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Ancient Origins of Cytoskeletal Crosstalk: Spectraplakin-like Proteins Precede the Emergence of Cortical Microtubule Stabilization Complexes as Crosslinkers. Int J Mol Sci 2022; 23:ijms23105594. [PMID: 35628404 PMCID: PMC9145010 DOI: 10.3390/ijms23105594] [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: 03/28/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Adhesion between cells and the extracellular matrix (ECM) is one of the prerequisites for multicellularity, motility, and tissue specialization. Focal adhesions (FAs) are defined as protein complexes that mediate signals from the ECM to major components of the cytoskeleton (microtubules, actin, and intermediate filaments), and their mutual communication determines a variety of cellular processes. In this study, human cytoskeletal crosstalk proteins were identified by comparing datasets with experimentally determined cytoskeletal proteins. The spectraplakin dystonin was the only protein found in all datasets. Other proteins (FAK, RAC1, septin 9, MISP, and ezrin) were detected at the intersections of FAs, microtubules, and actin cytoskeleton. Homology searches for human crosstalk proteins as queries were performed against a predefined dataset of proteomes. This analysis highlighted the importance of FA communication with the actin and microtubule cytoskeleton, as these crosstalk proteins exhibit the highest degree of evolutionary conservation. Finally, phylogenetic analyses elucidated the early evolutionary history of spectraplakins and cortical microtubule stabilization complexes (CMSCs) as model representatives of the human cytoskeletal crosstalk. While spectraplakins probably arose at the onset of opisthokont evolution, the crosstalk between FAs and microtubules is associated with the emergence of metazoans. The multiprotein complexes contributing to cytoskeletal crosstalk in animals gradually gained in complexity from the onset of metazoan evolution.
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Martin-Garcia JM, Botha S, Hu H, Jernigan R, Castellví A, Lisova S, Gil F, Calisto B, Crespo I, Roy-Chowdhury S, Grieco A, Ketawala G, Weierstall U, Spence J, Fromme P, Zatsepin N, Boer DR, Carpena X. Serial macromolecular crystallography at ALBA Synchrotron Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:896-907. [PMID: 35511023 PMCID: PMC9070724 DOI: 10.1107/s1600577522002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The increase in successful adaptations of serial crystallography at synchrotron radiation sources continues. To date, the number of serial synchrotron crystallography (SSX) experiments has grown exponentially, with over 40 experiments reported so far. In this work, we report the first SSX experiments with viscous jets conducted at ALBA beamline BL13-XALOC. Small crystals (15-30 µm) of five soluble proteins (lysozyme, proteinase K, phycocyanin, insulin and α-spectrin-SH3 domain) were suspended in lipidic cubic phase (LCP) and delivered to the X-ray beam with a high-viscosity injector developed at Arizona State University. Complete data sets were collected from all proteins and their high-resolution structures determined. The high quality of the diffraction data collected from all five samples, and the lack of specific radiation damage in the structures obtained in this study, confirm that the current capabilities at the beamline enables atomic resolution determination of protein structures from microcrystals as small as 15 µm using viscous jets at room temperature. Thus, BL13-XALOC can provide a feasible alternative to X-ray free-electron lasers when determining snapshots of macromolecular structures.
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Affiliation(s)
- Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Rebecca Jernigan
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Albert Castellví
- Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Fernando Gil
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Isidro Crespo
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
| | - Shatabdi Roy-Chowdhury
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Gihan Ketawala
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - John Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Department of Physics, Arizona State University, Tempe, AZ, USA
- ARC Centre of Excellence in Advance Molecular Physics, La Trobe Institute for Molecular ScienceImaging, Department of Chemistry and Physics, La Trobe University, Melbourne, Australia
| | | | - Xavi Carpena
- ALBA Synchrotron, Cerdanyola del Vallès, Barcelona, Spain
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53
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Kaewjanthong P, Sooksai S, Sasano H, Hutvagner G, Bajan S, McGowan E, Boonyaratanakornkit V. Cell-penetrating peptides containing the progesterone receptor polyproline domain inhibits EGF signaling and cell proliferation in lung cancer cells. PLoS One 2022; 17:e0264717. [PMID: 35235599 PMCID: PMC8890653 DOI: 10.1371/journal.pone.0264717] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/15/2022] [Indexed: 01/10/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) accounts for the majority (80–85%) of all lung cancers. All current available treatments have limited efficacy. The epidermal growth factor receptor (EGFR) plays a critical role in the development and progression of NSCLC, with high EGFR expression associated with increased cell proliferation and poor prognosis. Thus, interfering with EGFR signaling has been shown to effectively reduce cell proliferation and help in the treatment of NSCLC. We previously demonstrated that the progesterone receptor (PR) contains a polyproline domain (PPD) that directly interacts with Src homology 3 (SH3) domain-containing molecules and expression of PR-PPD peptides inhibits NSCLC cell proliferation. In this study, we investigated whether the introduction of PR-PPD by cell-penetrating peptides (CPPs) could inhibit EGF-induced cell proliferation in NSCLC cells. PR-PPD was attached to a cancer-specific CPP, Buforin2 (BR2), to help deliver the PR-PPD into NSCLC cells. Interestingly, addition of BR2-2xPPD peptides containing two PR-PPD repeats was more effective in inhibiting NSCLC proliferation and significantly reduced EGF-induced phosphorylation of Erk1/2. BR2-2xPPD treatment induced cell cycle arrest by inhibiting the expression of cyclin D1 and CDK2 genes in EGFR-wild type A549 cells. Furthermore, the combination treatment of EGFR-tyrosine kinase inhibitors (TKIs), including Gefitinib or Erlotinib, with BR2-2xPPD peptides further suppressed the growth of NSCLC PC9 cells harboring EGFR mutations as compared to EGFR-TKIs treatment alone. Importantly, BR2-2xPPD peptides mediated growth inhibition in acquired Gefitinib- and Erlotinib- resistant lung adenocarcinoma cells. Our data suggests that PR-PPD is the minimal protein domain sufficient to inhibit NSCLC cell growth and has the potential to be developed as a novel NSCLC therapeutic agent.
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Affiliation(s)
- Panthita Kaewjanthong
- Department of Clinical Chemistry and Graduate Program in Clinical Biochemistry and Molecular Medicine, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Sarintip Sooksai
- The Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Hironobu Sasano
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Australia
| | - Sarah Bajan
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Australia
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Australia
- Sunshine Coast Health Institute, Birtinya, Australia
| | - Eileen McGowan
- School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Viroj Boonyaratanakornkit
- Department of Clinical Chemistry and Graduate Program in Clinical Biochemistry and Molecular Medicine, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
- Age-related Inflammation and Degeneration Research Unit, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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54
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Hwang E, Kim H, Truong AD, Kim SJ, Song KD. Suppression of the Toll-like receptors 3 mediated pro-inflammatory
gene expressions by progenitor cell differentiation and proliferation factor in
chicken DF-1 cells. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:123-134. [PMID: 35174347 PMCID: PMC8819319 DOI: 10.5187/jast.2021.e130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Eunmi Hwang
- Division of Cosmetics and Biotechnology,
College of Life and Health Sciences, Hoseo University, Asan
31499, Korea
| | - Hyungkuen Kim
- Division of Cosmetics and Biotechnology,
College of Life and Health Sciences, Hoseo University, Asan
31499, Korea
| | - Anh Duc Truong
- Department of Agricultural Convergence
Technology, Jeonbuk National University, Jeonju 54896,
Korea
| | - Sung-Jo Kim
- Division of Cosmetics and Biotechnology,
College of Life and Health Sciences, Hoseo University, Asan
31499, Korea
- Corresponding author: Sung-Jo Kim, Division of
Cosmetics and Biotechnology, College of Life and Health Sciences, Hoseo
University, Asan 31499, Korea., Tel: +82-41-540-5571, E-mail:
| | - Ki-Duk Song
- Department of Agricultural Convergence
Technology, Jeonbuk National University, Jeonju 54896,
Korea
- Corresponding author: Ki-Duk Song, Department of
Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896,
Korea., Tel: +82-63-219-5523, E-mail:
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Landim-Vieira M, Childers MC, Wacker AL, Garcia MR, He H, Singh R, Brundage EA, Johnston JR, Whitson BA, Chase PB, Janssen PML, Regnier M, Biesiadecki BJ, Pinto JR, Parvatiyar MS. Post-translational modification patterns on β-myosin heavy chain are altered in ischemic and nonischemic human hearts. eLife 2022; 11:74919. [PMID: 35502901 PMCID: PMC9122498 DOI: 10.7554/elife.74919] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphorylation and acetylation of sarcomeric proteins are important for fine-tuning myocardial contractility. Here, we used bottom-up proteomics and label-free quantification to identify novel post-translational modifications (PTMs) on β-myosin heavy chain (β-MHC) in normal and failing human heart tissues. We report six acetylated lysines and two phosphorylated residues: K34-Ac, K58-Ac, S210-P, K213-Ac, T215-P, K429-Ac, K951-Ac, and K1195-Ac. K951-Ac was significantly reduced in both ischemic and nonischemic failing hearts compared to nondiseased hearts. Molecular dynamics (MD) simulations show that K951-Ac may impact stability of thick filament tail interactions and ultimately myosin head positioning. K58-Ac altered the solvent-exposed SH3 domain surface - known for protein-protein interactions - but did not appreciably change motor domain conformation or dynamics under conditions studied. Together, K213-Ac/T215-P altered loop 1's structure and dynamics - known to regulate ADP-release, ATPase activity, and sliding velocity. Our study suggests that β-MHC acetylation levels may be influenced more by the PTM location than the type of heart disease since less protected acetylation sites are reduced in both heart failure groups. Additionally, these PTMs have potential to modulate interactions between β-MHC and other regulatory sarcomeric proteins, ADP-release rate of myosin, flexibility of the S2 region, and cardiac myofilament contractility in normal and failing hearts.
