1
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Volpato A, Ollech D, Alvelid J, Damenti M, Müller B, York AG, Ingaramo M, Testa I. Extending fluorescence anisotropy to large complexes using reversibly switchable proteins. Nat Biotechnol 2023; 41:552-559. [PMID: 36217028 PMCID: PMC10110461 DOI: 10.1038/s41587-022-01489-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022]
Abstract
The formation of macromolecular complexes can be measured by detection of changes in rotational mobility using time-resolved fluorescence anisotropy. However, this method is limited to relatively small molecules (~0.1-30 kDa), excluding the majority of the human proteome and its complexes. We describe selective time-resolved anisotropy with reversibly switchable states (STARSS), which overcomes this limitation and extends the observable mass range by more than three orders of magnitude. STARSS is based on long-lived reversible molecular transitions of switchable fluorescent proteins to resolve the relatively slow rotational diffusivity of large complexes. We used STARSS to probe the rotational mobility of several molecular complexes in cells, including chromatin, the retroviral Gag lattice and activity-regulated cytoskeleton-associated protein oligomers. Because STARSS can probe arbitrarily large structures, it is generally applicable to the entire human proteome.
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Affiliation(s)
- Andrea Volpato
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dirk Ollech
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martina Damenti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Centre for Integrative Infectious Disease Research, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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2
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Pepanian A, Sommerfeld P, Kasprzyk R, Kühl T, Binbay FA, Hauser C, Löser R, Wodtke R, Bednarczyk M, Chrominski M, Kowalska J, Jemielity J, Imhof D, Pietsch M. Fluorescence Anisotropy Assay with Guanine Nucleotides Provides Access to Functional Analysis of Gαi1 Proteins. Anal Chem 2022; 94:14410-14418. [PMID: 36206384 DOI: 10.1021/acs.analchem.2c03176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gα proteins as part of heterotrimeric G proteins are molecular switches essential for G protein-coupled receptor- mediated intracellular signaling. The role of the Gα subunits has been examined for decades with various guanine nucleotides to elucidate the activation mechanism and Gα protein-dependent signal transduction. Several approaches describe fluorescent ligands mimicking the GTP function, yet lack the efficient estimation of the proteins' GTP binding activity and the fraction of active protein. Herein, we report the development of a reliable fluorescence anisotropy-based method to determine the affinity of ligands at the GTP-binding site and to quantify the fraction of active Gαi1 protein. An advanced bacterial expression protocol was applied to produce active human Gαi1 protein, whose GTP binding capability was determined with novel fluorescently labeled guanine nucleotides acting as high-affinity Gαi1 binders compared to the commonly used BODIPY FL GTPγS. This study thus contributes a new method for future investigations of the characterization of Gαi and other Gα protein subunits, exploring their corresponding signal transduction systems and potential for biomedical applications.
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Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Paul Sommerfeld
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - F Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Christoph Hauser
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Reik Löser
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Robert Wodtke
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.,Division of Biophysics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Joanna Kowalska
- Division of Biophysics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
| | - Markus Pietsch
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
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3
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Pérez-Juárez J, Tapia-Vieyra JV, Gutiérrez-Magdaleno G, Sánchez-Puig N. Altered Conformational Landscape upon Sensing Guanine Nucleotides in a Disease Mutant of Elongation Factor-like 1 (EFL1) GTPase. Biomolecules 2022; 12:biom12081141. [PMID: 36009035 PMCID: PMC9405973 DOI: 10.3390/biom12081141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
The final maturation step of the 60S ribosomal subunit requires the release of eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) to enter the pool of mature ribosomes capable of engaging in translation. This process is mediated by the concerted action of the Elongation Factor-like 1 (human EFL1, yeast Efl1) GTPase and its effector, the Shwachman-Bodian-Diamond syndrome protein (human SBDS, yeast Sdo1). Mutations in these proteins prevent the release of eIF6 and cause a disease known as Shwachman–Diamond Syndrome (SDS). While some mutations in EFL1 or SBDS result in insufficient proteins to meet the cell production of mature large ribosomal subunits, others do not affect the expression levels with unclear molecular defects. We studied the functional consequences of one such mutation using Saccharomyces cerevisiae Efl1 R1086Q, equivalent to human EFL1 R1095Q described in SDS patients. We characterised the enzyme kinetics and energetic basis outlining the recognition of this mutant to guanine nucleotides and Sdo1, and their interplay in solution. From our data, we propose a model where the conformational change in Efl1 depends on a long-distance network of interactions that are disrupted in mutant R1086Q, whereby Sdo1 and the guanine nucleotides no longer elicit the conformational changes previously described in the wild-type protein. These findings point to the molecular malfunction of an EFL1 mutant and its possible impact on SDS pathology.
