1
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Rajczewski A, Ndreu L, Vryonidis E, Hurben AK, Jamshidi S, Griffin TJ, Törnqvist MÅ, Tretyakova NY, Karlsson I. Mass Spectrometry-Based Strategies for Assessing Human Exposure Using Hemoglobin Adductomics. Chem Res Toxicol 2023; 36:2019-2030. [PMID: 37963067 PMCID: PMC10731639 DOI: 10.1021/acs.chemrestox.3c00294] [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: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Hemoglobin (Hb) adducts are widely used in human biomonitoring due to the high abundance of hemoglobin in human blood, its reactivity toward electrophiles, and adducted protein stability for up to 120 days. In the present paper, we compared three methods of analysis of hemoglobin adducts: mass spectrometry of derivatized N-terminal Val adducts, mass spectrometry of N-terminal adducted hemoglobin peptides, and limited proteolysis mass spectrometry . Blood from human donors was incubated with a selection of contact allergens and other electrophiles, after which hemoglobin was isolated and subjected to three analysis methods. We found that the FIRE method was able to detect and reliably quantify N-terminal adducts of acrylamide, acrylic acid, glycidic acid, and 2,3-epoxypropyl phenyl ether (PGE), but it was less efficient for 2-methyleneglutaronitrile (2-MGN) and failed to detect 1-chloro-2,4-dinitrobenzene (DNCB). By contrast, bottom-up proteomics was able to determine the presence of adducts from all six electrophiles at both the N-terminus and reactive hemoglobin side chains. Limited proteolysis mass spectrometry, studied for four contact allergens (three electrophiles and a metal salt), was able to determine the presence of covalent hemoglobin adducts with one of the three electrophiles (DNCB) and coordination complexation with the nickel salt. Together, these approaches represent complementary tools in the study of the hemoglobin adductome.
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Affiliation(s)
- Andrew
T. Rajczewski
- Department
of Biochemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Lorena Ndreu
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Efstathios Vryonidis
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Alexander K. Hurben
- Department
of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Sara Jamshidi
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
| | - Timothy J. Griffin
- Department
of Biochemistry, University of Minnesota, Minneapolis, Minnesota55455, United States
| | | | - Natalia Y. Tretyakova
- Department
of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota55455, United States
| | - Isabella Karlsson
- Department
of Environmental Science, Stockholm University, SE-10691Stockholm, Sweden
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2
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Kundlacz T, Schmidt C. Deciphering Solution and Gas-Phase Interactions between Peptides and Lipids by Native Mass Spectrometry. Anal Chem 2023; 95:17292-17299. [PMID: 37956985 PMCID: PMC10688224 DOI: 10.1021/acs.analchem.3c03428] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023]
Abstract
Many biological processes depend on the interactions between proteins and lipids. Accordingly, the analysis of protein-lipid complexes has become increasingly important. Native mass spectrometry is often used to identify and characterize specific protein-lipid interactions. However, it requires the transfer of the analytes into the gas phase, where electrostatic interactions are enhanced and hydrophobic interactions do not exist. Accordingly, the question remains whether interactions that are observed in the gas phase accurately reflect interactions that are formed in solution. Here, we systematically explore noncovalent interactions between the antimicrobial peptide LL-37 and glycerophospholipids containing different headgroups or varying in fatty acyl chain length. We observe differences in peak intensities for different peptide-lipid complexes, as well as their relative binding strength in the gas phase. Accordingly, we found that ion intensities and gas-phase stability correlate well for complexes formed by electrostatic interactions. Probing hydrophobic interactions by varying the length of fatty acyl chains, we detected differences in ion intensities based on hydrophobic interactions formed in solution. The relative binding strength of these peptide-lipid complexes revealed only minor differences originating from van der Waals interactions and different binding modes of lipid headgroups in solution. In summary, our results demonstrate that hydrophobic interactions are reflected by ion intensities, while electrostatic interactions, including van der Waals interactions, determine the gas-phase stability of complexes.
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Affiliation(s)
- Til Kundlacz
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Institute
of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary
Research Centre HALOmem, Institute of Biochemistry and Biotechnology,
Charles Tanford Protein Centre, Martin Luther
University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany
- Department
of Chemistry—Biochemistry, Johannes
Gutenberg University Mainz, Biocenter II, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
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3
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Li G, Wang Y, Sun C, Liu F. Determination of the microscopic acid dissociation constant of piperacillin and identification of dissociated molecular forms. Front Chem 2023; 11:1177128. [PMID: 37179774 PMCID: PMC10169600 DOI: 10.3389/fchem.2023.1177128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023] Open
Abstract
For amphoteric ß-lactam antibiotics, the acid dissociation constant (pK a) is a fundamental parameter to characterize physicochemical and biochemical properties of antibiotics and to predict persistence and removal of drugs. pK a of piperacillin (PIP) is determined by potentiometric titration with a glass electrode. Electrospray ionization mass spectrometry (ESI-MS) is creatively applied to verify the reasonable pK a value at every dissociation step. Two microscopic pK a values (3.37 ± 0.06 and 8.96 ± 0.10) are identified and attributed to the direct dissociation of the carboxylic acid functional group and one secondary amide group, respectively. Different from other ß-lactam antibiotics, PIP presents a dissociation pattern where direct dissociation is involved instead of protonation dissociation. Moreover, the degradation tendency of PIP in an alkaline solution may alter the dissociation pattern or dismiss the corresponding pK a of the amphoteric ß-lactam antibiotics. This work offers a reliable determination of the acid dissociation constant of PIP and a clear interpretation of the effect of stability of antibiotics on the dissociation process.