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Affiliation(s)
- Maicon Landim-Vieira
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Matthew C Childers
- Department of Bioengineering, College of Medicine, University of WashingtonSeattleUnited States
| | - Amanda L Wacker
- Department of Nutrition and Integrative Physiology, The Florida State UniversityTallahasseeUnited States
| | - Michelle Rodriquez Garcia
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Huan He
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States,Translational Science Laboratory, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Rakesh Singh
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States,Translational Science Laboratory, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Elizabeth A Brundage
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Jamie R Johnston
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Bryan A Whitson
- Department of Surgery, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - P Bryant Chase
- Department of Biological Science, The Florida State UniversityTallahasseeUnited States
| | - Paul ML Janssen
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Michael Regnier
- Department of Bioengineering, College of Medicine, University of WashingtonSeattleUnited States
| | - Brandon J Biesiadecki
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - J Renato Pinto
- Department of Biomedical Sciences, College of Medicine, The Florida State UniversityTallahasseeUnited States
| | - Michelle S Parvatiyar
- Department of Nutrition and Integrative Physiology, The Florida State UniversityTallahasseeUnited States
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56
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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: 3] [Impact Index Per Article: 1.0] [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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57
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Marcos-Torres FJ, Maurer D, Juniar L, Griese JJ. The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout. Nucleic Acids Res 2021; 49:10120-10135. [PMID: 34417623 PMCID: PMC8464063 DOI: 10.1093/nar/gkab711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 01/11/2023] Open
Abstract
The iron-dependent regulator IdeR is the main transcriptional regulator controlling iron homeostasis genes in Actinobacteria, including species from the Corynebacterium, Mycobacterium and Streptomyces genera, as well as the erythromycin-producing bacterium Saccharopolyspora erythraea. Despite being a well-studied transcription factor since the identification of the Diphtheria toxin repressor DtxR three decades ago, the details of how IdeR proteins recognize their highly conserved 19-bp DNA target remain to be elucidated. IdeR makes few direct contacts with DNA bases in its target sequence, and we show here that these contacts are not required for target recognition. The results of our structural and mutational studies support a model wherein IdeR mainly uses an indirect readout mechanism, identifying its targets via the sequence-dependent DNA backbone structure rather than through specific contacts with the DNA bases. Furthermore, we show that IdeR efficiently recognizes a shorter palindromic sequence corresponding to a half binding site as compared to the full 19-bp target previously reported, expanding the number of potential target genes controlled by IdeR proteins.
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Affiliation(s)
| | - Dirk Maurer
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Linda Juniar
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
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58
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Mompeán M, Oroz J, Laurents DV. Do polyproline II helix associations modulate biomolecular condensates? FEBS Open Bio 2021; 11:2390-2399. [PMID: 33934561 PMCID: PMC8409303 DOI: 10.1002/2211-5463.13163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/29/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Biomolecular condensates are microdroplets that form inside cells and serve to selectively concentrate proteins, RNAs and other molecules for a variety of physiological functions, but can contribute to cancer, neurodegenerative diseases and viral infections. The formation of these condensates is driven by weak, transient interactions between molecules. These weak associations can operate at the level of whole protein domains, elements of secondary structure or even moieties composed of just a few atoms. Different types of condensates do not generally combine to form larger microdroplets, suggesting that each uses a distinct class of attractive interactions. Here, we address whether polyproline II (PPII) helices mediate condensate formation. By combining with PPII-binding elements such as GYF, WW, profilin, SH3 or OCRE domains, PPII helices help form lipid rafts, nuclear speckles, P-body-like neuronal granules, enhancer complexes and other condensates. The number of PPII helical tracts or tandem PPII-binding domains can strongly influence condensate stability. Many PPII helices have a low content of proline residues, which hinders their identification. Recently, we characterized the NMR spectral properties of a Gly-rich, Pro-poor protein composed of six PPII helices. Based on those results, we predicted that many Gly-rich segments may form PPII helices and interact with PPII-binding domains. This prediction is being tested and could join the palette of verified interactions contributing to biomolecular condensate formation.
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Affiliation(s)
- Miguel Mompeán
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Javier Oroz
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
| | - Douglas V. Laurents
- Departamento de Química Física BiológicaInstituto de Química Física RocasolanoCSICMadridEspaña
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59
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Bianco PR. The mechanism of action of the SSB interactome reveals it is the first OB-fold family of genome guardians in prokaryotes. Protein Sci 2021; 30:1757-1775. [PMID: 34089559 PMCID: PMC8376408 DOI: 10.1002/pro.4140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/28/2022]
Abstract
The single-stranded DNA binding protein (SSB) is essential to all aspects of DNA metabolism in bacteria. This protein performs two distinct, but closely intertwined and indispensable functions in the cell. SSB binds to single-stranded DNA (ssDNA) and at least 20 partner proteins resulting in their regulation. These partners comprise a family of genome guardians known as the SSB interactome. Essential to interactome regulation is the linker/OB-fold network of interactions. This network of interactions forms when one or more PXXP motifs in the linker of SSB bind to an OB-fold in a partner, with interactome members involved in competitive binding between the linker and ssDNA to their OB-fold. Consequently, when linker-binding occurs to an OB-fold in an interactome partner, proteins are loaded onto the DNA. When linker/OB-fold interactions occur between SSB tetramers, cooperative ssDNA-binding results, producing a multi-tetrameric complex that rapidly protects the ssDNA. Within this SSB-ssDNA complex, there is an extensive and dynamic network of linker/OB-fold interactions that involves multiple tetramers bound contiguously along the ssDNA lattice. The dynamic behavior of these tetramers which includes binding mode changes, sliding as well as DNA wrapping/unwrapping events, are likely coupled to the formation and disruption of linker/OB-fold interactions. This behavior is essential to facilitating downstream DNA processing events. As OB-folds are critical to the essence of the linker/OB-fold network of interactions, and they are found in multiple interactome partners, the SSB interactome is classified as the first family of prokaryotic, oligosaccharide/oligonucleotide binding fold (OB-fold) genome guardians.
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MESH Headings
- Amino Acid Motifs
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding, Competitive
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Gene Regulatory Networks
- Genome, Bacterial
- Klebsiella pneumoniae/chemistry
- Klebsiella pneumoniae/genetics
- Klebsiella pneumoniae/metabolism
- Models, Molecular
- Oligonucleotides/chemistry
- Oligonucleotides/metabolism
- Oligosaccharides/chemistry
- Oligosaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Interaction Mapping
- Protein Multimerization
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Affiliation(s)
- Piero R. Bianco
- Department of Pharmaceutical Sciences, College of PharmacyUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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60
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Vazquez DS, Schilbert HM, Dodero VI. Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis. Int J Mol Sci 2021; 22:9278. [PMID: 34502187 PMCID: PMC8430993 DOI: 10.3390/ijms22179278] [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: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Gluten-related disorders (GRDs) are a group of diseases that involve the activation of the immune system triggered by the ingestion of gluten, with a worldwide prevalence of 5%. Among them, Celiac disease (CeD) is a T-cell-mediated autoimmune disease causing a plethora of symptoms from diarrhea and malabsorption to lymphoma. Even though GRDs have been intensively studied, the environmental triggers promoting the diverse reactions to gluten proteins in susceptible individuals remain elusive. It has been proposed that pathogens could act as disease-causing environmental triggers of CeD by molecular mimicry mechanisms. Additionally, it could also be possible that unrecognized molecular, structural, and physical parallels between gluten and pathogens have a relevant role. Herein, we report sequence, structural and physical similarities of the two most relevant gluten peptides, the 33-mer and p31-43 gliadin peptides, with bacterial pathogens using bioinformatics going beyond the molecular mimicry hypothesis. First, a stringent BLASTp search using the two gliadin peptides identified high sequence similarity regions within pathogen-derived proteins, e.g., extracellular proteins from Streptococcus pneumoniae and Granulicatella sp. Second, molecular dynamics calculations of an updated α-2-gliadin model revealed close spatial localization and solvent-exposure of the 33-mer and p31-43 peptide, which was compared with the pathogen-related proteins by homology models and localization predictors. We found putative functions of the identified pathogen-derived sequence by identifying T-cell epitopes and SH3/WW-binding domains. Finally, shape and size parallels between the pathogens and the superstructures of gliadin peptides gave rise to novel hypotheses about activation of innate immunity and dysbiosis. Based on our structural findings and the similarities with the bacterial pathogens, evidence emerges that these pathologically relevant gluten-derived peptides could behave as non-replicating pathogens opening new research questions in the interface of innate immunity, microbiome, and food research.
