Akt signaling pathway plays an essential role in regulating cell proliferation and apoptosis. Akt kinase is at the center of this signaling pathway and interacts with a variety of proteins. Akt is overexpressed in almost 80% of tumors. However, inhibiting Akt has serious clinical side effects so is not a suitable treatment for cancer. During recent years, Akt scaffold proteins have received increasing attention for their ability to regulate Akt signaling and have emerged as potential targets for cancer therapy. In this paper, we categorize Akt kinase scaffold proteins into four groups based on their cellular location: membrane-bound activator and inhibitor, cytoplasm, and endosome. We describe how these scaffolds interact with Akt kinase, how they affect Akt activity, and how they regulate the specificity of Akt signaling. We also discuss the clinical application of Akt scaffold proteins as targets for cancer therapy.
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Affiliation(s)
- Fan Bao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China.,Center of Stomatology, The First People's Hospital of Yunnan Province, Kunming, China.,The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Peiqi Hao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Su An
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Qian Hao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Mubashir Ejaz
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiao-Xi Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
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150
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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