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Affiliation(s)
- Guoao Li
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of water resource and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Yaling Wang
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
- National Engineering Research Center for Urban Environmental Pollution Control, Beijing, China
| | - Chengyi Sun
- Beijing Municipal Research Institute of Eco-Environmental Protection, Beijing, China
- National Engineering Research Center for Urban Environmental Pollution Control, Beijing, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of water resource and Environment, China University of Geosciences (Beijing), Beijing, China
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4
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Stachowski K, Norris A, Potter D, Wysocki V, Foster M. Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM. Nucleic Acids Res 2022; 50:1753-1769. [PMID: 35104890 PMCID: PMC8860596 DOI: 10.1093/nar/gkac032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
Cre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of palindromic recombinase binding elements and an asymmetric spacer region, by assembly of a tetrameric synaptic complex, cleavage of an opposing pair of strands, and formation of a Holliday junction intermediate. We used Cre and loxP variants to isolate the monomeric Cre-loxP (54 kDa), dimeric Cre2-loxP (110 kDa), and tetrameric Cre4-loxP2 assembly intermediates, and determined their structures using cryo-EM to resolutions of 3.9, 4.5 and 3.2 Å, respectively. Progressive and asymmetric bending of the spacer region along the assembly pathway enables formation of increasingly intimate interfaces between Cre protomers and illuminates the structural bases of biased loxP strand cleavage order and half-the-sites activity. Application of 3D variability analysis to the tetramer data reveals constrained conformational sampling along the pathway between protomer activation and Holliday junction isomerization. These findings underscore the importance of protein and DNA flexibility in Cre-mediated site selection, controlled activation of alternating protomers, the basis for biased strand cleavage order, and recombination efficiency. Such considerations may advance development of site-specific recombinases for use in gene editing applications.
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Affiliation(s)
- Kye Stachowski
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew S Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Devante Potter
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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5
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De León TS, Salum ML, Matsushita Y, Fukushima K, Monge ME, Erra-Balsells R. ESI-MS reveals preferential complex formation of carbohydrates with Z-sinapinic acid compared with the E-isomer. NEW J CHEM 2022. [DOI: 10.1039/d2nj02789e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ZSA + carbohydrate complex preferential formation and higher stability (ESI) support the previously proposed model for ZSA differential efficiency as the MALDI-MS matrix.
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Affiliation(s)
- Tobías Schmidt De León
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Pabellón II, 3er P., Ciudad Universitaria, 1428 Buenos Aires, Argentina
- CONICET, Universidad de Buenos Aires, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Facultad de Ciencias Exactas y Naturales Pabellón II, 3er P. Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - María Laura Salum
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Pabellón II, 3er P., Ciudad Universitaria, 1428 Buenos Aires, Argentina
- CONICET, Universidad de Buenos Aires, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Facultad de Ciencias Exactas y Naturales Pabellón II, 3er P. Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Yasuyuki Matsushita
- Laboratory of Forest Chemistry, Department of Forest and Environmental Resources Sciences, Graduate school of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0814, Japan
| | - Kazuhiko Fukushima
- Laboratory of Forest Chemistry, Department of Forest and Environmental Resources Sciences, Graduate school of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0814, Japan
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Argentina
| | - Rosa Erra-Balsells
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Pabellón II, 3er P., Ciudad Universitaria, 1428 Buenos Aires, Argentina
- CONICET, Universidad de Buenos Aires, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Facultad de Ciencias Exactas y Naturales Pabellón II, 3er P. Ciudad Universitaria, 1428 Buenos Aires, Argentina
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6
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Płonka D, Kotuniak R, Dąbrowska K, Bal W. Electrospray-Induced Mass Spectrometry Is Not Suitable for Determination of Peptidic Cu(II) Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2766-2776. [PMID: 34738801 PMCID: PMC8640992 DOI: 10.1021/jasms.1c00206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The toolset of mass spectrometry (MS) is still expanding, and the number of metal ion complexes researched this way is growing. The Cu(II) ion forms particularly strong peptide complexes of biological interest which are frequent objects of MS studies, but quantitative aspects of some reported results are at odds with those of experiments performed in solution. Cu(II) complexes are usually characterized by fast ligand exchange rates, despite their high affinity, and we speculated that such kinetic lability could be responsible for the observed discrepancies. In order to resolve this issue, we selected peptides belonging to the ATCUN family characterized with high and thoroughly determined Cu(II) binding constants and re-estimated them using two ESI-MS techniques: standard conditions in combination with serial dilution experiments and very mild conditions for competition experiments. The sample acidification, which accompanies the electrospray formation, was simulated with the pH-jump stopped-flow technique. Our results indicate that ESI-MS should not be used for quantitative studies of Cu(II)-peptide complexes because the electrospray formation process compromises the entropic contribution to the complex stability, yielding underestimations of complex stability constants.
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7
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Itai Bloch
- Biotechnology Department MIGAL-Galilee Research Institute Kiryat-Shmona 11016 Israel
| | - Maayan Gal
- Department of Oral Biology The Goldschleger School of Dental Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Nir London
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michal Sharon
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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8
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein-Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021; 60:19637-19642. [PMID: 34101963 PMCID: PMC8457057 DOI: 10.1002/anie.202104947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/23/2021] [Indexed: 12/22/2022]
Abstract
Understanding protein–ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)‐based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct‐MS method for rapid analysis of proteins directly from crude samples. Here, direct‐MS enables label‐free studies of protein–drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein–protein interactions, drug uptake and binding, and characterization of therapeutic proteins.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Itai Bloch
- Biotechnology Department, MIGAL-Galilee Research Institute, Kiryat-Shmona, 11016, Israel
| | - Maayan Gal
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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9
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Coulibaly K, Thauvin M, Melenbacher A, Testard C, Trigoni E, Vincent A, Stillman MJ, Vriz S, Policar C, Delsuc N. A di-Copper Peptidyl Complex Mimics the Activity of Catalase, a Key Antioxidant Metalloenzyme. Inorg Chem 2021; 60:9309-9319. [PMID: 34109781 DOI: 10.1021/acs.inorgchem.0c03718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalases (CAT) are antioxidant metalloenzymes necessary for life in oxygen-metabolizing cells to regulate H2O2 concentration by accelerating its dismutation. Many physiopathological situations are associated with oxidative stress resulting from H2O2 overproduction, during which antioxidant defenses are overwhelmed. We have used a combinatorial approach associated with an activity-based screening to discover a first peptidyl di-copper complex mimicking CAT. The complex was studied in detail and characterized for its CAT activity both in solutions and in cells using different analytical methods. The complex exhibited CAT activity in solutions and, more interestingly, on HyPer HeLa cells that possess a genetically encoded ratiometric fluorescent sensors of H2O2. These results highlight the efficiency of a combinatorial approach for the discovery of peptidyl complexes that exhibit catalytic activity.