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Affiliation(s)
- Diego S. Vazquez
- Grupo de Biología Estructural y Biotecnología (GBEyB-IMBICE), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, Ciudad Autónoma C1033AAJ, Buenos Aires, Argentina
| | - Hanna M. Schilbert
- Department of Chemistry, Organic Chemistry OCIII, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany;
| | - Veronica I. Dodero
- Department of Chemistry, Organic Chemistry OCIII, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany;
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61
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Ramberger E, Suarez-Artiles L, Perez-Hernandez D, Haji M, Popp O, Reimer U, Leutz A, Dittmar G, Mertins P. A universal peptide matrix interactomics approach to disclose motif dependent protein binding. Mol Cell Proteomics 2021; 20:100135. [PMID: 34391889 PMCID: PMC8453223 DOI: 10.1016/j.mcpro.2021.100135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Protein–protein interactions mediated by intrinsically disordered regions are often based on short linear motifs (SLiMs). SLiMs are implicated in signal transduction and gene regulation yet remain technically laborious and notoriously challenging to study. Here, we present an optimized method for a protein interaction screen on a peptide matrix (PRISMA) in combination with quantitative MS. The protocol was benchmarked with previously described SLiM-based protein–protein interactions using peptides derived from EGFR, SOS1, GLUT1, and CEBPB and extended to map binding partners of kinase activation loops. The detailed protocol provides practical considerations for setting up a PRISMA screen and subsequently implementing PRISMA on a liquid-handling robotic platform as a cost-effective high-throughput method. Optimized PRISMA can be universally applied to systematically study SLiM-based interactions and associated post-translational modifications or mutations to advance our understanding of the largely uncharacterized interactomes of intrinsically disordered protein regions. Optimized protocol for analysis of peptide–protein interactions with peptide arrays. Detection of interactions affected by mutations or post-translational modifications. Mapping of interaction sites with overlapping peptide sequences. Implementation on a liquid-handling robotic platform.
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lorena Suarez-Artiles
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Mohamad Haji
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin; Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK), Berlin, Germany.
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62
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The EphB6 Receptor: Kinase-Dead but Very Much Alive. Int J Mol Sci 2021; 22:ijms22158211. [PMID: 34360976 PMCID: PMC8347583 DOI: 10.3390/ijms22158211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 01/15/2023] Open
Abstract
The Eph receptor tyrosine kinase member EphB6 is a pseudokinase, and similar to other pseudoenzymes has not attracted an equivalent amount of interest as its enzymatically-active counterparts. However, a greater appreciation for the role pseudoenzymes perform in expanding the repertoire of signals generated by signal transduction systems has fostered more interest in the field. EphB6 acts as a molecular switch that is capable of modulating the signal transduction output of Eph receptor clusters. Although the biological effects of EphB6 activity are well defined, the molecular mechanisms of EphB6 function remain enigmatic. In this review, we use a comparative approach to postulate how EphB6 acts as a scaffold to recruit adaptor proteins to an Eph receptor cluster and how this function is regulated. We suggest that the evolutionary repurposing of EphB6 into a kinase-independent molecular switch in mammals has involved repurposing the kinase activation loop into an SH3 domain-binding site. In addition, we suggest that EphB6 employs the same SAM domain linker and juxtamembrane domain allosteric regulatory mechanisms that are used in kinase-positive Eph receptors to regulate its scaffold function. As a result, although kinase-dead, EphB6 remains a strategically active component of Eph receptor signaling.
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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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64
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Ortiz MA, Mikhailova T, Li X, Porter BA, Bah A, Kotula L. Src family kinases, adaptor proteins and the actin cytoskeleton in epithelial-to-mesenchymal transition. Cell Commun Signal 2021; 19:67. [PMID: 34193161 PMCID: PMC8247114 DOI: 10.1186/s12964-021-00750-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
Over a century of scientific inquiry since the discovery of v-SRC but still no final judgement on SRC function. However, a significant body of work has defined Src family kinases as key players in tumor progression, invasion and metastasis in human cancer. With the ever-growing evidence supporting the role of epithelial-mesenchymal transition (EMT) in invasion and metastasis, so does our understanding of the role SFKs play in mediating these processes. Here we describe some key mechanisms through which Src family kinases play critical role in epithelial homeostasis and how their function is essential for the propagation of invasive signals. Video abstract.
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Affiliation(s)
- Maria A Ortiz
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA.,Department of Urology, SUNY Upstate Medical University, Syracuse, USA
| | - Tatiana Mikhailova
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA
| | - Xiang Li
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA.,Department of Urology, SUNY Upstate Medical University, Syracuse, USA
| | - Baylee A Porter
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA.,Department of Urology, SUNY Upstate Medical University, Syracuse, USA
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA
| | - Leszek Kotula
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, USA. .,Department of Urology, SUNY Upstate Medical University, Syracuse, USA.
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65
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New Structural Perspectives in G Protein-Coupled Receptor-Mediated Src Family Kinase Activation. Int J Mol Sci 2021; 22:ijms22126489. [PMID: 34204297 PMCID: PMC8233884 DOI: 10.3390/ijms22126489] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
Src family kinases (SFKs) are key regulators of cell proliferation, differentiation, and survival. The expression of these non-receptor tyrosine kinases is strongly correlated with cancer development and tumor progression. Thus, this family of proteins serves as an attractive drug target. The activation of SFKs can occur via multiple signaling pathways, yet many of them are poorly understood. Here, we summarize the current knowledge on G protein-coupled receptor (GPCR)-mediated regulation of SFKs, which is of considerable interest because GPCRs are among the most widely used pharmaceutical targets. This type of activation can occur through a direct interaction between the two proteins or be allosterically regulated by arrestins and G proteins. We postulate that a rearrangement of binding motifs within the active conformation of arrestin-3 mediates Src regulation by comparison of available crystal structures. Therefore, we hypothesize a potentially different activation mechanism compared to arrestin-2. Furthermore, we discuss the probable direct regulation of SFK by GPCRs and investigate the intracellular domains of exemplary GPCRs with conserved polyproline binding motifs that might serve as scaffolding domains to allow such a direct interaction. Large intracellular domains in GPCRs are often understudied and, in general, not much is known of their contribution to different signaling pathways. The suggested direct interaction between a GPCR and a SFK could allow for a potential immediate allosteric regulation of SFKs by GPCRs and thereby unravel a novel mechanism of SFK signaling. This overview will help to identify new GPCR-SFK interactions, which could serve to explain biological functions or be used to modulate downstream effectors.
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66
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Alfaidi M, Scott ML, Orr AW. Sinner or Saint?: Nck Adaptor Proteins in Vascular Biology. Front Cell Dev Biol 2021; 9:688388. [PMID: 34124074 PMCID: PMC8187788 DOI: 10.3389/fcell.2021.688388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022] Open
Abstract
The Nck family of modular adaptor proteins, including Nck1 and Nck2, link phosphotyrosine signaling to changes in cytoskeletal dynamics and gene expression that critically modulate cellular phenotype. The Nck SH2 domain interacts with phosphotyrosine at dynamic signaling hubs, such as activated growth factor receptors and sites of cell adhesion. The Nck SH3 domains interact with signaling effectors containing proline-rich regions that mediate their activation by upstream kinases. In vascular biology, Nck1 and Nck2 play redundant roles in vascular development and postnatal angiogenesis. However, recent studies suggest that Nck1 and Nck2 differentially regulate cell phenotype in the adult vasculature. Domain-specific interactions likely mediate these isoform-selective effects, and these isolated domains may serve as therapeutic targets to limit specific protein-protein interactions. In this review, we highlight the function of the Nck adaptor proteins, the known differences in domain-selective interactions, and discuss the role of individual Nck isoforms in vascular remodeling and function.
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Affiliation(s)
- Mabruka Alfaidi
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Matthew L Scott
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States
| | - Anthony Wayne Orr
- Department of Pathology and Translational Pathobiology, Louisiana State University Health - Shreveport, Shreveport, LA, United States.,Department of Cell Biology and Anatomy, LSU Health - Shreveport, Shreveport, LA, United States.,Department of Molecular & Cellular Physiology, LSU Health - Shreveport, Shreveport, LA, United States
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67
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Luttman JH, Colemon A, Mayro B, Pendergast AM. Role of the ABL tyrosine kinases in the epithelial-mesenchymal transition and the metastatic cascade. Cell Commun Signal 2021; 19:59. [PMID: 34022881 PMCID: PMC8140471 DOI: 10.1186/s12964-021-00739-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
The ABL kinases, ABL1 and ABL2, promote tumor progression and metastasis in various solid tumors. Recent reports have shown that ABL kinases have increased expression and/or activity in solid tumors and that ABL inactivation impairs metastasis. The therapeutic effects of ABL inactivation are due in part to ABL-dependent regulation of diverse cellular processes related to the epithelial to mesenchymal transition and subsequent steps in the metastatic cascade. ABL kinases target multiple signaling pathways required for promoting one or more steps in the metastatic cascade. These findings highlight the potential utility of specific ABL kinase inhibitors as a novel treatment paradigm for patients with advanced metastatic disease. Video abstract.
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Affiliation(s)
- Jillian Hattaway Luttman
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Ashley Colemon
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Ann Marie Pendergast
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
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Novel Roles of SH2 and SH3 Domains in Lipid Binding. Cells 2021; 10:cells10051191. [PMID: 34068055 PMCID: PMC8152464 DOI: 10.3390/cells10051191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.
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69
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Sidibé H, Dubinski A, Vande Velde C. The multi-functional RNA-binding protein G3BP1 and its potential implication in neurodegenerative disease. J Neurochem 2021; 157:944-962. [PMID: 33349931 PMCID: PMC8248322 DOI: 10.1111/jnc.15280] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
Ras-GTPase-activating protein (GAP)-binding protein 1 (G3BP1) is a multi-functional protein that is best known for its role in the assembly and dynamics of stress granules. Recent studies have highlighted that G3BP1 also has other functions related to RNA metabolism. In the context of disease, G3BP1 has been therapeutically targeted in cancers because its over-expression is correlated with proliferation of cancerous cells and metastasis. However, evidence suggests that G3BP1 is essential for neuronal development and possibly neuronal maintenance. In this review, we will examine the many functions that are carried out by G3BP1 in the context of neurons and speculate how these functions are critical to the progression of neurodegenerative diseases. Additionally, we will highlight the similarities and differences between G3BP1 and the closely related protein G3BP2, which is frequently overlooked. Although G3BP1 and G3BP2 have both been deemed important for stress granule assembly, their roles may differ in other cellular pathways, some of which are specific to the CNS, and presents an opportunity for further exploration.