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Affiliation(s)
- Jesús Pérez-Juárez
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
| | - Juana Virginia Tapia-Vieyra
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
| | - Gabriel Gutiérrez-Magdaleno
- División de Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpan Avenida Vasco de Quiroga 4871, Ciudad de Mexico 05348, Mexico
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Correspondence: ; Tel.: +52-55-56224468
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4
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Mayer G, Shpilt Z, Kowalski H, Tshuva EY, Friedler A. Targeting Protein Interaction Hotspots Using Structured and Disordered Chimeric Peptide Inhibitors. ACS Chem Biol 2022; 17:1811-1823. [PMID: 35758642 DOI: 10.1021/acschembio.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The main challenge in inhibiting protein-protein interactions (PPI) for therapeutic purposes is designing molecules that bind specifically to the interaction hotspots. Adding to the complexity, such hotspots can be within both structured and disordered interaction interfaces. To address this, we present a strategy for inhibiting the structured and disordered hotspots of interactions using chimeric peptides that contain both structured and disordered parts. The chimeric peptides we developed are comprised of a cyclic structured part and a disordered part, which target both disordered and structured hotspots. We demonstrate our approach by developing peptide inhibitors for the interactions of the antiapoptotic iASPP protein. First, we developed a structured, α-helical stapled peptide inhibitor, derived from the N-terminal domain of MDM2. The peptide bound two hotspots on iASPP at the low micromolar range and had a cytotoxic effect on A2780 cancer cells with a half-maximal inhibitory concentration (IC50) value of 10 ± 1 μM. We then developed chimeric peptides comprising the structured stapled helical peptide and the disordered p53-derived LinkTer peptide that we previously showed to inhibit iASPP by targeting its disordered RT loop. The chimeric peptide targeted both structured and disordered domains in iASPP with higher affinity compared to the individual structured and disordered peptides and caused cancer cell death. Our strategy overcomes the inherent difficulty in inhibiting the interactions of proteins that possess structured and disordered regions. It does so by using chimeric peptides derived from different interaction partners that together target a much wider interface covering both the structured and disordered domains. This paves the way for developing such inhibitors for therapeutic purposes.
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Affiliation(s)
- Guy Mayer
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zohar Shpilt
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hadar Kowalski
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Edit Y Tshuva
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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5
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Solid Magnetoliposomes as Multi-Stimuli-Responsive Systems for Controlled Release of Doxorubicin: Assessment of Lipid Formulations. Biomedicines 2022; 10:biomedicines10051207. [PMID: 35625942 PMCID: PMC9138220 DOI: 10.3390/biomedicines10051207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/12/2022] Open
Abstract
Stimuli-responsive liposomes are a class of nanocarriers whose drug release occurs, preferentially, when exposed to a specific biological environment, to an external stimulus, or both. This work is focused on the design of solid magnetoliposomes (SMLs) as lipid-based nanosystems aiming to obtain multi-stimuli-responsive vesicles for doxorubicin (DOX) controlled release in pathological areas under the action of thermal, magnetic, and pH stimuli. The effect of lipid combinations on structural, colloidal stability, and thermodynamic parameters were evaluated. The results confirmed the reproducibility for SMLs synthesis based on nine lipid formulations (combining DPPC, DSPC, CHEMS, DOPE and/or DSPE-PEG), with structural and colloidal properties suitable for biological applications. A loss of stability and thermosensitivity was observed for formulations containing dioleoylphosphatidylethanolamine (DOPE) lipid. SMLs PEGylation is an essential step to enhance both their long-term storage stability and stealth properties. DOX encapsulation (encapsulation efficiency ranging between 87% and 96%) in the bilayers lowered its pKa, which favors the displacement of DOX from the acyl chains to the surface when changing from alkaline to acidic pH. The release profiles demonstrated a preferential release at acidic pH, more pronounced under mimetic mild-hyperthermia conditions (42 °C). Release kinetics varied with the lipid formulation, generally demonstrating hyperthermia temperatures and acidic pH as determining factors in DOX release; PEGylation was shown to act as a diffusion barrier on the SMLs surface. The integrated assessment and characterization of SMLs allows tuning lipid formulations that best respond to the needs for specific controlled release profiles of stimuli-responsive nanosystems as a multi-functional approach to cancer targeting and therapy.