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Affiliation(s)
- Koudedja Coulibaly
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marion Thauvin
- Collège de France, Centre Interdisciplinaire de Recherche en Biologie (CIRB), CNRS UMR7241/INSERM U1050, 75231 Paris, Cedex 05, France.,Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Adyn Melenbacher
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Clara Testard
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Evangelia Trigoni
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Amandine Vincent
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Sophie Vriz
- Collège de France, Centre Interdisciplinaire de Recherche en Biologie (CIRB), CNRS UMR7241/INSERM U1050, 75231 Paris, Cedex 05, France.,Faculty of Science, Université de Paris, 75006 Paris, France
| | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Nicolas Delsuc
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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10
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Santos IC, Brodbelt JS. Structural Characterization of Carbonic Anhydrase-Arylsulfonamide Complexes Using Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1370-1379. [PMID: 33683877 PMCID: PMC8377746 DOI: 10.1021/jasms.1c00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Numerous mass spectrometry-based strategies ranging from hydrogen-deuterium exchange to ion mobility to native mass spectrometry have been developed to advance biophysical and structural characterization of protein conformations and determination of protein-ligand interactions. In this study, we focus on the use of ultraviolet photodissociation (UVPD) to examine the structure of human carbonic anhydrase II (hCAII) and its interactions with arylsulfonamide inhibitors. Carbonic anhydrase, which catalyzes the conversion of carbon dioxide to bicarbonate, has been the target of countless thermodynamic and kinetic studies owing to its well-characterized active site, binding cavity, and mechanism of inhibition by hundreds of ligands. Here, we showcase the application of UVPD for evaluating structural changes of hCAII upon ligand binding on the basis of variations in fragmentation of hCAII versus hCAII-arylsulfonamide complexes, particularly focusing on the hydrophobic pocket. To extend the coverage in the midregion of the protein sequence, a supercharging agent was added to the solutions to increase the charge states of the complexes. The three arylsulfonamides examined in this study largely shift the fragmentation patterns in similar ways, despite their differences in binding affinities.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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11
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LILBID laser dissociation curves: a mass spectrometry-based method for the quantitative assessment of dsDNA binding affinities. Sci Rep 2020; 10:20398. [PMID: 33230224 PMCID: PMC7683618 DOI: 10.1038/s41598-020-76867-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/28/2020] [Indexed: 11/20/2022] Open
Abstract
One current goal in native mass spectrometry is the assignment of binding affinities to noncovalent complexes. Here we introduce a novel implementation of the existing laser-induced liquid bead ion desorption (LILBID) mass spectrometry method: this new method, LILBID laser dissociation curves, assesses binding strengths quantitatively. In all LILBID applications, aqueous sample droplets are irradiated by 3 µm laser pulses. Variation of the laser energy transferred to the droplet during desorption affects the degree of complex dissociation. In LILBID laser dissociation curves, laser energy transfer is purposely varied, and a binding affinity is calculated from the resulting complex dissociation. A series of dsDNAs with different binding affinities was assessed using LILBID laser dissociation curves. The binding affinity results from the LILBID laser dissociation curves strongly correlated with the melting temperatures from UV melting curves and with dissociation constants from isothermal titration calorimetry, standard solution phase methods. LILBID laser dissociation curve data also showed good reproducibility and successfully predicted the melting temperatures and dissociation constants of three DNA sequences. LILBID laser dissociation curves are a promising native mass spectrometry binding affinity method, with reduced time and sample consumption compared to melting curves or titrations.
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12
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Nguyen GTH, Leung WY, Tran TN, Wang H, Murray V, Donald WA. Mechanism for the Binding of Netropsin to Hairpin DNA Revealed Using Nanoscale Ion Emitters in Native Mass Spectrometry. Anal Chem 2019; 92:1130-1137. [PMID: 31778608 DOI: 10.1021/acs.analchem.9b04209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Netropsin is one of the first ligands to be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for developing potential anticancer and antibiotic agents. The mechanism by which netropsin binds to hairpin DNA remains controversial with two competing mechanisms having been proposed. In one mechanism, netropsin binding induces a hairpin-to-duplex DNA transition. Alternatively, netropsin binds in two thermodynamically different modes at a single duplexed AATT site. Here, results from native mass spectrometry (MS) with nanoscale ion emitters indicate that netropsin can simultaneously and sequentially bind to both hairpin and duplex DNA. Duplex DNA was not detected using conventional MS with larger emitters because nanoscale emitters significantly reduce the extent of salt adduction to ligand-DNA complex ions, including in the presence of relatively high concentrations of nonvolatile salts. Based on native MS and polyacrylamide gel electrophoresis results, the abundances of hairpin and duplex DNA are unaffected by the addition of netropsin. By native MS, the binding affinities for five ligand-DNA and DNA-DNA interactions can be rapidly obtained simultaneously. This research indicates a "simultaneous binding mechanism" for the interactions of netropsin with DNA.