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Affiliation(s)
- Hadjara Sidibé
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Alicia Dubinski
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
| | - Christine Vande Velde
- Department of NeurosciencesUniversité de Montréal, and CHUM Research CenterMontréalQCCanada
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70
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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Gulotta MR, Vittorio S, Gitto R, Perricone U, De Luca L. Exploring Molecular Contacts of MUC1 at CIN85 Binding Interface to Address Future Drug Design Efforts. Int J Mol Sci 2021; 22:2208. [PMID: 33672244 PMCID: PMC7927047 DOI: 10.3390/ijms22042208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
The modulation of protein-protein interactions (PPIs) by small molecules represents a valuable strategy for pharmacological intervention in several human diseases. In this context, computer-aided drug discovery techniques offer useful resources to predict the network of interactions governing the recognition process between protein partners, thus furnishing relevant information for the design of novel PPI modulators. In this work, we focused our attention on the MUC1-CIN85 complex as a crucial PPI controlling cancer progression and metastasis. MUC1 is a transmembrane glycoprotein whose extracellular domain contains a variable number of tandem repeats (VNTRs) regions that are highly glycosylated in normal cells and under-glycosylated in cancer. The hypo-glycosylation fosters the exposure of the backbone to new interactions with other proteins, such as CIN85, that alter the intracellular signalling in tumour cells. Herein, different computational approaches were combined to investigate the molecular recognition pattern of MUC1-CIN85 PPI thus unveiling new structural information useful for the design of MUC1-CIN85 PPI inhibitors as potential anti-metastatic agents.
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Affiliation(s)
- Maria Rita Gulotta
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90138 Palermo, Italy; (M.R.G.); (U.P.)
| | - Serena Vittorio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (R.G.); (L.D.L.)
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (R.G.); (L.D.L.)
| | - Ugo Perricone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90138 Palermo, Italy; (M.R.G.); (U.P.)
| | - Laura De Luca
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (R.G.); (L.D.L.)
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Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
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Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
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Lisboa J, Pereira C, Rifflet A, Ayala J, Terceti MS, Barca AV, Rodrigues I, Pereira PJB, Osorio CR, García-Del Portillo F, Gomperts Boneca I, do Vale A, Dos Santos NMS. A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria. mSphere 2021; 6:e00736-20. [PMID: 33536321 PMCID: PMC7860986 DOI: 10.1128/msphere.00736-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( PhotobacteriumNlpC-like protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG.IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
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Affiliation(s)
- Johnny Lisboa
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Cassilda Pereira
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Aline Rifflet
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Juan Ayala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mateus S Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alba V Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inês Rodrigues
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Macromolecular Structure Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco García-Del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Nuno M S Dos Santos
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
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74
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Sculpting Dendritic Spines during Initiation and Maintenance of Neuropathic Pain. J Neurosci 2021; 40:7578-7589. [PMID: 32998955 DOI: 10.1523/jneurosci.1664-20.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/21/2020] [Indexed: 12/21/2022] Open
Abstract
Accumulating evidence has established a firm role for synaptic plasticity in the pathogenesis of neuropathic pain. Recent advances have highlighted the importance of dendritic spine remodeling in driving synaptic plasticity within the CNS. Identifying the molecular players underlying neuropathic pain induced structural and functional maladaptation is therefore critical to understanding its pathophysiology. This process of dynamic reorganization happens in unique phases that have diverse pathologic underpinnings in the initiation and maintenance of neuropathic pain. Recent evidence suggests that pharmacological targeting of specific proteins during distinct phases of neuropathic pain development produces enhanced antinociception. These findings outline a potential new paradigm for targeted treatment and the development of novel therapies for neuropathic pain. We present a concise review of the role of dendritic spines in neuropathic pain and outline the potential for modulation of spine dynamics by targeting two proteins, srGAP3 and Rac1, critically involved in the regulation of the actin cytoskeleton.
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75
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In Silico Identification of Potential Druggable Binding Sites on CIN85 SH3 Domain. Int J Mol Sci 2021; 22:ijms22020534. [PMID: 33430321 PMCID: PMC7825788 DOI: 10.3390/ijms22020534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/01/2023] Open
Abstract
Protein-protein interactions (PPIs) play a pivotal role in the regulation of many physiological processes. The dysfunction of some PPIs interactions led to the alteration of different biological pathways causing various diseases including cancer. In this context, the inhibition of PPIs represents an attractive strategy for the design of new antitumoral agents. In recent years, computational approaches were successfully used to study the interactions between proteins, providing useful hints for the design of small molecules able to modulate PPIs. Targeting PPIs presents several challenges mainly due to the large and flat binding surface that lack the typical binding pockets of traditional drug targets. Despite these hurdles, substantial progress has been made in the last decade resulting in the identification of PPI modulators where some of them even found clinical use. This study focuses on MUC1-CIN85 PPI which is involved in the migration and invasion of cancer cells. Particularly, we investigated the presence of druggable binding sites on the CIN85 surface which provided new insights for the structure-based design of novel MUC1-CIN85 PPI inhibitors as anti-metastatic agents.
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76
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Advances in Understanding TKS4 and TKS5: Molecular Scaffolds Regulating Cellular Processes from Podosome and Invadopodium Formation to Differentiation and Tissue Homeostasis. Int J Mol Sci 2020; 21:ijms21218117. [PMID: 33143131 PMCID: PMC7663256 DOI: 10.3390/ijms21218117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Scaffold proteins are typically thought of as multi-domain "bridging molecules." They serve as crucial regulators of key signaling events by simultaneously binding multiple participants involved in specific signaling pathways. In the case of epidermal growth factor (EGF)-epidermal growth factor receptor (EGFR) binding, the activated EGFR contacts cytosolic SRC tyrosine-kinase, which then becomes activated. This process leads to the phosphorylation of SRC-substrates, including the tyrosine kinase substrates (TKS) scaffold proteins. The TKS proteins serve as a platform for the recruitment of key players in EGFR signal transduction, promoting cell spreading and migration. The TKS4 and the TKS5 scaffold proteins are tyrosine kinase substrates with four or five SH3 domains, respectively. Their structural features allow them to recruit and bind a variety of signaling proteins and to anchor them to the cytoplasmic surface of the cell membrane. Until recently, TKS4 and TKS5 had been recognized for their involvement in cellular motility, reactive oxygen species-dependent processes, and embryonic development, among others. However, a number of novel functions have been discovered for these molecules in recent years. In this review, we attempt to cover the diverse nature of the TKS molecules by discussing their structure, regulation by SRC kinase, relevant signaling pathways, and interaction partners, as well as their involvement in cellular processes, including migration, invasion, differentiation, and adipose tissue and bone homeostasis. We also describe related pathologies and the established mouse models.
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77
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Shen Y, Kalograiaki I, Prunotto A, Dunne M, Boulos S, Taylor NMI, Sumrall ET, Eugster MR, Martin R, Julian-Rodero A, Gerber B, Leiman PG, Menéndez M, Peraro MD, Cañada FJ, Loessner MJ. Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase. Chem Sci 2020; 12:576-589. [PMID: 34163788 PMCID: PMC8179006 DOI: 10.1039/d0sc04394j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity. Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.![]()
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Affiliation(s)
- Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Ioanna Kalograiaki
- Centro de Investigaciones Biológicas, Margarita Salas, Consejo Superior de Investigaciones Científicas Ramiro de Maeztu 9 28040 Madrid Spain.,Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain
| | - Alessio Prunotto
- Laboratory for Biomolecular Modeling, EPFL IBI-SV Station 19 1015 Lausanne Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Samy Boulos
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B Copenhagen 2200 Denmark
| | - Eric T Sumrall
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Marcel R Eugster
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Rebecca Martin
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Alicia Julian-Rodero
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Benjamin Gerber
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
| | - Petr G Leiman
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics 301 University Blvd Galveston TX 77555-0647 USA
| | - Margarita Menéndez
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain.,Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Cientificas Serrano 119 28006 Madrid Spain
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, EPFL IBI-SV Station 19 1015 Lausanne Switzerland
| | - Francisco Javier Cañada
- Centro de Investigaciones Biológicas, Margarita Salas, Consejo Superior de Investigaciones Científicas Ramiro de Maeztu 9 28040 Madrid Spain.,Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES) Avenida de Monforte de Lemos 3-5 28029 Madrid Spain
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich Schmelzbergstrasse 7 8092 Zurich Switzerland
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78
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Gerlach GJ, Carrock R, Stix R, Stollar EJ, Ball KA. A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway. PLoS Comput Biol 2020; 16:e1007815. [PMID: 32925900 PMCID: PMC7514057 DOI: 10.1371/journal.pcbi.1007815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/24/2020] [Accepted: 08/15/2020] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions are involved in a wide range of cellular processes. These interactions often involve intrinsically disordered proteins (IDPs) and protein binding domains. However, the details of IDP binding pathways are hard to characterize using experimental approaches, which can rarely capture intermediate states present at low populations. SH3 domains are common protein interaction domains that typically bind proline-rich disordered segments and are involved in cell signaling, regulation, and assembly. We hypothesized, given the flexibility of SH3 binding peptides, that their binding pathways include multiple steps important for function. Molecular dynamics simulations were used to characterize the steps of binding between the yeast Abp1p SH3 domain (AbpSH3) and a proline-rich IDP, ArkA. Before binding, the N-terminal segment 1 of ArkA is pre-structured and adopts a polyproline II helix, while segment 2 of ArkA (C-terminal) adopts a 310 helix, but is far less structured than segment 1. As segment 2 interacts with AbpSH3, it becomes more structured, but retains flexibility even in the fully engaged state. Binding simulations reveal that ArkA enters a flexible encounter complex before forming the fully engaged bound complex. In the encounter complex, transient nonspecific hydrophobic and long-range electrostatic contacts form between ArkA and the binding surface of SH3. The encounter complex ensemble includes conformations with segment 1 in both the forward and reverse orientation, suggesting that segment 2 may play a role in stabilizing the correct binding orientation. While the encounter complex forms quickly, the slow step of binding is the transition from the disordered encounter ensemble to the fully engaged state. In this transition, ArkA makes specific contacts with AbpSH3 and buries more hydrophobic surface. Simulating the binding between ApbSH3 and ArkA provides insight into the role of encounter complex intermediates and nonnative hydrophobic interactions for other SH3 domains and IDPs in general.