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6
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Bielak K, Hołubowicz R, Zoglowek A, Żak A, Kędzierski P, Ożyhar A, Dobryszycki P. N'-terminal- and Ca 2+-induced stabilization of high-order oligomers of full-length Danio rerio and Homo sapiens otolin-1. Int J Biol Macromol 2022; 209:1032-1047. [PMID: 35447266 DOI: 10.1016/j.ijbiomac.2022.04.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023]
Abstract
Otolin-1 is a C1q family member and a major component of the organic matrix of fish otoliths and human otoconia. To date, the protein molecular properties have not been characterized. In this work, we describe biochemical characterization and comparative studies on saccular-specific otolin-1 derived from Danio rerio and Homo sapiens. Due to the low abundance of proteins in the otoconial matrix, we developed a production and purification method for both recombinant homologues of otolin-1. Danio rerio and Homo sapiens otolin-1 forms higher-order oligomers that can be partially disrupted under reducing conditions. The presence of Ca2+ stabilizes the oligomers and significantly increases the thermal stability of the proteins. Despite the high sequence coverage, the oligomerization of Danio rerio otolin-1 is more affected by the reducing conditions and presence of Ca2+ than the human homologue. The results show differences in molecular behaviour, which may be reflected in Danio rerio and Homo sapiens otolin-1 role in otolith and otoconia formation.
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Affiliation(s)
- Klaudia Bielak
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Rafał Hołubowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Anna Zoglowek
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Andrzej Żak
- Electron Microscopy Laboratory, Faculty of Mechanical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Paweł Kędzierski
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Andrzej Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland.
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7
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Stidham S, Villareal V, Chellappa V, Yoder L, Alley O, Shreffler W, Spergel J, Fleischer D, Sampson H, Gilboa-Geffen A. Aptamer based point of care diagnostic for the detection of food allergens. Sci Rep 2022; 12:1303. [PMID: 35079047 PMCID: PMC8789827 DOI: 10.1038/s41598-022-05265-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Aptamers, due to their small size, strong target affinity, and ease of chemical modification, are ideally suited for molecular detection technologies. Here, we describe successful use of aptamer technology in a consumer device for the detection of peanut antigen in food. The novel aptamer-based protein detection method is robust across a wide variety of food matrices and sensitive to peanut protein at concentrations as low as 12.5 ppm (37.5 µg peanut protein in the sample). Integration of the assay into a sensitive, stable, and consumer friendly portable device will empower users to easily and quickly assess the presence of peanut allergens in foods before eating. With many food reactions occurring outside the home, the type of technology described here has significant potential to improve lives for children and families.
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8
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Jain P, Motosuke M. Fluorescence Anisotropy Studies on Bodipy (Pyrromethene 546) Dye as a Novel Thermal Probe. J Fluoresc 2022; 32:737-743. [DOI: 10.1007/s10895-021-02868-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022]
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9
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Hadeler A, Saikia A, Zacharias M, Springer S. Rapid peptide exchange on MHC class I by small molecules elucidates dynamics of bound peptide. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:167-174. [PMID: 36042776 PMCID: PMC9420430 DOI: 10.1016/j.crimmu.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022] Open
Abstract
Complexes of peptides with recombinant major histocompatibility complex class I molecules (rpMHCs) are an important tool for T cell detection, isolation, and activation in cancer immunotherapy. The rapid preparation of rpMHCs is aided by peptide exchange, for which several technologies exist. Here, we show peptide exchange with small-molecule alcohols and demonstrate that they accelerate the dissociation of pre-bound peptides, creating a novel method for rapid production of rpMHCs and increasing the understanding of the conformational flexibility of the MHC-bound peptides. Small alcohols can catalyze peptide exchange on MHC-I. C-terminal peptide binding plays an important role in ethanol mediated exchange. MHC-I ethanol peptide exchange is allotype dependent.
