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Russell Lewis B, Uddin MR, Moniruzzaman M, Kuo KM, Higgins AJ, Shah LMN, Sobott F, Parks JM, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein. Nat Commun 2023; 14:3900. [PMID: 37463890 PMCID: PMC10354078 DOI: 10.1038/s41467-023-39615-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli, AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Muhammad R Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Katie M Kuo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA
| | - Anna J Higgins
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Laila M N Shah
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Frank Sobott
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Jerry M Parks
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - James C Gumbart
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, GA, 30332, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK.
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2
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Obrador E, Jihad-Jebbar A, Salvador-Palmer R, López-Blanch R, Oriol-Caballo M, Moreno-Murciano MP, Navarro EA, Cibrian R, Estrela JM. Externally Applied Electromagnetic Fields and Hyperthermia Irreversibly Damage Cancer Cells. Cancers (Basel) 2023; 15:3413. [PMID: 37444524 DOI: 10.3390/cancers15133413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/13/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
At present, the applications and efficacy of non-ionizing radiations (NIR) in oncotherapy are limited. In terms of potential combinations, the use of biocompatible magnetic nanoparticles as heat mediators has been extensively investigated. Nevertheless, developing more efficient heat nanomediators that may exhibit high specific absorption rates is still an unsolved problem. Our aim was to investigate if externally applied magnetic fields and a heat-inducing NIR affect tumor cell viability. To this end, under in vitro conditions, different human cancer cells (A2058 melanoma, AsPC1 pancreas carcinoma, MDA-MB-231 breast carcinoma) were treated with the combination of electromagnetic fields (EMFs, using solenoids) and hyperthermia (HT, using a thermostated bath). The effect of NIR was also studied in combination with standard chemotherapy and targeted therapy. An experimental device combining EMFs and high-intensity focused ultrasounds (HIFU)-induced HT was tested in vivo. EMFs (25 µT, 4 h) or HT (52 °C, 40 min) showed a limited effect on cancer cell viability in vitro. However, their combination decreased viability to approximately 16%, 50%, and 21% of control values in A2058, AsPC1, and MDA-MB-231 cells, respectively. Increased lysosomal permeability, release of cathepsins into the cytosol, and mitochondria-dependent activation of cell death are the underlying mechanisms. Cancer cells could be completely eliminated by combining EMFs, HT, and standard chemotherapy or EMFs, HT, and anti-Hsp70-targeted therapy. As a proof of concept, in vivo experiments performed in AsPC1 xenografts showed that a combination of EMFs, HIFU-induced HT, standard chemotherapy, and a lysosomal permeabilizer induces a complete cancer regression.
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Affiliation(s)
- Elena Obrador
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Scientia BioTech, 46002 Valencia, Spain
| | - Ali Jihad-Jebbar
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
| | - Rosario Salvador-Palmer
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
| | - Rafael López-Blanch
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Scientia BioTech, 46002 Valencia, Spain
| | - María Oriol-Caballo
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Scientia BioTech, 46002 Valencia, Spain
| | | | - Enrique A Navarro
- Scientia BioTech, 46002 Valencia, Spain
- Department of Computer Sciences, Higher Technical School of Engineering, 46100 Burjassot, Spain
- IRTIC Institute, University of Valencia, 46980 Paterna, Spain
| | - Rosa Cibrian
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Scientia BioTech, 46002 Valencia, Spain
| | - José M Estrela
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain
- Scientia BioTech, 46002 Valencia, Spain
- Department of Physiology, Faculty of Pharmacy, University of Valencia, 46100 Burjassot, Spain
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Hammerschmid D, Calvaresi V, Bailey C, Russell Lewis B, Politis A, Morris M, Denbigh L, Anderson M, Reading E. Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies. Anal Chem 2023; 95:3002-3011. [PMID: 36706021 PMCID: PMC9909672 DOI: 10.1021/acs.analchem.2c04876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein-lipid nanodisc─both empty and loaded with the ∼115 kDa transmembrane protein AcrB─proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO2-coated and TiO2 beads and describe how solution conditions can be optimized to maximize not only the performance of our online but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even native cell membranes.
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Affiliation(s)
- Dietmar Hammerschmid
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Valeria Calvaresi
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Chloe Bailey
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | | | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Laetitia Denbigh
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Eamonn Reading
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
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4
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Kalaninová Z, Fojtík L, Chmelík J, Novák P, Volný M, Man P. Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2023; 2718:303-334. [PMID: 37665467 DOI: 10.1007/978-1-0716-3457-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydrogen/deuterium exchange (HDX) followed by mass spectrometry detection (MS) provides a fast, reliable, and detailed solution for the assessment of a protein structure. It has been widely recognized as an indispensable tool and already approved by several regulatory agencies as a structural technique for the validation of protein biopharmaceuticals, including antibody-based drugs. Antibodies are of a key importance in life and medical sciences but considered to be challenging analytical targets because of their compact structure stabilized by disulfide bonds and due to the presence of glycosylation. Despite these difficulties, there are already numerous excellent studies describing MS-based antibody structure characterization. In this chapter, we describe a universal HDX-MS workflow. Deeper attention is paid to sample handling, optimization procedures, and feasibility stages, as these elements of the HDX experiment are crucial for obtaining reliable detailed and spatially well-resolved information.
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Affiliation(s)
- Zuzana Kalaninová
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Fojtík
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Novák
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Michael Volný
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.
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