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Affiliation(s)
- Giang T H Nguyen
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Wai Yu Leung
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Thinh N Tran
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Huixin Wang
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia.,Mark Wainwright Analytical Centre , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - William A Donald
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
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13
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Recent advances in mass spectrometry studies of non-covalent complexes of macrocycles - A review. Anal Chim Acta 2019; 1081:32-50. [DOI: 10.1016/j.aca.2019.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/29/2022]
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14
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Zheng S, Yuan S, Hou Z, Li G, Chen Y, Pan Y, Liu Y, Huang G. Charge-dependent modulation of specific and nonspecific protein-metal ion interactions in nanoelectrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1502-1511. [PMID: 31151135 DOI: 10.1002/rcm.8493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Previous studies found that charge state could affect both specific and nonspecific binding of protein-metal ion interactions in nanoelectrospray ionization mass spectrometry (nESI-MS). However, the two kinds of interactions have been studied individually in spite of the problem that they often coexist in the same system. Thus, it is necessary to study the effects of charge state on specific and nonspecific protein-metal ion interactions in one system to reveal more accurate binding state. METHODS The HIV-1 nucleocapsid protein (NCp7(31-55)) which can bind specifically and nonspecifically to Zn2+ served as the model to show the charge-dependent protein-metal ion interactions. Hydrogen/deuterium exchange (HDX) and photodissociation (PD) were used to demonstrate that specific binding state was correlated with protein structure. In addition to NCp7(31-55), three other model proteins were used to investigate the reason for the charge-dependent nonspecific binding. RESULTS For specific binding, we proposed that protein ions with different charge states had different conformations. The HDX results showed that labile protons in the NCp7(31-55)-Zn complex were exchanged in a charge-state-dependent way. The PD experiments revealed differential fragment yields for different charge states. For nonspecific binding, higher charge states had more Zn2+ additions, but less SO4 2- additions. The effects of charge states on nonspecific binding levels were entirely the opposite for Zn2+ and SO4 2- . These results could reveal that the nonspecific binding was caused by electrostatic interaction. CONCLUSIONS For specific binding, NCp7(31-55) with lower charge states have folding and undenatured structures. The binding states of lower charge states can better reflect more native binding states. For nonspecific binding, when multiple metal ions adduct to proteins, the proteins have more net positive charges, which tend to generate higher charge ions during electrospray.
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Affiliation(s)
- Shihui Zheng
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Siming Yuan
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhuanghao Hou
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Gongyu Li
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yuting Chen
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
| | - Yangzhong Liu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Guangming Huang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
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15
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Bücher KS, Yan H, Creutznacher R, Ruoff K, Mallagaray A, Grafmüller A, Dirks JS, Kilic T, Weickert S, Rubailo A, Drescher M, Schmidt S, Hansman G, Peters T, Uetrecht C, Hartmann L. Fucose-Functionalized Precision Glycomacromolecules Targeting Human Norovirus Capsid Protein. Biomacromolecules 2018; 19:3714-3724. [PMID: 30071731 DOI: 10.1021/acs.biomac.8b00829] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Norovirus infection is the major cause of nonbacterial gastroenteritis in humans and has been the subject of numerous studies investigating the virus's biophysical properties and biochemical function with the aim of deriving novel and highly potent entry inhibitors to prevent infection. Recently, it has been shown that the protruding P domain dimer (P-dimer) of a GII.10 Norovirus strain exhibits two new binding sites for l-fucose in addition to the canonical binding sites. Thus, these sites provide a novel target for the design of multivalent fucose ligands as entry inhibitors of norovirus infections. In this current study, a first generation of multivalent fucose-functionalized glycomacromolecules was synthesized and applied as model structures to investigate the potential targeting of fucose binding sites in human norovirus P-dimer. Following previously established solid phase polymer synthesis, eight precision glycomacromolecules varying in number and position of fucose ligands along an oligo(amidoamine) backbone were obtained and then used in a series of binding studies applying native MS, NMR, and X-ray crystallography. We observed only one fucose per glycomacromolecule binding to one P-dimer resulting in similar binding affinities for all fucose-functionalized glycomacromolecules, which based on our current findings we attribute to the overall size of macromolecular ligands and possibly to steric hindrance.
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Affiliation(s)
- Katharina Susanne Bücher
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Kerstin Ruoff
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Andrea Grafmüller
- Max-Planck-Institute of Colloids and Interfaces , Department of Theory and Bio-Systems , Potsdam , Germany
| | - Jan Sebastian Dirks
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Turgay Kilic
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Sabrina Weickert
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Anna Rubailo
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Malte Drescher
- University of Konstanz , Department of Chemistry and Konstanz Research School Chemical Biology , Konstanz , Germany
| | - Stephan Schmidt
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
| | - Grant Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany and Department of Infectious Diseases, Virology , University of Heidelberg , Heidelberg , Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics , University of Lübeck , Lübeck , Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , Hamburg , Germany.,European XFEL GmbH , Schenefeld , Germany
| | - Laura Hartmann
- Heinrich-Heine-University Düsseldorf , Institute for Organic Chemistry and Macromolecular Chemistry , Düsseldorf , Germany
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16
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Chingin K, Barylyuk K. Charge-State-Dependent Variation of Signal Intensity Ratio between Unbound Protein and Protein-Ligand Complex in Electrospray Ionization Mass Spectrometry: The Role of Solvent-Accessible Surface Area. Anal Chem 2018; 90:5521-5528. [PMID: 29653057 DOI: 10.1021/acs.analchem.7b05349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Native electrospray ionization mass spectrometry (ESI-MS) is nowadays widely used for the direct and sensitive determination of protein complex stoichiometry and binding affinity constants ( Ka). A common yet poorly understood phenomenon in native ESI-MS is the difference between the charge-state distributions (CSDs) of the bound protein-ligand complex (PL) and unbound protein (P) signals. This phenomenon is typically attributed to experimental artifacts such as nonspecific binding or in-source dissociation and is considered highly undesirable, because the determined Ka values display strong variation with charge state. This situation raises serious concerns regarding the reliability of ESI-MS for the analysis of protein complexes. Here we demonstrate that, contrary to the common belief, the CSD difference between P and PL ions can occur without any loss of complex integrity, simply due to a change in the solvent-accessible surface area (ΔSASA) of the protein upon ligand binding in solution. The experimental CSD shifts for PL and P ions in ESI-MS are explained in relation to the magnitude of ΔSASA for diverse protein-ligand systems using a simple model based on the charged residue mechanism. Our analysis shows that the revealed ΔSASA factor should be considered rather general and be given attention for the correct spectral interpretation of protein complexes.