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10
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Méndez-Godoy A, García-Montalvo D, Martínez-Castilla LP, Sánchez-Puig N. Evolutionary and functional relationships in the ribosome biogenesis SBDS and EFL1 protein families. Mol Genet Genomics 2021; 296:1263-1278. [PMID: 34453201 DOI: 10.1007/s00438-021-01814-w] [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: 03/17/2021] [Accepted: 08/15/2021] [Indexed: 11/25/2022]
Abstract
Nascent ribosomal 60S subunits undergo the last maturation steps in the cytoplasm. The last one involves removing the anti-association factor eIF6 from the 60S ribosomal surface by the joint action of the Elongation Factor-like 1 (EFL1) GTPase and the SBDS protein. Herein, we studied the evolutionary relationship of the EFL1 and EF-2 protein families and the functional conservation within EFL1 orthologues. Phylogenetic analysis demonstrated that the EFL1 proteins are exclusive of eukaryotes and share an evolutionary origin with the EF-2 and EF-G protein families. EFL1 proteins originated by gene duplication from the EF-2 proteins and specialized in ribosome maturation while the latter retained their function in translation. Some organisms have more than one EFL1 protein resulting from alternative splicing, while others are encoded in different genes originated by gene duplication. However, the function of these alternative EFL1 proteins is still unknown. We performed GTPase activity and complementation assays to study the functional conservation of EFL1 homologs alone and together with their SBDS counterparts. None of the orthologues or cross-species combinations could replace the function of the corresponding yeast EFL1•SBDS binomial. The complementation of SBDS interspecies chimeras indicates that domain 2 is vital for its function together with EFL1 and the 60S subunit. The results suggest a functional species-specificity and possible co-evolution between EFL1, SBDS, and the 60S ribosomal subunit. These findings set the basis for further studies directed to understand the molecular evolution of these proteins and their impact on ribosome biogenesis and disease.
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Affiliation(s)
- Alfonso Méndez-Godoy
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México.,Unit of Biochemistry, Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Daniel García-Montalvo
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México
| | - León P Martínez-Castilla
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México, 04510, México.
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11
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Purohit V, Wang L, Yang H, Li J, Ney GM, Gumkowski ER, Vaidya AJ, Wang A, Bhardwaj A, Zhao E, Dolgalev I, Zamperone A, Abel EV, Magliano MPD, Crawford HC, Diolaiti D, Papagiannakopoulos TY, Lyssiotis CA, Simeone DM. ATDC binds to KEAP1 to drive NRF2-mediated tumorigenesis and chemoresistance in pancreatic cancer. Genes Dev 2021; 35:218-233. [PMID: 33446568 PMCID: PMC7849366 DOI: 10.1101/gad.344184.120] [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: 08/25/2020] [Accepted: 11/25/2020] [Indexed: 01/04/2023]
Abstract
Pancreatic ductal adenocarcinoma is a lethal disease characterized by late diagnosis, propensity for early metastasis and resistance to chemotherapy. Little is known about the mechanisms that drive innate therapeutic resistance in pancreatic cancer. The ataxia-telangiectasia group D-associated gene (ATDC) is overexpressed in pancreatic cancer and promotes tumor growth and metastasis. Our study reveals that increased ATDC levels protect cancer cells from reactive oxygen species (ROS) via stabilization of nuclear factor erythroid 2-related factor 2 (NRF2). Mechanistically, ATDC binds to Kelch-like ECH-associated protein 1 (KEAP1), the principal regulator of NRF2 degradation, and thereby prevents degradation of NRF2 resulting in activation of a NRF2-dependent transcriptional program, reduced intracellular ROS and enhanced chemoresistance. Our findings define a novel role of ATDC in regulating redox balance and chemotherapeutic resistance by modulating NRF2 activity.
