1
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Tunçer Çağlayan S, Gurbanov R. Modulation of bacterial membranes and cellular macromolecules by dimethyl sulfoxide: A dose-dependent study providing novel insights. Int J Biol Macromol 2024; 267:131581. [PMID: 38615866 DOI: 10.1016/j.ijbiomac.2024.131581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Using Escherichia coli as a model, this manuscript delves into the intricate interactions between dimethyl sulfoxide (DMSO) and membranes, cellular macromolecules, and the effects on various aspects of bacterial physiology. Given DMSO's wide-ranging use as a solvent in microbiology, we investigate the impacts of both non-growth inhibitory (1.0 % and 2.5 % v/v) and slightly growth-inhibitory (5.0 % v/v) concentrations of DMSO. The results demonstrate that DMSO causes alterations in bacterial membrane potential, influences the electrochemical characteristics of the cell surface, and exerts substantial effects on the composition and structure of cellular biomolecules. Genome-wide gene expression data from DMSO-treated E. coli was used to further investigate and bolster the results. The findings of this study provide valuable insights into the complex relationship between DMSO and biological systems, with potential implications in drug delivery and cellular manipulation. However, it is essential to exercise caution when utilizing DMSO to enhance the solubility and delivery of bioactive compounds, as even at low concentrations, DMSO exerts non-inert effects on cellular macromolecules and processes.
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Affiliation(s)
- Sinem Tunçer Çağlayan
- Vocational School of Health Services, Department of Medical Services and Techniques, Bilecik Şeyh Edebali University, 11100 Bilecik, Turkey.
| | - Rafig Gurbanov
- Department of Bioengineering, Bilecik Şeyh Edebali University, 11100 Bilecik, Turkey; Central Research Laboratory, Bilecik Şeyh Edebali University, 11100 Bilecik, Turkey
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2
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Skjærvø Ø, Togle A, Sutton H, Han X, Rauniyar N. Dimethyl sulfoxide as a gas phase charge-reducing agent for the determination of PEGylated proteins' intact mass. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38685882 DOI: 10.1039/d4ay00660g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Determination of PEGylated proteins' intact mass by mass spectrometry is challenging due to the molecules' large size, excessive charges, and instrument limitations. Previous efforts have been reported. However, signal variability, ion coalescence, and a generally low degree of robustness have been observed. In this work, we have explored the capabilities of post-column infusion of dimethyl sulfoxide (DMSO) following reversed-phase liquid chromatography-mass spectrometry (RP-LCMS) to determine PEG-filgrastim' intact mass, and to characterize its PEG moiety. The method was optimized around reproducibility (six preparations, and three injection replicates) with an in-house prepared PEG-filgrastim standard. The method showed a mass accuracy of ≤1.2 Da. The average molecular weight (MWEO=483) was 40 147.9 Da. The number average molecular weight (Mn) and the weight average molecular weight (Mw) were observed to be 40 101.1 and 40 113.9 Da, respectively, both with an RSD of 0.03%. The molecular weight distribution of ethylene oxide (EO), the polydispersity index (PDI), was 1.0003 for all preparations with a minimum and maximum number of EO units of 448 ± 2 and 516 ± 2, respectively. The method was finally applied to commercially available Neulasta® lots where the Mn and Mw were 39 995.8 and 40 008.8 Da, respectively, both with an RSD of 0.1%. The minimum and maximum EO units across the lots were observed to be 444.5 ± 1.5 and 514 ± 3, respectively. The PDI for all Neulasta® lots was 1.0003. This study provides an insightful characterization of Neulasta® and describes a robust LC-MS methodology for the characterization of the PEGylated proteins.
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Affiliation(s)
- Øystein Skjærvø
- Tanvex BioPharma USA, Inc., 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Alyssa Togle
- Tanvex BioPharma USA, Inc., 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Haley Sutton
- Tanvex BioPharma USA, Inc., 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Xuemei Han
- Tanvex BioPharma USA, Inc., 10394 Pacific Center Ct, San Diego, CA 92121, USA.
| | - Navin Rauniyar
- Tanvex BioPharma USA, Inc., 10394 Pacific Center Ct, San Diego, CA 92121, USA.
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3
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Sirotinskaya V, Bar Dolev M, Yashunsky V, Bahari L, Braslavsky I. Extended Temperature Range of the Ice-Binding Protein Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7395-7404. [PMID: 38527127 PMCID: PMC11008235 DOI: 10.1021/acs.langmuir.3c03710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Ice-binding proteins (IBPs) are expressed in various organisms for several functions, such as protecting them from freezing and freeze injuries. Via adsorption on ice surfaces, IBPs depress ice growth and recrystallization and affect nucleation and ice shaping. IBPs have shown promise in mitigating ice growth under moderate supercooling conditions, but their functionality under cryogenic conditions has been less explored. In this study, we investigate the impact of two types of antifreeze proteins (AFPs): type III AFP from fish and a hyperactive AFP from an insect, the Tenebrio molitor AFP, in vitrified dimethylsulfoxide (DMSO) solutions. We report that these AFPs depress devitrification at -80 °C. Furthermore, in cases where devitrification does occur, AFPs depress ice recrystallization during the warming stage. The data directly demonstrate that AFPs are active at temperatures below the regime of homogeneous nucleation. This research paves the way for exploring AFPs as potential enhancers of cryopreservation techniques, minimizing ice-growth-related damage, and promoting advancements in this vital field.
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Affiliation(s)
- Vera Sirotinskaya
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Maya Bar Dolev
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Faculty
of Biotechnology and Food Engineering, Technion, Haifa 3200003, Israel
| | - Victor Yashunsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
- The
Swiss Institute for Dryland Environmental and Energy Research, Ben Gurion University, Beer-Sheva 84105, Israel
| | - Liat Bahari
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ido Braslavsky
- Institute
of Biochemistry, Food Science, and Nutrition, Robert H. Smith Faculty
of Agriculture, Food and Environment, The
Hebrew University of Jerusalem, Rehovot 7610001, Israel
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4
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González-Gamboa I, Caparco AA, McCaskill J, Fuenlabrada-Velázquez P, Hays SS, Jin Z, Jokerst JV, Pokorski JK, Steinmetz NF. Inter-coat protein loading of active ingredients into Tobacco mild green mosaic virus through partial dissociation and reassembly of the virion. Sci Rep 2024; 14:7168. [PMID: 38532056 DOI: 10.1038/s41598-024-57200-0] [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: 08/01/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Chemical pesticide delivery is a fundamental aspect of agriculture. However, the extensive use of pesticides severely endangers the ecosystem because they accumulate on crops, in soil, as well as in drinking and groundwater. New frontiers in nano-engineering have opened the door for precision agriculture. We introduced Tobacco mild green mosaic virus (TMGMV) as a viable delivery platform with a high aspect ratio and favorable soil mobility. In this work, we assess the use of TMGMV as a chemical nanocarrier for agriculturally relevant cargo. While plant viruses are usually portrayed as rigid/solid structures, these are "dynamic materials," and they "breathe" in solution in response to careful adjustment of pH or bathing media [e.g., addition of solvent such as dimethyl sulfoxide (DMSO)]. Through this process, coat proteins (CPs) partially dissociate leading to swelling of the nucleoprotein complexes-allowing for the infusion of active ingredients (AI), such as pesticides [e.g., fluopyram (FLP), clothianidin (CTD), rifampicin (RIF), and ivermectin (IVM)] into the macromolecular structure. We developed a "breathing" method that facilitates inter-coat protein cargo loading, resulting in up to ~ 1000 AIs per virion. This is of significance since in the agricultural setting, there is a need to develop nanoparticle delivery strategies where the AI is not chemically altered, consequently avoiding the need for regulatory and registration processes of new compounds. This work highlights the potential of TMGMV as a pesticide nanocarrier in precision farming applications; the developed methods likely would be applicable to other protein-based nanoparticle systems.