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Affiliation(s)
- Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation , East China University of Technology , Guanglan Road 418 , Nanchang , Jiangxi , China 330013
| | - Konstantin Barylyuk
- Department of Biochemistry , University of Cambridge , Hopkins Building, Tennis Court Road , Cambridge CB2 1QW , United Kingdom
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17
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Zhao B, Zhuang X, Pi Z, Liu S, Liu Z, Song F. Determining the Effect of Catechins on SOD1 Conformation and Aggregation by Ion Mobility Mass Spectrometry Combined with Optical Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:734-741. [PMID: 29392684 DOI: 10.1007/s13361-017-1864-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 05/19/2023]
Abstract
The aggregation of Cu,Zn-superoxide dismutase (SOD1) plays an important role in the etiology of amyotrophic lateral sclerosis (ALS). For the disruption of ALS progression, discovering new drugs or compounds that can prevent SOD1 aggregation is important. In this study, ESI-MS was used to investigate the interaction of catechins and SOD1. The noncovalent complex of catechins that interact with SOD1 was found and retained in the gas phase under native ESI-MS condition. The conformation changes of SOD1 after binding with catechins were also explored via traveling wave ion mobility (IM) spectrometry. Epigallocatechin gallate (EGCG) can stabilize SOD1 conformation against unfolding in three catechins. To further evaluate the efficacy of EGCG, we monitored the fluorescence changes of dimer E2,E2,-SOD1(apo-SOD1, E:empty) with and without ligands under denaturation conditions, and found that EGCG can inhibit apo-SOD1 aggregation. In addition, the circular dichroism spectra of the samples showed that EGCG can decrease the β-sheet content of SOD1, which can produce aggregates. These results indicated that orthogonal separation dimension in the gas-phase IM coupled with ESI-MS (ESI-IM-MS) can potentially provide insight into the interaction between SOD1 and small molecules. The advantage is that it dramatically decreases the analysis time. Meantime, optical spectroscopy techniques can be used to confirm ESI-IM-MS results. Graphical Abstract ᅟ.
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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, 130022, China
- University of Science and Technology of China, Hefei, 230029, China
| | - Xiaoyu Zhuang
- 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, 130022, 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, 130022, 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, 130022, 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, 130022, 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, 130022, China.
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18
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Consta S, Oh MI, Sharawy M, Malevanets A. Macroion–Solvent Interactions in Charged Droplets. J Phys Chem A 2018; 122:5239-5250. [DOI: 10.1021/acs.jpca.8b01404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Mahmoud Sharawy
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Anatoly Malevanets
- Department of Electrical and Computer Engineering, The University of University of Western Ontario, London, Ontario, Canada N6A 5B9
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19
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Oh MI, Consta S. What factors determine the stability of a weak protein-protein interaction in a charged aqueous droplet? Phys Chem Chem Phys 2018; 19:31965-31981. [PMID: 29177351 DOI: 10.1039/c7cp05043g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Maintaining the interface of a weak transient protein complex transferred from bulk solution to the gaseous state via evaporating droplets is a critical question in the detection of the complex association (dissociation) constant by using electrospray ionization mass spectrometry (ESI-MS). Here we explore the factors that may affect the stability of a protein-protein interaction (PPI) using atomistic molecular dynamics (MD) modelling of a complex of ubiquitin (Ub) and the ubiquitin-associated domain (UbA) (RCSB PDB code ) and a non-covalent complex of diubiquitin (RCSB PDB code ) in aqueous droplets. A general method is presented to determine the protonation states of the complexes we investigate in particular, and that of a protein in general, under various pH conditions that an evaporating droplet acquires due to its change in size. We find that the combination of high temperature and high charge states of the protein complexes may destabilize the interface by creating new interfaces instead of a direct rupture of the initial stable interface. We provide evidence that highly charged protein complexes are found in droplets that form conical extrusions of the solvent on the surface due to charge-induced instability. This distinct droplet morphology leads to a higher solvent evaporation rate that assists in transferring the complex in the gaseous state without dissociation. The conical solvent protrusions expose on the droplet surface certain amino acids that otherwise would be solvated in a droplet with the protein complex of low charge states. The new vapor-protein interface does not have a direct effect on the stability of the PPI. A common way in experiments to stabilize the protein complexes in droplets is to reduce the protonation state of the proteins. Here we find that weakly bound protein complexes even at high protonation states can be stabilized by the presence of a small number of counterions, without affecting the protonation state of the protein. Our findings may provide guiding principles in ESI-MS experiments to stabilize weak transient PPIs.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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20
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Garcia-Alai MM, Heidemann J, Skruzny M, Gieras A, Mertens HDT, Svergun DI, Kaksonen M, Uetrecht C, Meijers R. Epsin and Sla2 form assemblies through phospholipid interfaces. Nat Commun 2018; 9:328. [PMID: 29362354 PMCID: PMC5780493 DOI: 10.1038/s41467-017-02443-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/30/2017] [Indexed: 01/22/2023] Open
Abstract
In clathrin-mediated endocytosis, adapter proteins assemble together with clathrin through interactions with specific lipids on the plasma membrane. However, the precise mechanism of adapter protein assembly at the cell membrane is still unknown. Here, we show that the membrane-proximal domains ENTH of epsin and ANTH of Sla2 form complexes through phosphatidylinositol 4,5-bisphosphate (PIP2) lipid interfaces. Native mass spectrometry reveals how ENTH and ANTH domains form assemblies by sharing PIP2 molecules. Furthermore, crystal structures of epsin Ent2 ENTH domain from S. cerevisiae in complex with PIP2 and Sla2 ANTH domain from C. thermophilum illustrate how allosteric phospholipid binding occurs. A comparison with human ENTH and ANTH domains reveal only the human ENTH domain can form a stable hexameric core in presence of PIP2, which could explain functional differences between fungal and human epsins. We propose a general phospholipid-driven multifaceted assembly mechanism tolerating different adapter protein compositions to induce endocytosis.