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Affiliation(s)
- Vinee Purohit
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Lidong Wang
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Huibin Yang
- Department of Radiation Oncology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Jiufeng Li
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Gina M Ney
- Department of Pediatric Oncology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Erica R Gumkowski
- Department of Molecular and Integrative Physiology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Akash J Vaidya
- Department of Molecular and Integrative Physiology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Annie Wang
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
- Department of Surgery, New York University, New York, New York 10016, USA
| | - Amit Bhardwaj
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Ende Zhao
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Igor Dolgalev
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Andrea Zamperone
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Ethan V Abel
- Department of Molecular and Integrative Physiology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Marina Pasca Di Magliano
- Department of Surgery, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
- Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Daniel Diolaiti
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
| | - Thales Y Papagiannakopoulos
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
- Department of Pathology, New York University, New York, New York 10016, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
- Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Diane M Simeone
- Perlmutter Cancer Center, New York University, New York, New York 10016, USA
- Department of Surgery, New York University, New York, New York 10016, USA
- Department of Pathology, New York University, New York, New York 10016, USA
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12
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Zhou X, Brown BA, Siegel AP, El Masry MS, Zeng X, Song W, Das A, Khandelwal P, Clark A, Singh K, Guda PR, Gorain M, Timsina L, Xuan Y, Jacobson SC, Novotny MV, Roy S, Agarwal M, Lee RJ, Sen CK, Clemmer DE, Ghatak S. Exosome-Mediated Crosstalk between Keratinocytes and Macrophages in Cutaneous Wound Healing. ACS NANO 2020; 14:12732-12748. [PMID: 32931251 PMCID: PMC7970718 DOI: 10.1021/acsnano.0c03064] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bidirectional cell-cell communication involving exosome-borne cargo such as miRNA has emerged as a critical mechanism for wound healing. Unlike other shedding vesicles, exosomes selectively package miRNA by SUMOylation of heterogeneous nuclear ribonucleoproteinA2B1 (hnRNPA2B1). In this work, we elucidate the significance of exosome in keratinocyte-macrophage crosstalk following injury. Keratinocyte-derived exosomes were genetically labeled with GFP-reporter (Exoκ-GFP) using tissue nanotransfection (TNT), and they were isolated from dorsal murine skin and wound-edge tissue by affinity selection using magnetic beads. Surface N-glycans of Exoκ-GFP were also characterized. Unlike skin exosome, wound-edge Exoκ-GFP demonstrated characteristic N-glycan ions with abundance of low-base-pair RNA and was selectively engulfed by wound macrophages (ωmϕ) in granulation tissue. In vitro addition of wound-edge Exoκ-GFP to proinflammatory ωmϕ resulted in conversion to a proresolution phenotype. To selectively inhibit miRNA packaging within Exoκ-GFPin vivo, pH-responsive keratinocyte-targeted siRNA-hnRNPA2B1 functionalized lipid nanoparticles (TLNPκ) were designed with 94.3% encapsulation efficiency. Application of TLNPκ/si-hnRNPA2B1 to the murine dorsal wound-edge significantly inhibited expression of hnRNPA2B1 by 80% in epidermis compared to the TLNPκ/si-control group. Although no significant difference in wound closure or re-epithelialization was observed, the TLNPκ/si-hnRNPA2B1 treated group showed a significant increase in ωmϕ displaying proinflammatory markers in the granulation tissue at day 10 post-wounding compared to the TLNPκ/si-control group. Furthermore, TLNPκ/si-hnRNPA2B1 treated mice showed impaired barrier function with diminished expression of epithelial junctional proteins, lending credence to the notion that unresolved inflammation results in leaky skin. This work provides insight wherein Exoκ-GFP is recognized as a major contributor that regulates macrophage trafficking and epithelial barrier properties postinjury.