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Affiliation(s)
- Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA
| | - Justin McCaskill
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Samuel S Hays
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA.
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Center for Engineering in Cancer, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA.
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5
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Feoli A, Sarno G, Castellano S, Sbardella G. DMSO-Related Effects on Ligand-Binding Properties of Lysine Methyltransferases G9a and SETD8. Chembiochem 2024; 25:e202300809. [PMID: 38205880 DOI: 10.1002/cbic.202300809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/12/2024]
Abstract
Being the standard solvent for preparing stock solutions of compounds for drug discovery, DMSO is always present in assay buffers in concentrations ranging from 0.1 % to 5 % (v/v). Even at the lowest concentrations, DMSO-containing solutions can have significant effects on individual proteins and possible pitfalls cannot be eliminated. Herein, we used two protein systems, the lysine methyltransferases G9a/KMT1 C and SETD8/KMT5 A, to study the effects of DMSO on protein stability and on the binding of the corresponding inhibitors, using different biophysical methods such as nano Differential Scanning Fluorimetry (nanoDSF), Differential Scanning Fluorimetry (DSF), microscale thermophoresis (MST), and surface plasmon resonance (SPR), all widely used in drug discovery screening campaigns. We demonstrated that the effects of DMSO are protein- and technique-dependent and cannot be predicted or extrapolated on the basis of previous studies using different proteins and/or different assays. Moreover, we showed that the application of orthogonal biophysical methods can lead to different binding affinity data, thus confirming the importance of using at least two different orthogonal assays in screening campaigns. This variability should be taken into account in the selection and characterization of hit compounds, in order to avoid data misinterpretation.
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Affiliation(s)
- Alessandra Feoli
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
| | - Giuliana Sarno
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
- PhD Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, I-84084, Fisciano, SA, Italy
| | - Sabrina Castellano
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
| | - Gianluca Sbardella
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
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6
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Bandak AF, Blower TR, Nitiss KC, Shah V, Nitiss J, Berger J. Using energy to go downhill-a genoprotective role for ATPase activity in DNA topoisomerase II. Nucleic Acids Res 2024; 52:1313-1324. [PMID: 38038260 PMCID: PMC10853770 DOI: 10.1093/nar/gkad1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023] Open
Abstract
Type II topoisomerases effect topological changes in DNA by cutting a single duplex, passing a second duplex through the break, and resealing the broken strand in an ATP-coupled reaction cycle. Curiously, most type II topoisomerases (topos II, IV and VI) catalyze DNA transformations that are energetically favorable, such as the removal of superhelical strain; why ATP is required for such reactions is unknown. Here, using human topoisomerase IIβ (hTOP2β) as a model, we show that the ATPase domains of the enzyme are not required for DNA strand passage, but that their loss elevates the enzyme's propensity for DNA damage. The unstructured C-terminal domains (CTDs) of hTOP2β strongly potentiate strand passage activity in ATPase-less enzymes, as do cleavage-prone mutations that confer hypersensitivity to the chemotherapeutic agent etoposide. The presence of either the CTD or the mutations lead ATPase-less enzymes to promote even greater levels of DNA cleavage in vitro, as well as in vivo. By contrast, aberrant cleavage phenotypes of these topo II variants is significantly repressed when the ATPase domains are present. Our findings are consistent with the proposal that type II topoisomerases acquired ATPase function to maintain high levels of catalytic activity while minimizing inappropriate DNA damage.
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Affiliation(s)
- Afif F Bandak
- Johns Hopkins University School of Medicine, Department of Biophysics and Biophysical Chemistry, Baltimore, MD 21205, USA
| | - Tim R Blower
- Johns Hopkins University School of Medicine, Department of Biophysics and Biophysical Chemistry, Baltimore, MD 21205, USA
| | - Karin C Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, 1601 Parkview Avenue, Rockford, IL 61107, USA
- Biomedical Sciences Department, University of Illinois College of Medicine, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Viraj Shah
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, 1601 Parkview Avenue, Rockford, IL 61107, USA
- Biomedical Sciences Department, University of Illinois College of Medicine, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - John L Nitiss
- Pharmaceutical Sciences Department, University of Illinois College of Pharmacy, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - James M Berger
- Johns Hopkins University School of Medicine, Department of Biophysics and Biophysical Chemistry, Baltimore, MD 21205, USA
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7
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Edwards AN, Blue AJ, Conforti JM, Cordes MS, Trakselis MA, Gallagher ES. Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity. Anal Bioanal Chem 2023; 415:6201-6212. [PMID: 37542535 DOI: 10.1007/s00216-023-04891-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
The biological role of the bacterial chloramphenicol (Chl)-resistance enzyme, chloramphenicol acetyltransferase (CAT), has seen renewed interest due to the resurgent use of Chl against multi-drug-resistant microbes. This looming threat calls for more rationally designed antibiotic derivatives that have improved antimicrobial properties and reduced toxicity in humans. Herein, we utilize native ion mobility spectrometry-mass spectrometry (IMS-MS) to investigate the gas-phase structure and thermodynamic stability of the type I variant of CAT from Escherichia coli (EcCATI) and several EcCATI:ligand-bound complexes. EcCATI readily binds multiple Chl without incurring significant changes to its gas-phase structure or stability. A non-hydrolyzable acetyl-CoA derivative (S-ethyl-CoA, S-Et-CoA) was used to kinetically trap EcCATI and Chl in a ternary, ligand-bound state (EcCATI:S-Et-CoA:Chl). Using collision-induced unfolding (CIU)-IMS-MS, we find that Chl dissociates from EcCATI:S-Et-CoA:Chl complexes at low collision energies, while S-Et-CoA remains bound to EcCATI even as protein unfolding occurs. Gas-phase binding constants further suggest that EcCATI binds S-Et-CoA more tightly than Chl. Both ligands exhibit negative cooperativity of subsequent ligand binding in their respective binary complexes. While we observe no significant change in structure or stability to EcCATI when bound to either or both ligands, we have elucidated novel gas-phase unfolding and dissociation behavior and provided a foundation for further characterization of alternative substrates and/or inhibitors of EcCATI.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Anthony J Blue
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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8
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Bandak AF, Blower TR, Nitiss KC, Shah V, Nitiss JL, Berger JM. Using energy to go downhill - a genoprotective role for ATPase activity in DNA topoisomerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.27.546777. [PMID: 37425896 PMCID: PMC10327052 DOI: 10.1101/2023.06.27.546777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Type II topoisomerases effect topological changes in DNA by cutting a single duplex, passing a second duplex through the break, and resealing the broken strand in an ATP-coupled reaction. Curiously, most type II topoisomerases (topos II, IV, and VI) catalyze DNA transformations that are energetically favorable, such as the removal of superhelical strain; why ATP is required for such reactions is unknown. Here, using human topoisomerase II β (hTOP2β) as a model, we show that the ATPase domains of the enzyme are not required for DNA strand passage, but that their loss leads to increased DNA nicking and double strand break formation by the enzyme. The unstructured C-terminal domains (CTDs) of hTOP2β strongly potentiate strand passage activity in the absence of the ATPase regions, as do cleavage-prone mutations that confer hypersensitivity to the chemotherapeutic agent etoposide. The presence of either the CTD or the mutations lead ATPase-less enzymes to promote even greater levels of DNA cleava in ge vitro , as well as in vivo . By contrast, the aberrant cleavage phenotypes of these topo II variants is significantly repressed when the ATPase domains are restored. Our findings are consistent with the proposal that type II topoisomerases acquired an ATPase function to maintain high levels of catalytic activity while minimizing inappropriate DNA damage.