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Affiliation(s)
- Gabriella J. Gerlach
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Rachel Carrock
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Robyn Stix
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
| | - Elliott J. Stollar
- School of Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - K. Aurelia Ball
- Department of Chemistry, Skidmore College, Saratoga Springs, New York, United States
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79
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Ahn J, Wu H, Lee K. Integrative Analysis Revealing Human Heart-Specific Genes and Consolidating Heart-Related Phenotypes. Front Genet 2020; 11:777. [PMID: 32903789 PMCID: PMC7438927 DOI: 10.3389/fgene.2020.00777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
Elucidating expression patterns of heart-specific genes is crucial for understanding developmental, physiological, and pathological processes of the heart. The aim of the present study is to identify functionally and pathologically important heart-specific genes by performing the Ingenuity Pathway Analysis (IPA). Through a median-based analysis of tissue-specific gene expression based on the Genotype-Tissue Expression (GTEx) data, we identified 56 genes with heart-specific or elevated expressions in the heart (heart-specific/enhanced), among which three common heart-specific/enhanced genes and four atrial appendage-specific/enhanced genes were unreported regarding the heart. Differential expression analysis further revealed 225 differentially expressed genes (DEGs) between atrial appendage and left ventricle. Our integrative analyses of those heart-specific/enhanced genes and DEGs with IPA revealed enriched heart-related traits and diseases, consolidating evidence of relationships between these genes and heart function. Our reports on comprehensive identification of heart-specific/enhanced genes and DEGs and their relation to pathways associated with heart-related traits and diseases provided molecular insights into essential regulators of cardiac physiology and pathophysiology and potential new therapeutic targets for heart diseases.
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Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - Huiguang Wu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
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80
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Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations. Biomolecules 2020; 10:biom10081097. [PMID: 32722039 PMCID: PMC7463635 DOI: 10.3390/biom10081097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/27/2022] Open
Abstract
Because proteins are fundamental to most biological processes, many genetic diseases can be traced back to single nucleotide variants (SNVs) that cause changes in protein sequences. However, not all SNVs that result in amino acid substitutions cause disease as each residue is under different structural and functional constraints. Influential studies have shown that protein–protein interaction interfaces are enriched in disease-associated SNVs and depleted in SNVs that are common in the general population. These studies focus primarily on folded (globular) protein domains and overlook the prevalent class of protein interactions mediated by intrinsically disordered regions (IDRs). Therefore, we investigated the enrichment patterns of missense mutation-causing SNVs that are associated with disease and cancer, as well as those present in the healthy population, in structures of IDR-mediated interactions with comparisons to classical globular interactions. When comparing the different categories of interaction interfaces, division of the interface regions into solvent-exposed rim residues and buried core residues reveal distinctive enrichment patterns for the various types of missense mutations. Most notably, we demonstrate a strong enrichment at the interface core of interacting IDRs in disease mutations and its depletion in neutral ones, which supports the view that the disruption of IDR interactions is a mechanism underlying many diseases. Intriguingly, we also found an asymmetry across the IDR interaction interface in the enrichment of certain missense mutation types, which may hint at an increased variant tolerance and urges further investigations of IDR interactions.
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81
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Sokolik CG, Qassem N, Chill JH. The Disordered Cellular Multi-Tasker WIP and Its Protein-Protein Interactions: A Structural View. Biomolecules 2020; 10:biom10071084. [PMID: 32708183 PMCID: PMC7407642 DOI: 10.3390/biom10071084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 01/21/2023] Open
Abstract
WASp-interacting protein (WIP), a regulator of actin cytoskeleton assembly and remodeling, is a cellular multi-tasker and a key member of a network of protein-protein interactions, with significant impact on health and disease. Here, we attempt to complement the well-established understanding of WIP function from cell biology studies, summarized in several reviews, with a structural description of WIP interactions, highlighting works that present a molecular view of WIP's protein-protein interactions. This provides a deeper understanding of the mechanisms by which WIP mediates its biological functions. The fully disordered WIP also serves as an intriguing example of how intrinsically disordered proteins (IDPs) exert their function. WIP consists of consecutive small functional domains and motifs that interact with a host of cellular partners, with a striking preponderance of proline-rich motif capable of interactions with several well-recognized binding partners; indeed, over 30% of the WIP primary structure are proline residues. We focus on the binding motifs and binding interfaces of three important WIP segments, the actin-binding N-terminal domain, the central domain that binds SH3 domains of various interaction partners, and the WASp-binding C-terminal domain. Beyond the obvious importance of a more fundamental understanding of the biology of this central cellular player, this approach carries an immediate and highly beneficial effect on drug-design efforts targeting WIP and its binding partners. These factors make the value of such structural studies, challenging as they are, readily apparent.
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82
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Li X, Li J, Martinez EC, Froese A, Passariello CL, Henshaw K, Rusconi F, Li Y, Yu Q, Thakur H, Nikolaev VO, Kapiloff MS. Calcineurin Aβ-Specific Anchoring Confers Isoform-Specific Compartmentation and Function in Pathological Cardiac Myocyte Hypertrophy. Circulation 2020; 142:948-962. [PMID: 32611257 DOI: 10.1161/circulationaha.119.044893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The Ca2+/calmodulin-dependent phosphatase calcineurin is a key regulator of cardiac myocyte hypertrophy in disease. An unexplained paradox is how the β isoform of the calcineurin catalytic A-subunit (CaNAβ) is required for induction of pathological myocyte hypertrophy, despite calcineurin Aα expression in the same cells. It is unclear how the pleiotropic second messenger Ca2+ drives excitation-contraction coupling while not stimulating hypertrophy by calcineurin in the normal heart. Elucidation of the mechanisms conferring this selectivity in calcineurin signaling should reveal new strategies for targeting the phosphatase in disease. METHODS Primary adult rat ventricular myocytes were studied for morphology and intracellular signaling. New Förster resonance energy transfer reporters were used to assay Ca2+ and calcineurin activity in living cells. Conditional gene deletion and adeno-associated virus-mediated gene delivery in the mouse were used to study calcineurin signaling after transverse aortic constriction in vivo. RESULTS CIP4 (Cdc42-interacting protein 4)/TRIP10 (thyroid hormone receptor interactor 10) was identified as a new polyproline domain-dependent scaffold for CaNAβ2 by yeast 2-hybrid screen. Cardiac myocyte-specific CIP4 gene deletion in mice attenuated pressure overload-induced pathological cardiac remodeling and heart failure. Blockade of CaNAβ polyproline-dependent anchoring using a competing peptide inhibited concentric hypertrophy in cultured myocytes; disruption of anchoring in vivo using an adeno-associated virus gene therapy vector inhibited cardiac hypertrophy and improved systolic function after pressure overload. Live cell Förster resonance energy transfer biosensor imaging of cultured myocytes revealed that Ca2+ levels and calcineurin activity associated with the CIP4 compartment were increased by neurohormonal stimulation, but minimally by pacing. Conversely, Ca2+ levels and calcineurin activity detected by nonlocalized Förster resonance energy transfer sensors were induced by pacing and minimally by neurohormonal stimulation, providing functional evidence for differential intracellular compartmentation of Ca2+ and calcineurin signal transduction. CONCLUSIONS These results support a structural model for Ca2+ and CaNAβ compartmentation in cells based on an isoform-specific mechanism for calcineurin protein-protein interaction and localization. This mechanism provides an explanation for the specific role of CaNAβ in hypertrophy and its selective activation under conditions of pathologic stress. Disruption of CaNAβ polyproline-dependent anchoring constitutes a rational strategy for therapeutic targeting of CaNAβ-specific signaling responsible for pathological cardiac remodeling in cardiovascular disease deserving of further preclinical investigation.
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Affiliation(s)
- Xiaofeng Li
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Jinliang Li
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Eliana C Martinez
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Alexander Froese
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.F., V.O.N.)
| | - Catherine L Passariello
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Kathryn Henshaw
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Francesca Rusconi
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.)
| | - Yang Li
- Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Qian Yu
- Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Hrishikesh Thakur
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany (A.F., V.O.N.)
| | - Michael S Kapiloff
- Interdisciplinary Stem Cell Institute, Department of Pediatrics, Leonard M. Miller School of Medicine, University of Miami, FL (X.L., J.L., E.C.M., C.L.P., K.H., F.R., H.T., M.S.K.).,Departments of Ophthalmology and Medicine, Stanford Cardiovascular Institute, Stanford University, Palo Alto, CA (J.L., Y.L., Q.Y., H.T., M.S.K.)