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Affiliation(s)
- Maria M Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Johannes Heidemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Michal Skruzny
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Anna Gieras
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
- University Medical Center Hamburg - Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marko Kaksonen
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany.
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
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21
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Consta S, Sharawy M, Oh MI, Malevanets A. Advances in Modeling the Stability of Noncovalent Complexes in Charged Droplets with Applications in Electrospray Ionization-MS Experiments. Anal Chem 2017; 89:8192-8202. [DOI: 10.1021/acs.analchem.7b01941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Styliani Consta
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Mahmoud Sharawy
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Myong In Oh
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Anatoly Malevanets
- Department
of Electrical and Computer Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada
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22
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Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
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Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
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23
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Zhuang X, Gavriilidou AFM, Zenobi R. Influence of Alkylammonium Acetate Buffers on Protein-Ligand Noncovalent Interactions Using Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:341-346. [PMID: 27830529 DOI: 10.1007/s13361-016-1526-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
We investigate the influence of three volatile alkylammonium acetate buffers on binding affinities for protein-ligand interactions determined by native electrospray ionization-mass spectrometry (ESI-MS). Four different types of proteins were chosen for this study. A charge-reduction effect was observed for all the cases studied, in comparison to the ions formed in ammonium acetate solution. When increasing the collision energy, the complexes of trypsin and the ligand were found to be more stable when sprayed from alkylammonium acetate buffers than from ammonium acetate. The determined dissociation constant (Kd) also exhibited a drop (up to 40%) when ammonium acetate was replaced by alkylammonium acetate buffers for the case of lysozyme and the ligand. The prospective uses of these ammonium acetate analogs in native ESI-MS are discussed in this paper as well. Graphical Abstract ᅟ.
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Affiliation(s)
- Xiaoyu Zhuang
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
- 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, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Agni F M Gavriilidou
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland.
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24
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Oh MI, Consta S. Stability of a Transient Protein Complex in a Charged Aqueous Droplet with Variable pH. J Phys Chem Lett 2017; 8:80-85. [PMID: 27936321 DOI: 10.1021/acs.jpclett.6b02319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has the potential to become a high-throughput robust experimental method for the detection of protein-protein equilibrium constants. Poorly understood processes that affect the stability of weak noncovalent protein complexes in the intervening droplet environment are a significant factor that precludes the advancement of the method. We use molecular dynamics to study the stability of a ubiquitin and ubiquitin-associated domain complex (RCSB PDB code 2MRO ) in an aqueous droplet with changing size and charge concentration. We present evidence that a weak protein complex changes conformation and may dissociate in shrinking droplets. Then, the droplets containing these dissociated proteins divide. Our findings suggest that in some cases ESI-MS does not measure the correct association constants. The study intends to stimulate research for systematic development of experimental protocols that stabilize weakly bound protein interfaces in droplets.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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25
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Biswas S, Sen S, Im J, Biswas S, Krstic P, Ashcroft B, Borges C, Zhao Y, Lindsay S, Zhang P. Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions. ACS NANO 2016; 10:11304-11316. [PMID: 28024337 DOI: 10.1021/acsnano.6b06466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.
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Affiliation(s)
| | | | | | | | - Predrag Krstic
- Institute for Advanced Computational Science, Stony Brook University , Stony Brook, New York 11794-5250, United States
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26
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Rocca R, Moraca F, Costa G, Nadai M, Scalabrin M, Talarico C, Distinto S, Maccioni E, Ortuso F, Artese A, Alcaro S, Richter SN. Identification of G-quadruplex DNA/RNA binders: Structure-based virtual screening and biophysical characterization. Biochim Biophys Acta Gen Subj 2016; 1861:1329-1340. [PMID: 28025082 DOI: 10.1016/j.bbagen.2016.12.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Recent findings demonstrated that, in mammalian cells, telomere DNA (Tel) is transcribed into telomeric repeat-containing RNA (TERRA), which is involved in fundamental biological processes, thus representing a promising anticancer target. For this reason, the discovery of dual (as well as selective) Tel/TERRA G-quadruplex (G4) binders could represent an innovative strategy to enhance telomerase inhibition. METHODS Initially, docking simulations of known Tel and TERRA active ligands were performed on the 3D coordinates of bimolecular G4 Tel DNA (Tel2) and TERRA (TERRA2). Structure-based pharmacophore models were generated on the best complexes and employed for the virtual screening of ~257,000 natural compounds. The 20 best candidates were submitted to biophysical assays, which included circular dichroism and mass spectrometry at different K+ concentrations. RESULTS Three hits were here identified and characterized by biophysical assays. Compound 7 acts as dual Tel2/TERRA2 G4-ligand at physiological KCl concentration, while hits 15 and 17 show preferential thermal stabilization for Tel2 DNA. The different molecular recognition against the two targets was also discussed. CONCLUSIONS Our successful results pave the way to further lead optimization to achieve both increased selectivity and stabilizing effect against TERRA and Tel DNA G4s. GENERAL SIGNIFICANCE The current study combines for the first time molecular modelling and biophysical assays applied to bimolecular DNA and RNA G4s, leading to the identification of innovative ligand chemical scaffolds with a promising anticancer profile. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Carmine Talarico
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, via Ospedale 72, Cagliari 09124, Italy
| | - Elias Maccioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, via Ospedale 72, Cagliari 09124, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
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27
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Im J, Biswas S, Liu H, Zhao Y, Sen S, Biswas S, Ashcroft B, Borges C, Wang X, Lindsay S, Zhang P. Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling. Nat Commun 2016; 7:13868. [PMID: 28000682 PMCID: PMC5187581 DOI: 10.1038/ncomms13868] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM–MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.