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9
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Avilan L, Lichtenstein BR, König G, Zahn M, Allen MD, Oliveira L, Clark M, Bemmer V, Graham R, Austin HP, Dominick G, Johnson CW, Beckham GT, McGeehan JE, Pickford AR. Concentration-Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering. CHEMSUSCHEM 2023; 16:e202202277. [PMID: 36811288 DOI: 10.1002/cssc.202202277] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Enzyme-based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis (IsPETase) is capable of PET hydrolysis under mild conditions but suffers from concentration-dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET-degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable IsPETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.
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Affiliation(s)
- Luisana Avilan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Bruce R Lichtenstein
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Gerhard König
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Mark D Allen
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Liliana Oliveira
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Matilda Clark
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Victoria Bemmer
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Rosie Graham
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Harry P Austin
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, D-17487, Greifswald, Germany
| | - Graham Dominick
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - Gregg T Beckham
- BOTTLE Consortium, Golden, CO 80401, United States
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
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10
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Zhang H, Li Y, Zhang YF, Qiao XJ, Sun LY, Li J, Wang YY, Han YF. Solvato-Controlled Assembly and Structural Transformation of Emissive Poly-NHC-Based Organometallic Cages and Their Applications in Amino Acid Sensing and Fluorescence Imaging. Chemistry 2023; 29:e202300209. [PMID: 36762405 DOI: 10.1002/chem.202300209] [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: 01/20/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/11/2023]
Abstract
Stimuli-induced structural transformation of supramolecular cages has drawn increasing attention because of their sensitive feature to external variations as model systems to simulate biological processes. However, combining structural transformation and useful functions has remained a difficult task. This study reports the solvato-controlled self-assembly of two unique topologies with different emission characteristics, a water-soluble Ag8 L4 cage (A) and an Ag4 L2 cage (B), produced from the same sulfonate-pendant tetraphenylethene (TPE) bridged tetrakis-(1,2,4-triazolium) ligand. Both cages show interesting solvent-responsive reversible structural transformation, and the change of fluorescence signals can efficiently track the process. Additionally, water-soluble cage A exhibits unique properties in thermochromism, thiol amino acid sensing, and subcellular imaging in aqueous media.
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Affiliation(s)
- Heng Zhang
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Yang Li
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Yi-Fan Zhang
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Xiu-Juan Qiao
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Li-Ying Sun
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Jianli Li
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Yao-Yu Wang
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
| | - Ying-Feng Han
- Key Laboratory of Synthetic and, Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, P. R. China
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11
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Sugahara G, Ishida Y, Lee JJ, Li M, Tanaka Y, Eoh H, Higuchi Y, Saito T. Long-term cell fate and functional maintenance of human hepatocyte through stepwise culture configuration. FASEB J 2023; 37:e22750. [PMID: 36607308 PMCID: PMC9830592 DOI: 10.1096/fj.202201292rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
Human hepatocyte culture system represents by far the most physiologically relevant model for our understanding of liver biology and diseases; however, its versatility has been limited due to the rapid and progressive loss of genuine characteristics, indicating the inadequacy of in vitro milieu for fate maintenance. This study, therefore, is designed to define environmental requirements necessary to sustain the homeostasis of terminally differentiated hepatocytes. Our study reveals that the supplementation of dimethyl sulfoxide (DMSO) is indispensable in mitigating fate deterioration and promoting adaptation to the in vitro environment, resulting in the restoration of tight cell-cell contact, cellular architecture, and polarity. The morphological recovery was overall accompanied by the restoration of hepatocyte marker gene expression, highlighting the interdependence between the cellular architecture and the maintenance of cell fate. However, beyond the recovery phase culture, DMSO supplementation is deemed detrimental due to the potent inhibitory effect on a multitude of hepatocyte functionalities while its withdrawal results in the loss of cell fate. In search of DMSO substitute, our screening of organic substances led to the identification of dimethyl sulfone (DMSO2), which supports the long-term maintenance of proper morphology, marker gene expression, and hepatocytic functions. Moreover, hepatocytes maintained DMSO2 exhibited clinically relevant toxicity in response to prolonged exposure to xenobiotics as well as alcohol. These observations suggest that the stepwise culture configuration consisting of the consecutive supplementation of DMSO and DMSO2 confers the microenvironment essential for the fate and functional maintenance of terminally differentiated human hepatocytes.