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83
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Visconti L, Toto A, Jarvis JA, Troilo F, Malagrinò F, De Simone A, Gianni S. Demonstration of Binding Induced Structural Plasticity in a SH2 Domain. Front Mol Biosci 2020; 7:89. [PMID: 32528972 PMCID: PMC7247818 DOI: 10.3389/fmolb.2020.00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/17/2020] [Indexed: 01/13/2023] Open
Abstract
SH2 domains are common protein interaction domains able to recognize short aminoacidic sequences presenting a phosphorylated tyrosine (pY). In spite of their fundamental importance for cell physiology there is a lack of information about the mechanism by which these domains recognize and bind their natural ligands. The N-terminal SH2 (N-SH2) domain of PI3K mediates the interaction with different scaffolding proteins and is known to recognize a specific pY-X-X-M consensus sequence. These interactions are at the cross roads of different molecular pathways and play a key role for cell development and division. By combining mutagenesis, chemical kinetics and NMR, here we provide a complete characterization of the interaction between N-SH2 and a peptide mimicking the scaffolding protein Gab2. Our results highlight that N-SH2 is characterized by a remarkable structural plasticity, with the binding reaction being mediated by a diffused structural region and not solely by the residues located in the binding pocket. Furthermore, the analysis of kinetic data allow us to pinpoint an allosteric network involving residues far from the binding pocket involved in specificity. Results are discussed on the light of previous works on the binding properties of SH2 domains.
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Affiliation(s)
- Lorenzo Visconti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - James A Jarvis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Francesca Troilo
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Rome, Italy
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84
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Understanding the Mechanism of Recognition of Gab2 by the N-SH2 Domain of SHP2. Life (Basel) 2020; 10:life10060085. [PMID: 32545165 PMCID: PMC7345789 DOI: 10.3390/life10060085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/08/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Gab2 is a scaffold protein with a crucial role in colocalizing signaling proteins and it is involved in the regulation of several important molecular pathways. SHP2 is a protein phosphatase that binds, through its two SH2 domains, specific consensus sequences presenting a phosphorylated tyrosine located on the disordered tail of Gab2. To shed light on the details of such a fundamental interaction for the physiology of the cell, we present a complete mutational analysis of the kinetics of binding between the N-SH2 domain of SHP2 and a peptide mimicking a specific region of Gab2. By analyzing kinetic data, we determined structural features of the transition state of the N-SH2 domain binding to Gab2, highlighting a remarkable cooperativity of the binding reaction. Furthermore, comparison of these data with ones previously obtained for another SH2 domain suggests the presence of underlying general features characterizing the binding process of SH2 domains. Data are discussed under the light of previous works on SH2 domains.
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85
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Quinlan MA, Robson MJ, Ye R, Rose KL, Schey KL, Blakely RD. Ex vivo Quantitative Proteomic Analysis of Serotonin Transporter Interactome: Network Impact of the SERT Ala56 Coding Variant. Front Mol Neurosci 2020; 13:89. [PMID: 32581705 PMCID: PMC7295033 DOI: 10.3389/fnmol.2020.00089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022] Open
Abstract
Altered serotonin (5-HT) signaling is associated with multiple brain disorders, including major depressive disorder (MDD), obsessive-compulsive disorder (OCD), and autism spectrum disorder (ASD). The presynaptic, high-affinity 5-HT transporter (SERT) tightly regulates 5-HT clearance after release from serotonergic neurons in the brain and enteric nervous systems, among other sites. Accumulating evidence suggests that SERT is dynamically regulated in distinct activity states as a result of environmental and intracellular stimuli, with regulation perturbed by disease-associated coding variants. Our lab identified a rare, hypermorphic SERT coding substitution, Gly56Ala, in subjects with ASD, finding that the Ala56 variant stabilizes a high-affinity outward-facing conformation (SERT∗) that leads to elevated 5-HT uptake in vitro and in vivo. Hyperactive SERT Ala56 appears to preclude further activity enhancements by p38α mitogen-activated protein kinase (MAPK) and can be normalized by pharmacological p38α MAPK inhibition, consistent with SERT Ala56 mimicking, constitutively, a high-activity conformation entered into transiently by p38α MAPK activation. We hypothesize that changes in SERT-interacting proteins (SIPs) support the shift of SERT into the SERT∗ state which may be captured by comparing the composition of SERT Ala56 protein complexes with those of wildtype (WT) SERT, defining specific interactions through comparisons of protein complexes recovered using preparations from SERT–/– (knockout; KO) mice. Using quantitative proteomic-based approaches, we identify a total of 459 SIPs, that demonstrate both SERT specificity and sensitivity to the Gly56Ala substitution, with a striking bias being a loss of SIP interactions with SERT Ala56 compared to WT SERT. Among this group are previously validated SIPs, such as flotillin-1 (FLOT1) and protein phosphatase 2A (PP2A), whose functions are believed to contribute to SERT microdomain localization and regulation. Interestingly, our studies nominate a number of novel SIPs implicated in ASD, including fragile X mental retardation 1 protein (FMR1) and SH3 and multiple ankyrin repeat domains protein 3 (SHANK3), of potential relevance to long-standing evidence of serotonergic contributions to ASD. Further investigation of these SIPs, and the broader networks they engage, may afford a greater understanding of ASD as well as other brain and peripheral disorders associated with perturbed 5-HT signaling.
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Affiliation(s)
- Meagan A Quinlan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States.,Department of Pharmacology, Vanderbilt University, Nashville, TN, United States.,Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, FL, United States
| | - Matthew J Robson
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, United States
| | - Ran Ye
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Randy D Blakely
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States.,Brain Institute, Florida Atlantic University, Jupiter, FL, United States
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86
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Cheong HSJ, Nona M, Guerra SB, VanBerkum MF. The first quarter of the C-terminal domain of Abelson regulates the WAVE regulatory complex and Enabled in axon guidance. Neural Dev 2020; 15:7. [PMID: 32359359 PMCID: PMC7196227 DOI: 10.1186/s13064-020-00144-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
Background Abelson tyrosine kinase (Abl) plays a key role in axon guidance in linking guidance receptors to actin dynamics. The long C-terminal domain (CTD) of Drosophila Abl is important for this role, and previous work identified the ‘first quarter’ (1Q) of the CTD as essential. Here, we link the physical interactions of 1Q binding partners to Abl’s function in axon guidance. Methods Protein binding partners of 1Q were identified by GST pulldown and mass spectrometry, and validated using axon guidance assays in the embryonic nerve cord and motoneurons. The role of 1Q was assessed genetically, utilizing a battery of Abl transgenes in combination with mutation or overexpression of the genes of pulled down proteins, and their partners in actin dynamics. The set of Abl transgenes had the following regions deleted: all of 1Q, each half of 1Q (‘eighths’, 1E and 2E) or a PxxP motif in 2E, which may bind SH3 domains. Results GST pulldown identified Hem and Sra-1 as binding partners of 1Q, and our genetic analyses show that both proteins function with Abl in axon guidance, with Sra-1 likely interacting with 1Q. As Hem and Sra-1 are part of the actin-polymerizing WAVE regulatory complex (WRC), we extended our analyses to Abi and Trio, which interact with Abl and WRC members. Overall, the 1Q region (and especially 2E and its PxxP motif) are important for Abl’s ability to work with WRC in axon guidance. These areas are also important for Abl’s ability to function with the actin regulator Enabled. In comparison, 1E contributes to Abl function with the WRC at the midline, but less so with Enabled. Conclusions The 1Q region, and especially the 2E region with its PxxP motif, links Abl with the WRC, its regulators Trio and Abi, and the actin regulator Ena. Removing 1E has specific effects suggesting it may help modulate Abl’s interaction with the WRC or Ena. Thus, the 1Q region of Abl plays a key role in regulating actin dynamics during axon guidance.
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Affiliation(s)
| | - Mark Nona
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
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87
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Ding W, Tan HY, Zhang JX, Wilczek LA, Hsieh KR, Mulkin JA, Bianco PR. The mechanism of Single strand binding protein-RecG binding: Implications for SSB interactome function. Protein Sci 2020; 29:1211-1227. [PMID: 32196797 PMCID: PMC7184773 DOI: 10.1002/pro.3855] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023]
Abstract
The Escherichia coli single-strand DNA binding protein (SSB) is essential to viability where it functions to regulate SSB interactome function. Here it binds to single-stranded DNA and to target proteins that comprise the interactome. The region of SSB that links these two essential protein functions is the intrinsically disordered linker. Key to linker function is the presence of three, conserved PXXP motifs that mediate binding to oligosaccharide-oligonucleotide binding folds (OB-fold) present in SSB and its interactome partners. Not surprisingly, partner OB-fold deletions eliminate SSB binding. Furthermore, single point mutations in either the PXXP motifs or, in the RecG OB-fold, obliterate SSB binding. The data also demonstrate that, and in contrast to the view currently held in the field, the C-terminal acidic tip of SSB is not required for interactome partner binding. Instead, we propose the tip has two roles. First, and consistent with the proposal of Dixon, to regulate the structure of the C-terminal domain in a biologically active conformation that prevents linkers from binding to SSB OB-folds until this interaction is required. Second, as a secondary binding domain. Finally, as OB-folds are present in SSB and many of its partners, we present the SSB interactome as the first family of OB-fold genome guardians identified in prokaryotes.