Carbohydrates are common biological molecules, but display huge stereochemical complexity that often cannot be elucidated by mass spectrometry. Here the authors show that recognition tunnelling can distinguish individual stereoisomers, utilizing picomole quantities of analytes.
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Affiliation(s)
- JongOne Im
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizonan State University, Tempe, Arizona 85287, USA
| | - Sovan Biswas
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Hao Liu
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Yanan Zhao
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
| | - Suman Sen
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Sudipta Biswas
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Brian Ashcroft
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
| | - Chad Borges
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Xu Wang
- School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA.,School of Molecular Sciences, Arizonan State University, Tempe, Arizona 85287, USA.,Department of Physics, Arizonan State University, Tempe, Arizona 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizonan State University, Tempe, Arizona 85287, USA
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28
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Mehmood S, Marcoux J, Gault J, Quigley A, Michaelis S, Young SG, Carpenter EP, Robinson CV. Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24. Nat Chem 2016; 8:1152-1158. [PMID: 27874871 PMCID: PMC5123592 DOI: 10.1038/nchem.2591] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
Off-target binding of hydrophobic drugs can lead to unwanted side effects, either through specific or non-specific binding to unintended membrane protein targets. However, distinguishing the binding of drugs to membrane proteins from that of detergents, lipids and cofactors is challenging. Here, we use high-resolution mass spectrometry to study the effects of HIV protease inhibitors on the human zinc metalloprotease ZMPSTE24. This intramembrane protease plays a major role in converting prelamin A to mature lamin A. We monitored the proteolysis of farnesylated prelamin A peptide by ZMPSTE24 and unexpectedly found retention of the C-terminal peptide product with the enzyme. We also resolved binding of zinc, lipids and HIV protease inhibitors and showed that drug binding blocked prelamin A peptide cleavage and conferred stability to ZMPSTE24. Our results not only have relevance for the progeria-like side effects of certain HIV protease inhibitor drugs, but also highlight new approaches for documenting off-target drug binding.
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Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Julien Marcoux
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Quigley
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Stephen G Young
- Departments of Medicine and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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29
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Chingin K, Barylyuk K, Chen H. On the preservation of non-covalent protein complexes during electrospray ionization. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0377. [PMID: 27644969 PMCID: PMC5031642 DOI: 10.1098/rsta.2015.0377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 06/06/2023]
Abstract
The application range of electrospray ionization mass spectrometry for the quantitative determination of stoichiometries and binding constants for non-covalent protein complexes is broadly discussed. The underlying fundamental question is whether or not the original molecular equilibrium can be preserved during the ionization process and be revealed by subsequent mass spectrometry analysis. Here, we take a new look at this question by discussing recent studies in droplet chemistry.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Guanglan Road 418, Nanchang, Jiangxi 330013, People's Republic of China
| | - Konstantin Barylyuk
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Guanglan Road 418, Nanchang, Jiangxi 330013, People's Republic of China
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30
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Pedro L, Van Voorhis WC, Quinn RJ. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1520-30. [PMID: 27225419 PMCID: PMC4972871 DOI: 10.1007/s13361-016-1417-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 05/28/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ.
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Affiliation(s)
- Liliana Pedro
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | | | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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31
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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32
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Composition of thiacalix[4]arene complexes with monovalent metal ions in the gas phase: MALDI mass spectrometry. Russ Chem Bull 2016. [DOI: 10.1007/s11172-015-1078-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Li H, Ha E, Donaldson RP, Jeremic AM, Vertes A. Rapid assessment of human amylin aggregation and its inhibition by copper(II) ions by laser ablation electrospray ionization mass spectrometry with ion mobility separation. Anal Chem 2016; 87:9829-9837. [PMID: 26352401 DOI: 10.1021/acs.analchem.5b02217] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Native electrospray ionization (ESI) mass spectrometry (MS) is often used to monitor noncovalent complex formation between peptides and ligands. The relatively low throughput of this technique, however, is not compatible with extensive screening. Laser ablation electrospray ionization (LAESI) MS combined with ion mobility separation (IMS) can analyze complex formation and provide conformation information within a matter of seconds. Islet amyloid polypeptide (IAPP) or amylin, a 37-amino acid residue peptide, is produced in pancreatic beta-cells through proteolytic cleavage of its prohormone. Both amylin and its precursor can aggregate and produce toxic oligomers and fibrils leading to cell death in the pancreas that can eventually contribute to the development of type 2 diabetes mellitus. The inhibitory effect of the copper(II) ion on amylin aggregation has been recently discovered, but details of the interaction remain unknown. Finding other more physiologically tolerated approaches requires large scale screening of potential inhibitors. Here, we demonstrate that LAESI-IMS-MS can reveal the binding stoichiometry, copper oxidation state, and the dissociation constant of human amylin-copper(II) complex. The conformations of hIAPP in the presence of copper(II) ions were also analyzed by IMS, and preferential association between the β-hairpin amylin monomer and the metal ion was found. The copper(II) ion exhibited strong association with the -HSSNN- residues of the amylin. In the absence of copper(II), amylin dimers were detected with collision cross sections consistent with monomers of β-hairpin conformation. When copper(II) was present in the solution, no dimers were detected. Thus, the copper(II) ions disrupt the association pathway to the formation of β-sheet rich amylin fibrils. Using LAESI-IMS-MS for the assessment of amylin-copper(II) interactions demonstrates the utility of this technique for the high-throughput screening of potential inhibitors of amylin oligomerization and fibril formation. More generally, this rapid technique opens the door for high-throughput screening of potential inhibitors of amyloid protein aggregation.