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Affiliation(s)
- Go Sugahara
- University of Southern California, Keck School of Medicine, Department of Medicine, Division of Gastrointestinal and Liver Diseases, Los Angeles, California, USA.,Research and Development Department, PhoenixBio, Co., Ltd, Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Yuji Ishida
- University of Southern California, Keck School of Medicine, Department of Medicine, Division of Gastrointestinal and Liver Diseases, Los Angeles, California, USA.,Research and Development Department, PhoenixBio, Co., Ltd, Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Jae Jin Lee
- University of Southern California, Keck School of Medicine, Department of Molecular Microbiology & Immunology, Los Angeles, California, USA
| | - Meng Li
- University of Southern California, Norris Medical Library, Bioinformatics Service Program, Los Angeles, California, USA
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
| | - Hyungjin Eoh
- University of Southern California, Keck School of Medicine, Department of Molecular Microbiology & Immunology, Los Angeles, California, USA
| | - Yusuke Higuchi
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Takeshi Saito
- University of Southern California, Keck School of Medicine, Department of Medicine, Division of Gastrointestinal and Liver Diseases, Los Angeles, California, USA.,USC Research Center for Liver Diseases, Los Angeles, California, USA.,Corresponding author: Takeshi Saito, M.D., Ph.D., Associate Professor of Medicine, Molecular Microbiology & Immunology, and Pathology, USC Research Center for Liver Diseases, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine of USC, University of Southern California, 2011 Zonal Avenue, HMR 801A, Los Angeles, CA 90033-9141, Phone: +1-323-442-2260, Fax:+1-323-442-5425,
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12
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Protein cysteine S-glycosylation: oxidative hydrolysis of protein S-glycosidic bonds in aqueous alkaline environments. Amino Acids 2023; 55:61-74. [PMID: 36460841 PMCID: PMC9877059 DOI: 10.1007/s00726-022-03208-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/13/2022] [Indexed: 12/03/2022]
Abstract
Some glycoproteins contain carbohydrates S-linked to cysteine (Cys) residues. However, relatively few S-glycosylated proteins have been detected, due to the lack of an effective research methodology. This work outlines a general concept for the detection of S-glycosylation sites in proteins. The approach was verified by exploratory experiments on a model mixture of β-S-glucosylated polypeptides obtained by the chemical transformation of lysozyme P00698. The model underwent two processes: (1) oxidative hydrolysis of S-glycosidic bonds under alkaline conditions to expose the thiol group of Cys residues; (2) thiol S-alkylation leading to thiol S-adduct formation at the former S-glycosylation sites. Oxidative hydrolysis was conducted in aqueous urea, dimethyl sulfoxide, or trifluoroethanol, with silver nitrate as the reaction promoter, in the presence of triethylamine and/or pyridine. The concurrent formation of stable protein silver thiolates, gluconic acid, and silver nanoclusters was observed. The essential de-metalation of protein silver thiolates using dithiothreitol preceded the S-labeling of Cys residues with 4-vinyl pyridine or a fluorescent reagent. The S-labeled model was sequenced by tandem mass spectrometry to obtain data on the modifications and their distribution over the protein chains. This enabled the efficiency of both S-glycosidic bonds hydrolysis and S-glycosylation site labeling to be evaluated. Suggestions are also given for testing this novel strategy on real proteomic samples.
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13
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Recombinant Thaumatin-Like Protein (rTLP) and Chitinase (rCHI) from Vitis vinifera as Models for Wine Haze Formation. Molecules 2022; 27:molecules27196409. [PMID: 36234944 PMCID: PMC9573663 DOI: 10.3390/molecules27196409] [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: 09/06/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Cross-linking net aggregates of thermolabile thaumatin-like proteins (TLPs) and chitinases (CHIs) are the primary source of haze in white wines. Although bentonite fining is still routinely used in winemaking, alternative methods to selectively remove haze proteins without affecting wine organoleptic properties are needed. The availability of pure TLPs and CHIs would facilitate the research for the identification of such technological advances. Therefore, we proposed the usage of recombinant TLP (rTLP) and CHI (rCHI), expressed by Komagataella phaffii, as haze-protein models, since they showed similar characteristics (aggregation potential, melting point, functionality, glycosylation levels and bentonite adsorption) to the native-haze proteins from Vitis vinifera. Hence, rTLP and rCHI can be applied to study haze formation mechanisms on a molecular level and to explore alternative fining methods by screening proteolytic enzymes and ideal adsorptive resins.
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14
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Chakrabarty S, Deshmukh SH, Barman A, Bagchi S, Ghosh A. On-Off Infrared Absorption of the S═O Vibrational Probe of Dimethyl Sulfoxide. J Phys Chem B 2022; 126:4501-4508. [PMID: 35674725 DOI: 10.1021/acs.jpcb.1c10558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dimethyl sulfoxide (DMSO), a polar solvent molecule, is used in a wide range of therapeutic and pharmacological applications. Different intermolecular interactions, such as dimerization and hydrogen bonding with water, are crucial to understanding the role of DMSO in applications. Herein, we study DMSO in various solvation environments to decipher the environment-dependent dimerization and hydrogen-bonding propensity. We use a combination of infrared spectroscopy, quantum mechanical calculations, and molecular dynamics simulations to reach our conclusions. Although DMSO can exist in a dynamic equilibrium between monomers and dimers, our results show that the relative intensity of the S═O stretch and the CH3 rocking modes is a spectroscopic indicator of the extent of DMSO dimerization in solution. The dimerization (self-association) is seen to be maximum in neat DMSO. When dissolved in different solvents, the dimerization propensity decreases with increasing solvent polarity. In the presence of a protic solvent, such as water, DMSO forms a hydrogen bond with the solvent molecules, thereby reducing the extent of dimerization. Further, we estimate the hydrogen-bond occupancy of DMSO. Our results show that DMSO predominantly exists as doubly hydrogen-bonded in water.
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Affiliation(s)
- Suranjana Chakrabarty
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Samadhan H Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anjan Barman
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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15
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Dugan LD, Bier ME. Mechanospray Ionization MS of Proteins Including in the Folded State and Polymers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:772-782. [PMID: 35420806 DOI: 10.1021/jasms.1c00344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mechanospray ionization (MoSI) is a technique that produces ions directly from solution-like electrospray ionization (ESI) but without the need of a high voltage. In MoSI, mechanical vibrations aerosolize solution phase analytes, whereby the resulting microdroplets can be directed into the inlet orifice of a mass spectrometer. In this work, MoSI is applied to biomolecules up to 80 kDa in mass in both denatured and native conditions as well as polymers up to 12 kDa in mass. The various MoSI devices used in these analyses were all comprised of a piezoelectric annulus attached to a central metallic disk containing an array of 4 to 7 μm diameter holes. The devices vibrated in the 100-170 kHz range to generate a beam of microdroplets that ultimately resulted in ion formation. A linear quadrupole ion trap (LIT) and orbitrap mass spectrometer were used in the analysis to investigate higher mass proteins at both native (folded) and denatured (unfolded) conditions. MoSI native mass spectra of proteins acquired on the orbitrap and LIT instrument demonstrated that proteins could remain intact and in a folded state. In the case of native MS of holomyoglobin, the intact folded protein remained mostly bound noncovalently to the heme group, and typically, the spectra showed reduced loss of the heme group by MoSI as compared to ESI. In both non-native and native protein analyses examples, broader often multimodal distributions to lower charge states were observed. When using the LIT instrument, a significant increase in the relative abundance of dimers was observed by MoSI as compared to ESI. The softness of the MoSI technique was evidenced by the lack of fragmentation, the formation of dimers as also noted by others ( J. Mass Spectrom. 2016, 424-429) and under native conditions, the retention of proteins in one or more presumed folded structures and for holomyoglobin the high retention of the heme group. When analyzing polyethylene glycol (PEG) and polypropylene glycol (PPG), MoSI also generated a broader distribution to lower charge states than ESI. By using the improved separation of peaks at lower charge states and all the charge states available, MoSI data should provide an improved ionization method to obtain more accurate mass and dispersity values for some polymers.