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Affiliation(s)
- Wenfei Ding
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Hui Yin Tan
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndianaUnited States
| | - Jia Xiang Zhang
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
| | - Luke A. Wilczek
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
- Present address:
Department of ChemistryBrown UniversityProvidenceRhode IslandUnited States
| | - Karin R. Hsieh
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Jeffrey A. Mulkin
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
| | - Piero R. Bianco
- Center for Single Molecule BiophysicsUniversity at BuffaloBuffaloNew YorkUnited States
- Department of BiochemistryUniversity at BuffaloBuffaloNew YorkUnited States
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88
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Bianco PR. DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication forks in Escherichia coli. Genes (Basel) 2020; 11:E471. [PMID: 32357475 PMCID: PMC7290993 DOI: 10.3390/genes11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 01/25/2023] Open
Abstract
In Escherichia coli, DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so that repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls helicase-fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart.
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, NY 14221, USA
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89
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Navinés-Ferrer A, Martín M. Long-Tailed Unconventional Class I Myosins in Health and Disease. Int J Mol Sci 2020; 21:ijms21072555. [PMID: 32272642 PMCID: PMC7177449 DOI: 10.3390/ijms21072555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 01/21/2023] Open
Abstract
Long-tailed unconventional class I myosin, Myosin 1E (MYO1E) and Myosin 1F (MYO1F) are motor proteins that use chemical energy from the hydrolysis of adenosine triphosphate (ATP) to produce mechanical work along the actin cytoskeleton. On the basis of their motor properties and structural features, myosins perform a variety of essential roles in physiological processes such as endocytosis, exocytosis, cell adhesion, and migration. The long tailed unconventional class I myosins are characterized by having a conserved motor head domain, which binds actin and hydrolyzes ATP, followed by a short neck with an isoleucine-glutamine (IQ) motif, which binds calmodulin and is sensitive to calcium, and a tail that contains a pleckstrin homology domain (PH), a tail homology 1 domain (TH1), wherein these domains allow membrane binding, a tail homology 2 domain (TH2), an ATP-insensitive actin-binding site domain, and a single Src homology 3 domain (SH3) susceptible to binding proline rich regions in other proteins. Therefore, these motor proteins are able to bind actin, plasma membrane, and other molecules (adaptor, kinases, membrane proteins) that contribute to their function, ranging from increasing membrane tension to molecular trafficking and cellular adhesion. MYO1E and MYO1F function in host self-defense, with a better defined role in innate immunity in cell migration and phagocytosis. Impairments of their function have been identified in patients suffering pathologies ranging from tumoral processes to kidney diseases. In this review, we summarize our current knowledge of specific features and functions of MYO1E and MYO1F in various tissues, as well as their involvement in disease.
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Affiliation(s)
- A. Navinés-Ferrer
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine, University of Barcelona, 08036 Barcelona, Spain
- Laboratory of Clinic and Experimental Respiratory Immunoallergy, IDIBAPS, 08036 Barcelona, Spain
| | - M. Martín
- Biochemistry and Molecular Biology Unit, Biomedicine Department, Faculty of Medicine, University of Barcelona, 08036 Barcelona, Spain
- Laboratory of Clinic and Experimental Respiratory Immunoallergy, IDIBAPS, 08036 Barcelona, Spain
- ARADyAL research network, Carlos III Health Institute, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-93-4024541; Fax: +34-93-4035882
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90
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Yin H, Zhao J, Han S, Cui C, Wang Y, Li D, Zhu Q. Molecular characterization, tissue distribution, and functional analysis of the STAC3 gene in chicken. 3 Biotech 2020; 10:171. [PMID: 32206505 DOI: 10.1007/s13205-020-2161-2] [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: 02/08/2020] [Accepted: 03/02/2020] [Indexed: 11/29/2022] Open
Abstract
The Src homology 3 and cysteine-rich domain 3 gene (STAC3) encodes a protein containing both a cysteine-rich domain and two Src (sarcoma) homology 3 domains (SH3). STAC3 is specifically expressed in skeletal muscle and plays an important role in skeletal muscle development, but the explicit sequence and function of chicken SATC3 remain unknown. In the current study, we found the full-length chicken STAC3 cDNA to be 1383 bp long, with a 1092 bp open reading frame that harbors one cysteine-rich C1 domain and two SH3 domains. Tissue distribution analysis reveals chicken STAC3 mRNA only in skeletal muscle among 12 chicken tissues examined by reverse transcription PCR. Both cholecystokinin octapeptide analysis and a 5-ethynyl-2'-deoxyuridine assay suggest that neither STAC3 overexpression nor knockdown has any effect on the proliferation of chicken skeletal muscle satellite cells. However, STAC3 knockdown significantly increases the mRNA expression of MyoG, MyoD, Mb, and MyHC, and the protein abundance of MyHC and MyoG, whereas the opposite result is found in STAC3 overexpressed cells. We conclude that the STAC3 gene is expressed specifically in skeletal muscle and is a negative regulator of skeletal muscle satellite cell differentiation in chicken.
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Affiliation(s)
- Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Jing Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Shunshun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Can Cui
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130 Sichuan People's Republic of China
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91
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Structural basis for substrate specificity and catalysis of α1,6-fucosyltransferase. Nat Commun 2020; 11:973. [PMID: 32080177 PMCID: PMC7033129 DOI: 10.1038/s41467-020-14794-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Core-fucosylation is an essential biological modification by which a fucose is transferred from GDP-β-L-fucose to the innermost N-acetylglucosamine residue of N-linked glycans. A single human enzyme α1,6-fucosyltransferase (FUT8) is the only enzyme responsible for this modification via the addition of an α-1,6-linked fucose to N-glycans. To date, the details of substrate recognition and catalysis by FUT8 remain unknown. Here, we report the crystal structure of FUT8 complexed with GDP and a biantennary complex N-glycan (G0), which provides insight into both substrate recognition and catalysis. FUT8 follows an SN2 mechanism and deploys a series of loops and an α-helix which all contribute in forming the binding site. An exosite, formed by one of these loops and an SH3 domain, is responsible for the recognition of branched sugars, making contacts specifically to the α1,3 arm GlcNAc, a feature required for catalysis. This information serves as a framework for inhibitor design, and helps to assess its potential as a therapeutic target.
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92
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Chlamydia-induced curvature of the host-cell plasma membrane is required for infection. Proc Natl Acad Sci U S A 2020; 117:2634-2644. [PMID: 31964834 PMCID: PMC7007526 DOI: 10.1073/pnas.1911528117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During invasion of host cells, Chlamydia pneumoniae secretes the effector protein CPn0678, which facilitates internalization of the pathogen by remodeling the target cell's plasma membrane and recruiting sorting nexin 9 (SNX9), a central multifunctional endocytic scaffold protein. We show here that the strongly amphipathic N-terminal helix of CPn0678 mediates binding to phospholipids in both the plasma membrane and synthetic membranes, and is sufficient to induce extensive membrane tubulations. CPn0678 interacts via its conserved C-terminal polyproline sequence with the Src homology 3 domain of SNX9. Thus, SNX9 is found at bacterial entry sites, where C. pneumoniae is internalized via EGFR-mediated endocytosis. Moreover, depletion of human SNX9 significantly reduces internalization, whereas ectopic overexpression of CPn0678-GFP results in a dominant-negative effect on endocytotic processes in general, leading to the uptake of fewer chlamydial elementary bodies and diminished turnover of EGFR. Thus, CPn0678 is an early effector involved in regulating the endocytosis of C. pneumoniae in an EGFR- and SNX9-dependent manner.
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93
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Photobiomodulation and the expression of genes related to the JAK/STAT signalling pathway in wounded and diabetic wounded cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 204:111791. [PMID: 31981991 DOI: 10.1016/j.jphotobiol.2020.111791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/11/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022]
Abstract
Photobiomodulation therapy (PBMT) is a curative technique that uses low intensity light to relegate pain and inflammation, and accelerate tissue repair. At a molecular level, the effects of photobiomodulation (PBM) are not fully established. The present study aimed to assess the impact of PBM on the alteration of genes linked to Janus kinase-Signal transducer and activator of transcription (JAK-STAT) signalling in wounded and diabetic wounded cells in vitro. Cells were irradiated using a diode laser at a wavelength of 660 nm and an energy density of 5 J/cm2. RNA was extracted from cells 48 h post-irradiation, and was used to synthesise complementary deoxyribonucleic acid (cDNA) that was used in PCR arrays to profile for 84 JAK/STAT signalling related genes. Irradiation at a wavelength of 660 nm and an energy density of 5 J/cm2 significantly regulated genes related to the JAK/STAT signalling pathway in wounded and diabetic wounded cells. In irradiated wounded cells, 19 genes were significantly regulated, of which two were up-regulated and 17 were down-regulated, while 73 genes were significantly regulated in irradiated diabetic wounded cells of which 46 were up-regulated and 27 were down-regulated. This data suggests that PBM modulates gene transcription for protein synthesis and activates cellular signalling, and may indeed be helpful in enhancing diabetic wound repair.