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Affiliation(s)
- Xiaoju Zhou
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Brooke A. Brown
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Amanda P. Siegel
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Integrated Nanosystems Development Institute, Indiana University–Purdue University Indianapolis, IN, 46202, USA
| | - Mohamed S. El Masry
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Plastic and Reconstructive Surgery, Zagazig University, 44519, Egypt
| | - Xuyao Zeng
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Woran Song
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Amitava Das
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Puneet Khandelwal
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Andrew Clark
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kanhaiya Singh
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Poornachander R. Guda
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mahadeo Gorain
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Lava Timsina
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Outcomes Research, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yi Xuan
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mangilal Agarwal
- Integrated Nanosystems Development Institute, Indiana University–Purdue University Indianapolis, IN, 46202, USA
| | - Robert J. Lee
- Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
| | - Chandan K. Sen
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Corresponding Authors: Subhadip Ghatak, PhD, Tel: 317-278-2711; , David E. Clemmer, PhD, Tel: 812-855-8259;
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Corresponding Authors: Subhadip Ghatak, PhD, Tel: 317-278-2711; , David E. Clemmer, PhD, Tel: 812-855-8259;
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Delre P, Alberga D, Gijsbers A, Sánchez-Puig N, Nicolotti O, Saviano M, Siliqi D, Mangiatordi GF. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics. J Biomol Struct Dyn 2020; 38:5219-5229. [PMID: 31838967 DOI: 10.1080/07391102.2019.1704883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shwachman-Diamond Syndrome (SDS) is an autosomal recessive disorder whose patients present mutations in two ribosome assembly proteins, the Shwachman-Bodian-Diamond Syndrome protein (SBDS) and the Elongation Factor-Like 1 (EFL1). Due to the lack of knowledge of the molecular mechanisms responsible for SDS pathogenesis, current therapy is nonspecific and focuses only at alleviating the symptoms. Building on the recent observation that EFL1 single-point mutations clinically manifest as SDS-like phenotype, we carried out comparative Molecular Dynamics (MD) simulations on three mutants, T127A, M882K and R1095Q and wild type EFL1. As supported by small angle X-ray scattering experiments, the obtained data improve the static EFL1 model resulting from the Cryo-electron microscopy and clearly show that all the mutants experience a peculiar rotation, around the hinge region, of domain IV with respect to domains I and II leading to a different conformation respect to that of wild type protein. This study supports the notion that EFL1 function is governed by an allosteric mechanism involving the concerted action of GTPase domain (domain I) and the domain IV and can help point towards new approaches to SDS treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pietro Delre
- Dipartimento di Chimica, Università Degli Studi di Bari "Aldo Moro", Bari, Italy.,Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
| | | | - Abril Gijsbers
- The Maastricht Multimodal Molecular Imaging Institute (M4I), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Nuria Sánchez-Puig
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze Del Farmaco, Università̀ Degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Michele Saviano
- Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
| | - Dritan Siliqi
- Consiglio Nazionale Delle Ricerche, Istituto di Cristallografia, Bari, Italy
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14
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Fluorescence Anisotropy Sensor Comprising a Dual Hollow-Core Antiresonant Fiber Polarization Beam Splitter. SENSORS 2020; 20:s20113321. [PMID: 32545205 PMCID: PMC7308924 DOI: 10.3390/s20113321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022]
Abstract
Fluorescence anisotropy imaging and sensing is a widely recognized method for studying molecular orientation and mobility. However, introducing this technique to in vivo systems is a challenging task, especially when one considers multiphoton excitation methods. Past two decades have brought a possible solution to this issue in the form of hollow-core antiresonant fibers (HC-ARFs). The continuous development of their fabrication technology has resulted in the appearance of more and more sophisticated structures. One of the most promising concepts concerns dual hollow-core antiresonant fibers (DHC-ARFs), which can be used to split and combine optical signals, effectively working as optical fiber couplers. In this paper, the design of a fluorescence anisotropy sensor based on a DHC-ARF structure is presented. The main purpose of the proposed DHC-ARF is multiphoton-excited fluorescence spectroscopy; however, other applications are also possible.