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Affiliation(s)
- Liam D Dugan
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Mark E Bier
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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16
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Reimer L, Haikal C, Gram H, Theologidis V, Kovacs G, Ruesink H, Baun A, Nielsen J, Otzen DE, Li JY, Jensen PH. Low dose DMSO treatment induces oligomerization and accelerates aggregation of α-synuclein. Sci Rep 2022; 12:3737. [PMID: 35260646 PMCID: PMC8904838 DOI: 10.1038/s41598-022-07706-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 02/10/2022] [Indexed: 01/05/2023] Open
Abstract
Dimethyl sulfoxide (DMSO) is a highly utilized small molecule that serves many purposes in scientific research. DMSO offers unique polar, aprotic and amphiphilic features, which makes it an ideal solvent for a wide variety of both polar and nonpolar molecules. Furthermore, DMSO is often used as a cryoprotectant in cell-based research. However, recent reports suggest that DMSO, even at low concentration, might interfere with important cellular processes, and cause macromolecular changes to proteins where a shift from α-helical to β-sheet structure can be observed. To investigate how DMSO might influence current research, we assessed biochemical and cellular impacts of DMSO treatment on the structure of the aggregation-prone protein α-synuclein, which plays a central role in the etiology of Parkinson’s disease, and other brain-related disorders, collectively termed the synucleinopathies. Here, we found that addition of DMSO increased the particle-size of α-synuclein, and accelerated the formation of seeding-potent fibrils in a dose-dependent manner. These fibrils made in the presence of DMSO were indistinguishable from fibrils made in pure PBS, when assessed by proteolytic digestion, cytotoxic profile and their ability to seed cellular aggregation of α-synuclein. Moreover, as evident through binding to the MJFR-14-6-4-2 antibody, which preferentially recognizes aggregated forms of α-synuclein, and a bimolecular fluorescence complementation assay, cells exposed to DMSO experienced increased aggregation of α-synuclein. However, no observable α-synuclein abnormalities nor differences in neuronal survival were detected after oral DMSO-treatment in either C57BL/6- or α-synuclein transgenic F28 mice. In summary, we demonstrate that low concentrations of DMSO makes α-synuclein susceptible to undergo aggregation both in vitro and in cells. This may affect experimental outcomes when studying α-synuclein in the presence of DMSO, and should call for careful consideration when such experiments are planned.
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Affiliation(s)
- Lasse Reimer
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark. .,Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
| | - Caroline Haikal
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Hjalte Gram
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Vasileios Theologidis
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Gergo Kovacs
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Harm Ruesink
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Andreas Baun
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center - iNANO, Aarhus University, Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center - iNANO, Aarhus University, Aarhus C, Denmark
| | - Jia-Yi Li
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, Lund, Sweden.,Institute of Health Sciences, China Medical University, 110112, Shenyang, People's Republic of China
| | - Poul Henning Jensen
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
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18
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Kang SK, Lee MJ, Ryu HH, Lee J, Lee MS. Dimethyl Sulfoxide Enhances Kaposi’s Sarcoma-Associated Herpesvirus Production During Lytic Replication. Front Microbiol 2021; 12:778525. [PMID: 34975802 PMCID: PMC8716793 DOI: 10.3389/fmicb.2021.778525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/19/2021] [Indexed: 02/05/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is an etiologic agent of Kaposi’s sarcoma, primary effusion lymphoma, and multicentric Castleman disease. In studies of KSHV, efficient virus production and isolation are essential. Reactivation of KSHV can be initiated by treating latently infected cells with chemicals, such as 12-O-tetradecanoyl-phorbol-13-acetate and sodium butyrate. These chemicals have been used as tools to induce lytic replication and viral production in KSHV-producing cell lines. Dimethyl sulfoxide (DMSO) is an organosulfur compound that is frequently used as an aprotic solvent similar to water. In experiments exploring signaling pathways in KSHV-infected cells, DMSO treatment alone as a vehicle affected the lytic gene expression of KSHV. However, to the best of our knowledge, the effects of DMSO on KSHV-producing cells have not yet been reported. Therefore, in this study, we investigated whether DMSO could be used as a reagent to enhance viral production during lytic replication in KSHV-producing cells and assessed the underlying mechanisms. The effects of DMSO on KSHV production were analyzed in iSLK BAC16 cells, which have been widely used for recombinant KSHV production. We found that the production of KSHV virions was significantly increased by treatment with DMSO during the induction of lytic replication. Mechanistically, lytic genes of KSHV were enhanced by DMSO treatment, which was correlated with virion production. Additionally, DMSO induced the phosphorylation of JNK during lytic replication, and inhibition of JNK abolished the effects of DMSO on lytic replication and virion production. Our findings showed that additional treatment with DMSO during the induction of lytic replication significantly improved the yield of KSHV production.
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Affiliation(s)
- Su-Kyung Kang
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Myung-Ju Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Ho-Hyun Ryu
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Jisu Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, South Korea
- Eulji Biomedical Science Research Institute, Eulji University School of Medicine, Daejeon, South Korea
- *Correspondence: Myung-Shin Lee,
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19
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Vallejo DD, Kang J, Coghlan J, Ramírez CR, Polasky DA, Kurulugama RT, Fjeldsted JC, Schwendeman AA, Ruotolo BT. Collision-Induced Unfolding Reveals Stability Differences in Infliximab Therapeutics under Native and Heat Stress Conditions. Anal Chem 2021; 93:16166-16174. [PMID: 34808055 DOI: 10.1021/acs.analchem.1c03946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU) assays of monoclonal antibody (mAb)-based biotherapeutics have proven sensitive to disulfide bridge structures, glycosylation patterns, and small molecule conjugation levels. Despite promising prior reports detailing the capabilities of IM-MS and CIU to differentiate biosimilars, generic mAb therapeutics, there remain questions surrounding the sensitivity of CIU to mAb structure changes that occur upon stress, the reproducibility of such measurements across IM-MS platforms, and the correlation between CIU and differential scanning calorimetry (DSC) datasets. In this report, we describe a comprehensive IM-MS and CIU dataset acquired for three Infliximabs: Remicade, Inflectra, and Renflexis. We subject each infliximab sample to forced degradation through heat stress and observe broadly similar yet subtly different stability patterns for these three biotherapeutics. We find that CIU is capable of tracking differences in mAb higher-order structure (HOS) imparted during forced heat stress degradation and that DSC is less sensitive to these alterations in comparison. Furthermore, we collected our comprehensive IM-MS and CIU data across two instrument platforms (Waters G2 and Agilent 6560), with both producing similar abilities to differentiate mAbs while also revealing minor differences between the results obtained on the two instruments. Finally, we demonstrate that CIU-based heatmaps and classification allow for rapid assessment of the most differentiating charge states for the analysis of infliximab, and using multiplexed classification, we conservatively estimate a 30-fold improvement in the time required to perform mAb stability and HOS measurements over standard DSC tools.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jukyung Kang
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jill Coghlan
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Daniel A Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - John C Fjeldsted
- Agilent Technologies, Santa Clara, California 95051, United States
| | - Anna A Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Xie A, Tsvetkova I, Liu Y, Ye X, Hewavitharanage P, Dragnea B, Cadena-Nava RD. Hydrophobic Cargo Encapsulation into Virus Protein Cages by Self-Assembly in an Aprotic Organic Solvent. Bioconjug Chem 2021; 32:2366-2376. [PMID: 34730939 DOI: 10.1021/acs.bioconjchem.1c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While extensive studies of virus capsid assembly in environments mimicking in vivo conditions have led to an understanding of the thermodynamic driving forces at work, applying this knowledge to virus assembly in other solvents than aqueous buffers has not been attempted yet. In this study, Brome mosaic virus (BMV) capsid proteins were shown to preserve their self-assembly abilities in an aprotic polar solvent, dimethyl sulfoxide (DMSO). This facilitated protein cage encapsulation of nanoparticles and dye molecules that favor organic solvents, such as β-NaYF4-based upconversion nanoparticles and BODIPY dye. Assembly was found to be robust relative to a surprisingly broad range of DMSO concentrations. Cargos with poor initial stability in aqueous solutions were readily encapsulated at high DMSO concentrations and then transferred to aqueous solvents, where they remained stable and preserved their function for months.