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Affiliation(s)
- Hang Li
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, D.C. 20052, United States
| | - Emmeline Ha
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, D.C. 20052, United States
| | - Robert P Donaldson
- Department of Biological Sciences, The George Washington University, Washington, D.C. 20052, United States
| | - Aleksandar M Jeremic
- Department of Biological Sciences, The George Washington University, Washington, D.C. 20052, United States
| | - Akos Vertes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, D.C. 20052, United States
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34
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Chen F, Gülbakan B, Weidmann S, Fagerer SR, Ibáñez AJ, Zenobi R. Applying mass spectrometry to study non-covalent biomolecule complexes. MASS SPECTROMETRY REVIEWS 2016; 35:48-70. [PMID: 25945814 DOI: 10.1002/mas.21462] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 05/10/2023]
Abstract
Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Basri Gülbakan
- Institute of Child Health, Division of Pediatric Basic Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Simon Weidmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Stephan R Fagerer
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Alfredo J Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
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35
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Santos IC, Waybright VB, Fan H, Ramirez S, Mesquita RBR, Rangel AOSS, Fryčák P, Schug KA. Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1204-1212. [PMID: 25832030 DOI: 10.1007/s13361-015-1113-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 06/04/2023]
Abstract
Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac-L-Lys(Ac)-D-Ala-D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac-L-Lys(Ac)-D-Ala-L-Ala, Ac-L-Lys(Ac)-L-Ala-D-Ala, and Ac-L-Lys(Ac)-L-Ala-L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes.
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Affiliation(s)
- Inês C Santos
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401, Porto, Portugal
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36
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Yan B, Yesilbag Tonga G, Hou S, Fedick PW, Yeh YC, Alfonso FS, Mizuhara T, Vachet RW, Rotello VM. Mass spectrometric detection of nanoparticle host-guest interactions in cells. Anal Chem 2014; 86:6710-4. [PMID: 24873526 PMCID: PMC4082387 DOI: 10.1021/ac501682y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Synthetic host–guest chemistry
is a versatile tool for biomedical
applications. Characterization and detection of host–guest
complexes in biological systems, however, is challenging due to the
complexity of the biological milieu. Here, we describe and apply a
mass spectrometric method to monitor the association and dissociation
of nanoparticle (NP)-based host–guest interactions that integrates
NP-assisted laser desorption/ionization (LDI) and matrix assisted
laser desoption/ionization (MALDI) mass spectrometry. This LDI/MALDI
approach reveals how NP surface functionality affects host–guest
interactions in cells, information difficult to achieve using other
techniques.
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Affiliation(s)
- Bo Yan
- Department of Chemistry, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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37
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Frankevich V, Barylyuk K, Chingin K, Nieckarz R, Zenobi R. Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein. Chemphyschem 2013; 14:929-35. [DOI: 10.1002/cphc.201200959] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/22/2013] [Indexed: 01/19/2023]
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38
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Chen F, Gülbakan B, Zenobi R. Direct access to aptamer–protein complexes via MALDI-MS. Chem Sci 2013. [DOI: 10.1039/c3sc51410b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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39
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Dai Y, Guo M, Peng J, Shen W, Li M, He R, Zhu C, Lin SH. Noncovalent interaction and its influence on excited-state behavior: A theoretical study on the mixed coaggregates of dicyanonaphthalene and pyrazoline. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.11.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Mealman TD, Zhou M, Affandi T, Chacón KN, Aranguren ME, Blackburn NJ, Wysocki VH, McEvoy MM. N-terminal region of CusB is sufficient for metal binding and metal transfer with the metallochaperone CusF. Biochemistry 2012; 51:6767-75. [PMID: 22812620 DOI: 10.1021/bi300596a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Gram-negative bacteria, such as Escherichia coli, utilize efflux resistance systems in order to expel toxins from their cells. Heavy-metal resistance is mediated by resistance nodulation cell division (RND)-based efflux pumps composed of a tripartite complex that includes an RND-transporter, an outer-membrane factor (OMF), and a membrane fusion protein (MFP) that spans the periplasmic space. MFPs are necessary for complex assembly and have been hypothesized to play an active role in substrate efflux. Crystal structures of MFPs are available, however incomplete, as large portions of the apparently disordered N- and C-termini are unresolved. Such is the case for CusB, the MFP of the E. coli Cu(I)/Ag(I) efflux pump CusCFBA. In this work, we have investigated the structure and function of the N-terminal region of CusB, which includes the metal-binding site and is missing from previously determined crystal structures. Results from mass spectrometry and X-ray absorption spectroscopy show that the isolated N-terminal 61 residues (CusB-NT) bind metal in a 1:1 stoichiometry with a coordination site composed of M21, M36, and M38, consistent with full-length CusB. NMR spectra show that CusB-NT is mostly disordered in the apo state; however, some slight structure is adopted upon metal binding. Much of the intact protein's function is maintained in this fragment as CusB-NT binds metal in vivo and in vitro, and metal is transferred between the metallochaperone CusF and CusB-NT in vitro. Functional analysis in vivo shows that full-length CusB is necessary in an intact polypeptide for full metal resistance, though CusB-NT alone can contribute partial metal resistance. These findings reinforce the theory that the role of CusB is not only to bind metal but also to play an active role in efflux.
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Affiliation(s)
- Tiffany D Mealman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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