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Paul S, Hossain SS, M BD, Samanta A. Interactions between a Bioflavonoid and c-MYC Promoter G-Quadruplex DNA: Ensemble and Single-Molecule Investigations. J Phys Chem B 2019; 123:2022-2031. [DOI: 10.1021/acs.jpcb.9b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Bala Divya M
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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16
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Cooperative energetic effects elicited by the yeast Shwachman-Diamond syndrome protein (Sdo1) and guanine nucleotides modulate the complex conformational landscape of the elongation factor-like 1 (Efl1) GTPase. Biophys Chem 2019; 247:13-24. [PMID: 30780079 DOI: 10.1016/j.bpc.2019.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 12/13/2022]
Abstract
One of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (human EFL1, yeast Efl1) GTPase and the Shwachman-Diamond syndrome protein (human SBDS, yeast Sdo1) to release the eukaryotic translation initiation factor 6 (human eIF6, yeast Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes. However, the nature of such conformational changes or the mechanism by which they are prompted are still largely unknown. In previous studies, it has been established that this GTPase interacts with its cofactor in solution in an inverted orientation with respect to the binding mode derived from 60S ribosome subunit cryo-EM data. To shed new light on this conundrum, we characterized calorimetrically the energetic basis describing the recognition of Efl1 to GT(D)P, Sdo1 and their intercommunication in solution. A structural-based analysis of the binding signatures indicates that Efl1 has a large structural flexibility. The mutual effects of Sdo1 and nucleotides on Efl1 modulate in a very specific and robust way the complex conformational landscape of Efl1, resembling the behavior observed with other GTPases and their cofactors.
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17
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Gijsbers A, Montagut DC, Méndez-Godoy A, Altamura D, Saviano M, Siliqi D, Sánchez-Puig N. Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations. Int J Mol Sci 2018; 19:E4012. [PMID: 30545121 PMCID: PMC6321010 DOI: 10.3390/ijms19124012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
The Shwachman-Diamond Syndrome (SDS) is a disorder arising from mutations in the genes encoding for the Shwachman-Bodian-Diamond Syndrome (SBDS) protein and the GTPase known as Elongation Factor Like-1 (EFL1). Together, these proteins remove the anti-association factor eIF6 from the surface of the pre-60S ribosomal subunit to promote the formation of mature ribosomes. SBDS missense mutations can either destabilize the protein fold or affect surface epitopes. The molecular alterations resulting from the latter remain largely unknown, although some evidence suggest that binding to EFL1 may be affected. We further explored the effect of these SBDS mutations on the interaction with EFL1, and showed that all tested mutations disrupted the binding to EFL1. Binding was either severely weakened or almost abolished, depending on the assessed mutation. In higher eukaryotes, SBDS is essential for development, and lack of the protein results in early lethality. The existence of patients whose only source of SBDS consists of that with surface missense mutations highlights the importance of the interaction with EFL1 for their function. Additionally, we studied the interaction mechanism of the proteins in solution and demonstrated that binding consists of two independent and cooperative events, with domains 2⁻3 of SBDS directing the initial interaction with EFL1, followed by docking of domain 1. In solution, both proteins exhibited large flexibility and consisted of an ensemble of conformations, as demonstrated by Small Angle X-ray Scattering (SAXS) experiments.
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Affiliation(s)
- Abril Gijsbers
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Diana Carolina Montagut
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Alfonso Méndez-Godoy
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - Davide Altamura
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/O, 70126 Bari, Italy.
| | - Nuria Sánchez-Puig
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Ciudad de México 04510, Mexico.
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18
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Zhang X, Hu H. Investigating and characterizing the binding activity of the immobilized calmodulin to calmodulin-dependent protein kinase I binding domain with atomic force microscopy. Chem Cent J 2017; 11:128. [PMID: 29214517 PMCID: PMC5718999 DOI: 10.1186/s13065-017-0360-7] [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: 08/23/2017] [Accepted: 11/30/2017] [Indexed: 12/03/2022] Open
Abstract
Protein–protein interactions are responsible for many biological processes, and the study of how proteins undergo a conformational change induced by other proteins in the immobilized state can help us to understand a protein’s function and behavior, empower the current knowledge on molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. In this study, a bottom-up approach was utilized to fabricate micro/nanometer-scale protein patterns. One cysteine mutated calmodulin (CaM), as a model protein, was immobilized on thiol-terminated pattern surfaces. Atomic Force Microscopy (AFM) was then employed as a tool to investigate the interactions between CaM and CaM kinase I binding domain, and show that the immobilized CaM retains its activity to interact with its target protein. Our work demonstrate the potential of employing AFM to the research and assay works evolving surface-based protein–protein interactions biosensors, bioelectronics or drug screening.
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Affiliation(s)
- Xiaoning Zhang
- College of Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Hongmei Hu
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316021, China
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