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Affiliation(s)
- Amberly Xie
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Irina Tsvetkova
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Yang Liu
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xingchen Ye
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Priyadarshine Hewavitharanage
- Chemistry Department, University of Southern Indiana, 8600 University Boulevard, Evansville, Indiana 47712, United States
| | - Bogdan Dragnea
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Ruben D Cadena-Nava
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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21
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El-Shaffey HM, Gross EJ, Hall YD, Ohata J. An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method. J Am Chem Soc 2021; 143:12974-12979. [PMID: 34387473 DOI: 10.1021/jacs.1c06092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
While a diverse set of design strategies have produced various chemical tools for biomolecule labeling in aqueous media, the development of nonaqueous, biomolecule-compatible media for bioconjugation has significantly lagged behind. In this report, we demonstrate that an aprotic ionic liquid serves as a novel reaction solvent for protein bioconjugation without noticeable loss of the biomolecule functions. The ionic liquid bioconjugation approach led to discovery of a novel triphenylphosphine-mediated amine-azide coupling reaction that forges a stable tetrazene linkage on unprotected peptides and proteins. This strategy of using untraditional media would provide untapped opportunities for expanding the scope of chemical approaches for bioconjugation.
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Affiliation(s)
- Hisham M El-Shaffey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Elizabeth J Gross
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yvonne D Hall
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jun Ohata
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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22
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Chee SMQ, Wongsantichon J, Yi LS, Sana B, Frosi Y, Robinson RC, Ghadessy FJ. Functional display of bioactive peptides on the vGFP scaffold. Sci Rep 2021; 11:10127. [PMID: 33980885 PMCID: PMC8115314 DOI: 10.1038/s41598-021-89421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Grafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein–protein interactions.
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Affiliation(s)
- Sharon Min Qi Chee
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lau Sze Yi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Barindra Sana
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Yuri Frosi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Farid J Ghadessy
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore.
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23
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Choi R, Zhou M, Shek R, Wilson JW, Tillery L, Craig JK, Salukhe IA, Hickson SE, Kumar N, James RM, Buchko GW, Wu R, Huff S, Nguyen TT, Hurst BL, Cherry S, Barrett LK, Hyde JL, Van Voorhis WC. High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity. PLoS One 2021; 16:e0250019. [PMID: 33886614 PMCID: PMC8062000 DOI: 10.1371/journal.pone.0250019] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer's therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.
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Affiliation(s)
- Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Roger Shek
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jesse W. Wilson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Logan Tillery
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Justin K. Craig
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Indraneel A. Salukhe
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Sarah E. Hickson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Rhema M. James
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- School of Molecular Bioscience, Washington State University, Pullman, WA, United States of America
| | - Ruilian Wu
- Bioenergy and Biome Sciences, Los Alamos National Laboratory (LANL), Los Alamos, NM, United States of America
| | - Sydney Huff
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Tu-Trinh Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, United States of America
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lynn K. Barrett
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jennifer L. Hyde
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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24
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Konermann L, Aliyari E, Lee JH. Mobile Protons Limit the Stability of Salt Bridges in the Gas Phase: Implications for the Structures of Electrosprayed Protein Ions. J Phys Chem B 2021; 125:3803-3814. [PMID: 33848419 DOI: 10.1021/acs.jpcb.1c00944] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrosprayed protein ions can retain native-like conformations. The intramolecular contacts that stabilize these compact gas-phase structures remain poorly understood. Recent work has uncovered abundant salt bridges in electrosprayed proteins. Salt bridges are zwitterionic BH+/A- contacts. The low dielectric constant in the vacuum strengthens electrostatic interactions, suggesting that salt bridges could be a key contributor to the retention of compact protein structures. A problem with this assertion is that H+ are mobile, such that H+ transfer can convert salt bridges into neutral B0/HA0 contacts. This possible salt bridge annihilation puts into question the role of zwitterionic motifs in the gas phase, and it calls for a detailed analysis of BH+/A- versus B0/HA0 interactions. Here, we investigate this issue using molecular dynamics (MD) simulations and electrospray experiments. MD data for short model peptides revealed that salt bridges with static H+ have dissociation energies around 700 kJ mol-1. The corresponding B0/HA0 contacts are 1 order of magnitude weaker. When considering the effects of mobile H+, BH+/A- bond energies were found to be between these two extremes, confirming that H+ migration can significantly weaken salt bridges. Next, we examined the protein ubiquitin under collision-induced unfolding (CIU) conditions. CIU simulations were conducted using three different MD models: (i) Positive-only runs with static H+ did not allow for salt bridge formation and produced highly expanded CIU structures. (ii) Zwitterionic runs with static H+ resulted in abundant salt bridges, culminating in much more compact CIU structures. (iii) Mobile H+ simulations allowed for the dynamic formation/annihilation of salt bridges, generating CIU structures intermediate between scenarios (i) and (ii). Our results uncover that mobile H+ limit the stabilizing effects of salt bridges in the gas phase. Failure to consider the effects of mobile H+ in MD simulations will result in unrealistic outcomes under CIU conditions.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Justin H Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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25
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Heterogeneous Off-Target Effects of Ultra-Low Dose Dimethyl Sulfoxide (DMSO) on Targetable Signaling Events in Lung Cancer In Vitro Models. Int J Mol Sci 2021; 22:ijms22062819. [PMID: 33802212 PMCID: PMC8001778 DOI: 10.3390/ijms22062819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Targetable alterations in cancer offer novel opportunities to the drug discovery process. However, pre-clinical testing often requires solubilization of these drugs in cosolvents like dimethyl sulfoxide (DMSO). Using a panel of cell lines commonly used for in vitro drug screening and pre-clinical testing, we explored the DMSO off-target effects on functional signaling networks, drug targets, and downstream substrates. Eight Non-Small Cell Lung Cancer (NSCLC) cell lines were incubated with three concentrations of DMSO (0.0008%, 0.002%, and 0.004% v/v) over time. Expression and activation levels of 187 proteins, of which 137 were kinases and downstream substrates, were captured using the Reverse Phase Protein Array (RPPA). The DMSO effect was heterogeneous across cell lines and varied based on concentration, exposure time, and cell line. Of the 187 proteins measured, all were statistically different in at least one comparison at the highest DMSO concentration, followed by 99.5% and 98.9% at lower concentrations. Only 46% of the proteins were found to be statistically different in more than 5 cell lines, indicating heterogeneous response across models. These cell line specific alterations modulate response to in vitro drug screening. Ultra-low DMSO concentrations have broad and heterogeneous effects on targetable signaling proteins. Off-target effects need to be carefully evaluated in pre-clinical drug screening and testing.