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Zhou P, Yan F, Miao Q, Chen Z, Wang H. Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode? J Biomol Struct Dyn 2020; 39:310-318. [DOI: 10.1080/07391102.2019.1709547] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
- Center for Information in BioMedicine, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
| | - Fugang Yan
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Qingqing Miao
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Zheng Chen
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Heyi Wang
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
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95
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Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang ECY, Davison AJ, Wilkinson GWG, Stanton RJ, Huttlin EL, Weekes MP. Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. eLife 2019; 8:e49894. [PMID: 31873071 PMCID: PMC6959991 DOI: 10.7554/elife.49894] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023] Open
Abstract
Human cytomegalovirus (HCMV) extensively modulates host cells, downregulating >900 human proteins during viral replication and degrading ≥133 proteins shortly after infection. The mechanism of degradation of most host proteins remains unresolved, and the functions of many viral proteins are incompletely characterised. We performed a mass spectrometry-based interactome analysis of 169 tagged, stably-expressed canonical strain Merlin HCMV proteins, and two non-canonical HCMV proteins, in infected cells. This identified a network of >3400 virus-host and >150 virus-virus protein interactions, providing insights into functions for multiple viral genes. Domain analysis predicted binding of the viral UL25 protein to SH3 domains of NCK Adaptor Protein-1. Viral interacting proteins were identified for 31/133 degraded host targets. Finally, the uncharacterised, non-canonical ORFL147C protein was found to interact with elements of the mRNA splicing machinery, and a mutational study suggested its importance in viral replication. The interactome data will be important for future studies of herpesvirus infection.
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Affiliation(s)
- Luis V Nobre
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Katie Nightingale
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Benjamin J Ravenhill
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Lior Soday
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - James A Davies
- Division of Infection and ImmunityCardiff University School of MedicineCardiffUnited Kingdom
| | - Sepehr Seirafian
- Division of Infection and ImmunityCardiff University School of MedicineCardiffUnited Kingdom
| | - Eddie CY Wang
- Division of Infection and ImmunityCardiff University School of MedicineCardiffUnited Kingdom
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Gavin WG Wilkinson
- Division of Infection and ImmunityCardiff University School of MedicineCardiffUnited Kingdom
| | - Richard J Stanton
- Division of Infection and ImmunityCardiff University School of MedicineCardiffUnited Kingdom
| | - Edward L Huttlin
- Department of Cell BiologyHarvard Medical SchoolBostonUnited States
| | - Michael P Weekes
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUnited Kingdom
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96
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Kim MK, Kim B, Kwon JO, Song MK, Jung S, Lee ZH, Kim HH. ST5 Positively Regulates Osteoclastogenesis via Src/Syk/calcium Signaling Pathways. Mol Cells 2019; 42:810-819. [PMID: 31707778 PMCID: PMC6883977 DOI: 10.14348/molcells.2019.0189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023] Open
Abstract
For physiological or pathological understanding of bone disease caused by abnormal behavior of osteoclasts (OCs), functional studies of molecules that regulate the generation and action of OCs are required. In a microarray approach, we found the suppression of tumorigenicity 5 (ST5) gene is upregulated by receptor activator of nuclear factor-κB ligand (RANKL), the OC differentiation factor. Although the roles of ST5 in cancer and β-cells have been reported, the function of ST5 in bone cells has not yet been investigated. Knockdown of ST5 by siRNA reduced OC differentiation from primary precursors. Moreover, ST5 downregulation decreased expression of NFATc1, a key transcription factor for osteoclastogenesis. In contrast, overexpression of ST5 resulted in the opposite phenotype of ST5 knockdown. In immunocytochemistry experiments, the ST5 protein is colocalized with Src in RANKL-committed cells. In addition, ST5 enhanced activation of Src and Syk, a Src substrate, in response to RANKL. ST5 reduction caused a decrease in RANKL-evoked calcium oscillation and inhibited translocation of NFATc1 into the nucleus. Taken together, these findings provide the first evidence of ST5 involvement in positive regulation of osteoclastogenesis via Src/Syk/calcium signaling.
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Affiliation(s)
- Min Kyung Kim
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Bongjun Kim
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Jun-Oh Kwon
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Min-Kyoung Song
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Suhan Jung
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Zang Hee Lee
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
| | - Hong-Hee Kim
- Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080,
Korea
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97
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The Nebulin Family LIM and SH3 Proteins Regulate Postsynaptic Development and Function. J Neurosci 2019; 40:526-541. [PMID: 31754010 PMCID: PMC6961999 DOI: 10.1523/jneurosci.0334-19.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Neuronal dendrites have specialized actin-rich structures called dendritic spines that receive and integrate most excitatory synaptic inputs. The stabilization of dendrites and spines during neuronal maturation is essential for proper neural circuit formation. Changes in dendritic morphology and stability are largely mediated by regulation of the actin cytoskeleton; however, the underlying mechanisms remain to be fully elucidated. Here, we present evidence that the nebulin family members LASP1 and LASP2 play an important role in the postsynaptic development of rat hippocampal neurons from both sexes. We find that both LASP1 and LASP2 are enriched in dendritic spines, and their knockdown impairs spine development and synapse formation. Furthermore, LASP2 exerts a distinct role in dendritic arbor and dendritic spine stabilization. Importantly, the actin-binding N-terminal LIM domain and nebulin repeats of LASP2 are required for spine stability and dendritic arbor complexity. These findings identify LASP1 and LASP2 as novel regulators of neuronal circuitry.SIGNIFICANCE STATEMENT Proper regulation of the actin cytoskeleton is essential for the structural stability of dendrites and dendritic spines. Consequently, the malformation of dendritic structures accompanies numerous neurologic disorders, such as schizophrenia and autism. Nebulin family members are best known for their role in regulating the stabilization and function of actin thin filaments in muscle. The two smallest family members, LASP1 and LASP2, are more structurally diverse and are expressed in a broader array of tissues. While both LASP1 and LASP2 are highly expressed in the brain, little is currently known about their function in the nervous system. In this study, we demonstrate the first evidence that LASP1 and LASP2 are involved in the formation and long-term maintenance of dendrites and dendritic spines.
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98
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Guerra MJ, González‐Jamett AM, Báez‐Matus X, Navarro‐Quezada N, Martínez AD, Neely A, Cárdenas AM. The Ca2+channel subunit CaVβ2a‐subunit down‐regulates voltage‐activated ion current densities by disrupting actin‐dependent traffic in chromaffin cells. J Neurochem 2019; 151:703-715. [DOI: 10.1111/jnc.14851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/01/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Affiliation(s)
- María J. Guerra
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Arlek M. González‐Jamett
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Ximena Báez‐Matus
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Nieves Navarro‐Quezada
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Agustín D. Martínez
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Alan Neely
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
| | - Ana M. Cárdenas
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencia de Valparaíso, Instituto de Neurociencia Universidad de Valparaíso Valparaíso Chile
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99
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Nie Y, Zhu J, Ramelot TA, Kennedy MA, Liu M, He T, Yang Y. Solution NMR structure and ligand identification of human Gas7 SH3 domain reveal a typical SH3 fold but a non-canonical ligand-binding mode. Biochem Biophys Res Commun 2019; 516:1190-1195. [PMID: 31296381 DOI: 10.1016/j.bbrc.2019.07.004] [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: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 10/26/2022]
Abstract
Growth arrest specific 7 (Gas7) protein is a cytoskeleton regulator playing a crucial role in neural cell development and function, and has been implicated in Alzheimer disease, schizophrenia and cancers. In human, three Gas7 isoforms can be expressed from a single Gas7 gene, while only the longest isoform, hGas7c, possesses an SH3 domain at the N-terminus. To date, the structure and function of hGas7 SH3 domain are still unclear. Here, we reported the solution NMR structure of hGas7 SH3 domain (hGas7-SH3), which displays a typical SH3 β-barrel fold comprising five β-strands and one 310-helix. Structural and sequence comparison showed that hGas7-SH3 shares high similarity with Abl SH3 domain, which binds to a high-affinity proline-rich peptide P41 in a canonical SH3-ligand binding mode through two hydrophobic pockets and a specificity site in the RT-loop. However, unlike Abl-SH3, only six residues in the RT-loop and two residues adjacent to but not in the two hydrophobic pockets of hGas7-SH3 showed significant chemical shift perturbations in NMR titrations, suggesting a low affinity and a non-canonical binding mode of hGas7-SH3 for P41. Furthermore, four peptides selected from phage-displayed libraries also bound weakly to hGas7-SH3, and the binding region of hGas7-SH3 was mainly located in the RT-loop as well. The ligand identifications through structural similarity searching and peptide library screening in this study imply that although hGas7-SH3 adopts a typical SH3 fold, it probably possesses distinctive ligand-binding specificity.
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Affiliation(s)
- Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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100
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Abstract
Herpesviridae is a vast family of enveloped DNA viruses that includes eight distinct human pathogens, responsible for diseases that range from almost asymptomatic to severe and life-threatening. Epstein-Barr virus infects B-cells and epithelial cells, causing infectious mononucleosis, as well as a number of cancers. Epstein-Barr infection cannot be cured since neither vaccine nor antiviral drug treatments are available. All herpesviruses contain a linear double-stranded DNA genome, enclosed within an icosahedral capsid. Viral portal protein plays a key role in the procapsid assembly and DNA packaging. The portal is the entrance and exit pore for the viral genome, making it an attractive pharmacological target for the development of new antivirals. Here we present the atomic structure of the portal protein of Epstein-Barr virus, solved by cryo-electron microscopy at 3.5 Å resolution. The detailed architecture of this protein suggests that it plays a functional role in DNA retention during packaging. The Epstein-Barr virus (EBV) is a dangerous human pathogen responsible for mononucleosis and several types of cancers. Here the authors describe a high-resolution atomic structure of the EBV portal, which serves as the entrance and exit pore for the viral genome and is a potential pharmacological target for the development of antivirals.
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