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26
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The dynamic changes of glycogen molecular structure in Escherichia coli BL21(DE3). Carbohydr Polym 2021; 259:117773. [PMID: 33674016 DOI: 10.1016/j.carbpol.2021.117773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 01/12/2023]
Abstract
Diurnal alteration of glycogen molecular structure has been identified in healthy mice. Recently, both fragile (disintegration in dimethyl sulfoxide) and stable (not disintegrating in DMSO) glycogen particles were found in Escherichia coli. However, how glycogen structure changes dynamically in E. coli is not clear. The question examined here is whether fragile, stable glycogen α particles occur in bacteria, following a similar pattern as in mice. In this study, we examine the dynamic changes of glycogen molecular structure over 24-h in E. coli BL21(DE3), using transmission electron microscopy, size exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis at representative time points. It was found that glycogen structure was mainly fragile at the synthesis stage and largely stable during the degradation stage. qRT-PCR results indicated that balance of anabolic and catabolic gene expression levels in glycogen metabolism could be a key factor affecting the fragility of glycogen α particles in bacteria.
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27
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Han Z, Christiansen A, Meena, Liau G. Relative Quantification of Na V1.1 Protein in Mouse Brains Using a Meso Scale Discovery-Electrochemiluminescence (MSD-ECL) Method. Bio Protoc 2021; 11:e3910. [PMID: 33732797 DOI: 10.21769/bioprotoc.3910] [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: 09/16/2020] [Revised: 12/14/2020] [Accepted: 02/03/2021] [Indexed: 11/02/2022] Open
Abstract
Densitometric analysis is often used to quantify NaV1.1 protein on immunoblots, although the sensitivity and dilution linearity of the method are usually poor. Here we present a protocol for quantification of NaV1.1 in mouse brain tissues using a Meso Scale Discovery-Electrochemiluminescence (MSD-ECL) method. MSD-ECL is based on ELISA (enzyme-linked immunosorbent assay) and uses electrochemiluminescence to produce measurable signals. Two different antibodies are used in this assay to capture and detect NaV1.1 respectively in brain tissue lysate. The specificity of the antibodies is confirmed by Scn1a gene knock-out tissue. The calibration curve standards used in this assay were generated with mouse liver lysate spiked with mouse brain lysate, instead of using a recombinant protein. We showed that this method was qualified and used for quantification of NaV1.1 in mouse brain tissues with specificity, accuracy and precision.
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Affiliation(s)
- Zhou Han
- Stoke Therapeutics, Inc., Bedford, MA, USA
| | | | - Meena
- Stoke Therapeutics, Inc., Bedford, MA, USA
| | - Gene Liau
- Stoke Therapeutics, Inc., Bedford, MA, USA
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28
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Amjadi Oskouie A, Abiri A. Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity? Anal Biochem 2020; 613:113744. [PMID: 32325085 DOI: 10.1016/j.ab.2020.113744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/11/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022]
Abstract
Regulation of transcription and replication by the tetrad patterns of DNA has drawn the attention of many scientists. In this perspective article, we discuss some disparaged parameters in the study of G-quadruplex structures (G4-tetrads). Besides, the implication of "destabilization as a side-effect" by these ligands on quadruplexes is explained. The lack of strict control of in vitro cell-free experiments in terms of ionic concentration, pH, epigenetic modifications, (macro)molecular crowding, and solvent effects is evident in many previous studies. The role of these factors in ligands binding and their possible effects in G-quadruplex structures are also represented.
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Affiliation(s)
- Akbar Amjadi Oskouie
- Department of Biology, Ardabil Branch, Islamic Azad University, Ardabil, Iran; Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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29
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Pavitt AS, Tratnyek PG. Electrochemical characterization of natural organic matter by direct voltammetry in an aprotic solvent. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1664-1683. [PMID: 31576393 DOI: 10.1039/c9em00313d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The complex and indeterminant composition of NOM makes characterization of its redox properties challenging. Approaches that have been taken to address this challenge include chemical probe reactions, potentiometric titrations, chronocoulometry, and voltammetry. In this study, we revisit the use of direct voltammetric methods in aprotic solvents by applying an expanded and refined suite of methods to a large set of NOM samples and model compounds (54 NOM samples from 10 different sources, 7 NOM model compounds, and 2 fresh extracts of plant materials that are high in redox-active quinonoid model compounds dissolved in DMSO). Refinements in the methods of fitting the data obtained by staircase cyclic voltammetry (SCV) provided improved definition of peaks, and square wave voltammetry (SWV), performed under the same conditions as SCV, provided even more reliable identification and quantitation of peaks. Further evidence is provided that DMSO improves the electrode response by unfolding some of the tertiary structure of NOM polymers, thereby allowing greater contact between redox active functional groups and the electrode surface. We averaged experimental peak potentials for all NOM compounds and calculated potentials in water. Average values for Epa1, Epc1, and Ep1 in DMSO were -0.866 ± 0.069, -1.35 ± 0.071, and -0.831 ± 0.051 V vs. Ag/Ag+, and -0.128, -0.613, and -0.0930 V vs. SHE in water. In addition to peak potentials, the breadth of SCV peaks was quantified as a way to characterize the degree to which the redox activity of NOM is due to a continuum of contributing functional groups. The average breadth values were 1.63 ± 0.24, 1.28 ± 0.34, and 0.648 ± 0.15 V for Epa1, Epc1, and Ep1 respectively. Comparative analysis of the overall dataset-from SCV and SWV on all NOMs and model compounds-revealed that NOM redox properties vary over a narrower range than expected based on model compound properties. This lack of diversity in redox properties of NOM is similar to conclusions from other recent work on the molecular structure of NOM, all of which could be the result of selectivity in the common extraction methods used to obtain the materials.
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Affiliation(s)
- Ania S Pavitt
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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30
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Vallejo DD, Polasky DA, Kurulugama RT, Eschweiler JD, Fjeldsted JC, Ruotolo BT. A Modified Drift Tube Ion Mobility-Mass Spectrometer for Charge-Multiplexed Collision-Induced Unfolding. Anal Chem 2019; 91:8137-8146. [PMID: 31194508 DOI: 10.1021/acs.analchem.9b00427] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Collision-induced unfolding (CIU) of protein ions and their noncovalent complexes offers relatively rapid access to a rich portfolio of biophysical information, without the need to tag or purify proteins prior to analysis. Such assays have been characterized extensively for a range of therapeutic proteins, proving exquisitely sensitive to alterations in protein sequence, structure, and post-translational modification state. Despite advantages over traditional probes of protein stability, improving the throughput and information content of gas-phase protein unfolding assays remains a challenge for current instrument platforms. In this report, we describe modifications to an Agilent 6560 drift tube ion mobility-mass spectrometer in order to perform robust, simultaneous CIU across all precursor ions detected. This approach dramatically increases the speed associated with typical CIU assays, which typically involve mass selection of narrow m/ z regions prior to collisional activation, and thus their development requires a comprehensive assessment of charge-stripping reactions that can unintentionally pollute CIU data with chemical noise when more than one precursor ion is allowed to undergo simultaneous activation. By studying the unfolding and dissociation of intact antibody ions, a key analyte class associated with biotherapeutics, we reveal a predictive relationship between the precursor charge state, the amount of buffer components bound to the ions of interest, and the amount of charge stripping detected. We then utilize our knowledge of antibody charge stripping to rapidly capture CIU data for a range of antibody subclasses and subtypes across all charge states simultaneously, demonstrating a strong charge state dependence on the information content of CIU. Finally, we demonstrate that CIU data collection times can be further reduced by scanning fewer voltage steps, enabling us to optimize the throughput of our improved CIU methods and confidently differentiate antibody variant ions using ∼20% of the data typically collected during CIU. Taken together, our results characterize a new instrument platform for biotherapeutic stability measurements with dramatically improved throughput and information content.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Daniel A Polasky
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | | | - Joseph D Eschweiler
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States.,AbbVie , North Chicago , Illinois 60064 , United States
| | - John C Fjeldsted
- Agilent Technologies , Santa Clara , California 95051 , United States
| | - Brandon T Ruotolo
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
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31
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Dixit SM, Ruotolo BT. A Semi-Empirical Framework for Interpreting Traveling Wave Ion Mobility Arrival Time Distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:956-966. [PMID: 30815838 DOI: 10.1007/s13361-019-02133-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
The inherent structural heterogeneity of biomolecules is an important biophysical property that is essential to their function, but is challenging to characterize experimentally. We present a workflow that rapidly and quantitatively assesses the conformational heterogeneity of peptides and proteins in the gas phase using traveling wave ion mobility (TWIM) arrival time distributions (ATDs). We have established a set of semi-empirical equations that model the TWIM ATD peak width and resolution across a wide range of wave amplitudes (V) and wave velocities (v). In addition, a conformational broadening parameter, δ, can be extracted from this analysis that reports on the contribution of conformational heterogeneity to the broadening of TWIM ATD peak width during ion mobility separation. We use this δ value to evaluate the conformational heterogeneity of a set of helical peptides, and our analysis correlates well with previous peak width observations reported for these ions. Furthermore, we use molecular dynamics simulations to independently investigate the general flexibility of these peptides in the gas phase, and generate similar trends found in experimental TWIM data. Finally, we extended our analysis to Avidin, a 64-kDa homotetramer, and quantify the structural heterogeneity of this intact complex using TWIM ATD data as a function of cross-linking. We observe an initial reduction in δ values as a function of cross-linker concentration, demonstrating the sensitivity of our δ value analysis to changes in flexibility of the assembly.
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Affiliation(s)
- Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA.
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32
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Zhao B, Zhuang X, Bian X, Pi Z, Liu S, Liu Z, Song F. Effects of aprotic solvents on the stability of metal-free superoxide dismutase probed by native electrospray ionization-ion mobility-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:351-358. [PMID: 30734979 DOI: 10.1002/jms.4341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Considering that aprotic solvents are often used as cosolvents in investigating the interactions between small molecules and proteins, we assessed the effects of five aprotic solvents represented by dimethylformamide (DMF) on the structure stabilities of metal-free SOD1 (apo-SOD1) by native electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS). These aprotic solvents include DMF, 1,3-dimethyl-2-imidazolidinone (DMI), dimethyl sulfoxide (DMSO), acetonitrile (ACN), and tetrahydrofuran (THF). Results indicated that DMI, DMSO, and DMF at low percentage concentration could reduce the average charge and the dimer dissociation of apo-SOD1. By contrast, ACN and THF at low concentration have no similar effect. DMF was selected as a representative solvent to further investigate the detailed effects on the structure stability of apo-SOD1 by using collision-induced dissociation and unfolding. The results reveal that the addition of minimal DMF to an aqueous protein solution can protect against the unfolding and dissociation of dimer, even under destabilizing conditions (such as low pH or high cone voltage). When the different percentage concentrations of DMF were added, the average collision cross section of apo-SOD1 showed that apo-SOD1 became compacted when the DMF concentration increased from 0% to 1% and eventually started extending when increased from 1% to 20%. The results indicated that DMF has similar effects to DMSO in native mass spectrometry (MS) and it can also be used as a cosolvent besides DMSO in investigating the stabilities of proteins and the interactions between small molecules and proteins.
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Affiliation(s)
- Bing Zhao
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
| | - Xiaoyu Zhuang
- School of Pharmacy, Fudan University, Shanghai, China
| | - Xinyu Bian
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
| | - Zifeng Pi
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Shu Liu
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Zhiqiang Liu
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fengrui Song
- National Center of Mass Spectrometry in Changchun & Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
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33
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Jeffreys LN, Poddar H, Golovanova M, Levy CW, Girvan HM, McLean KJ, Voice MW, Leys D, Munro AW. Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs. Sci Rep 2019; 9:1577. [PMID: 30733479 PMCID: PMC6367340 DOI: 10.1038/s41598-018-37330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.
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Affiliation(s)
- Laura N Jeffreys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Harshwardhan Poddar
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Marina Golovanova
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Colin W Levy
- Manchester Protein Structure Facility (MPSF), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Hazel M Girvan
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom.
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Polasky DA, Dixit SM, Fantin SM, Ruotolo BT. CIUSuite 2: Next-Generation Software for the Analysis of Gas-Phase Protein Unfolding Data. Anal Chem 2019; 91:3147-3155. [DOI: 10.1021/acs.analchem.8b05762] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah M. Fantin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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