1
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Shui T, Li A, Chae M, Xu CC, Bressler DC. Valorization strategies for hazardous proteinaceous waste from rendering production - Recent advances in specified risk materials (SRMs) conversion. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131339. [PMID: 37058938 DOI: 10.1016/j.jhazmat.2023.131339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Strict bans on specific risk materials (SRMs) are in place to prevent the spread of bovine spongiform encephalopathy (BSE). SRMs are characterized as tissues in cattle where misfolded proteins, the potential source of BSE infection, are concentrated. As a result of these bans, SRMs must be strictly isolated and disposed of, resulting in great costs for rendering companies. The increasing yield and the landfill of SRMs also exacerbated the burden on the environment. To cope with the emergence of SRMs, novel disposal methods and feasible value-added conversion routes are needed. The focus of this review is on the valorization progress achieved in the conversion of peptides derived from SRMs via an alternative disposal method, thermal hydrolysis. Promising value-added conversion of SRM-derived peptides into tackifiers, wood adhesives, flocculants, and bioplastics, is introduced. The potential conjugation strategies that can be adapted to SRM-derived peptides for desired properties are also critically reviewed. The purpose of this review is to discover a technical platform through which other hazardous proteinaceous waste, SRMs, can be treated as a high-demand feedstock for the production of renewable materials.
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Affiliation(s)
- Tao Shui
- School of Materials Science and Engineering, Southeast University, Nanjing, China; Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - An Li
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Michael Chae
- Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Chunbao Charles Xu
- Department of Chemical and Biochemical Engineering, Western University, London, Ontario N6A 5B9, Canada
| | - David C Bressler
- Biorefining Conversions and Fermentation Laboratory, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada.
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2
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Oligonucleotide conjugated antibody strategies for cyclic immunostaining. Sci Rep 2021; 11:23844. [PMID: 34903759 PMCID: PMC8668956 DOI: 10.1038/s41598-021-03135-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022] Open
Abstract
A number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely used methods are limited by harmful signal removal techniques, difficulties with reagent production and antigen sensitivity. Multiplexed immunostaining employing oligonucleotide (oligos)-barcoded antibodies is an alternative approach that is growing in popularity. However, challenges remain in consistent conjugation of oligos to antibodies with maintained antigenicity as well as non-destructive, robust and cost-effective signal removal methods. Herein, a variety of oligo conjugation and signal removal methods were evaluated in the development of a robust oligo conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) methodology. Both non- and site-specific conjugation strategies were assessed to label antibodies, where site-specific conjugation resulted in higher retained binding affinity and antigen-specific staining. A variety of fluorescence signal removal methods were also evaluated, where incorporation of a photocleavable link (PCL) resulted in full fluorescence signal removal with minimal tissue disruption. In summary, this work resulted in an optimized Ab-oligo cyCIF platform capable of generating high dimensional images to characterize the spatial proteomics of the hallmarks of cancer.
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3
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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4
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Kratzer U, Sommersdorf C, Maier S, Wagner TR, Templin M, Joos TO, Rothbauer U, Zeck A, Poetz O. Tris(hydroxymethyl)aminomethane Compatibility with N-Hydroxysuccinimide Ester Chemistry: Biotinylation of Peptides and Proteins in TRIS Buffer. Bioconjug Chem 2021; 32:1960-1965. [PMID: 34406760 DOI: 10.1021/acs.bioconjchem.1c00283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Hydroxysuccinimide esters of small molecules are widely used to modify biomolecules such as antibodies or proteins. Primary amine groups preferably react with the ester to form covalent amide bonds. Currently, protocols strongly recommend replacing the buffer reagent tris(hydroxymethyl)aminomethane, and it has even been proposed as a stop reagent. Here, we show that TRIS indeed does not interfere with biotinylation of biomolecules with NHS chemistry.
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Affiliation(s)
- Ulrich Kratzer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | | | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- SIGNATOPE GmbH, 72770 Reutlingen, Germany
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5
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Abstract
Cross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a "light" and a "heavy" cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
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6
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Smith S, Goodge K, Delaney M, Struzyk A, Tansey N, Frey M. A Comprehensive Review of the Covalent Immobilization of Biomolecules onto Electrospun Nanofibers. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2142. [PMID: 33121181 PMCID: PMC7692479 DOI: 10.3390/nano10112142] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 01/08/2023]
Abstract
Biomolecule immobilization has attracted the attention of various fields such as fine chemistry and biomedicine for their use in several applications such as wastewater, immunosensors, biofuels, et cetera. The performance of immobilized biomolecules depends on the substrate and the immobilization method utilized. Electrospun nanofibers act as an excellent substrate for immobilization due to their large surface area to volume ratio and interconnectivity. While biomolecules can be immobilized using adsorption and encapsulation, covalent immobilization offers a way to permanently fix the material to the fiber surface resulting in high efficiency, good specificity, and excellent stability. This review aims to highlight the various covalent immobilization techniques being utilized and their benefits and drawbacks. These methods typically fall into two categories: (1) direct immobilization and (2) use of crosslinkers. Direct immobilization techniques are usually simple and utilize the strong electrophilic functional groups on the nanofiber. While crosslinkers are used as an intermediary between the nanofiber substrate and the biomolecule, with some crosslinkers being present in the final product and others simply facilitating the reactions. We aim to provide an explanation of each immobilization technique, biomolecules commonly paired with said technique and the benefit of immobilization over the free biomolecule.
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Affiliation(s)
- Soshana Smith
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, NY 14853, USA; (K.G.); (N.T.); (M.F.)
| | - Katarina Goodge
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, NY 14853, USA; (K.G.); (N.T.); (M.F.)
| | - Michael Delaney
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; (M.D.); (A.S.)
| | - Ariel Struzyk
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; (M.D.); (A.S.)
| | - Nicole Tansey
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, NY 14853, USA; (K.G.); (N.T.); (M.F.)
| | - Margaret Frey
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, NY 14853, USA; (K.G.); (N.T.); (M.F.)
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7
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Kohl B, Brüderlin M, Ritz D, Schmidt A, Hiller S. Protocol for High-Yield Production of Photo-Leucine-Labeled Proteins in Escherichia coli. J Proteome Res 2020; 19:3100-3108. [PMID: 32412763 DOI: 10.1021/acs.jproteome.0c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UV-cross-linking mass spectrometry is an emerging technique to obtain structural information of biomacromolecules and their complexes in vivo and in vitro. In particular, certain photo-reactive amino acids (pA) such as photo-leucine (pLeu) and photo-methionine can provide unique short-distance information on the structural core regions of proteins. Here, we present a protocol for high-yield incorporation of pLeu in proteins recombinantly expressed in Escherichia coli. The protein of interest is expressed at high cell densities, which reduces the required amount of the pA by a factor of 10, as compared to the standard protocols, while maintaining high incorporation rates. For the two chaperones, trigger factor and SecB, up to 3 mg of pLeu-labeled protein were thus obtained from 100 mL of cell culture, with label incorporation rates of up to 34%. For trigger factor, UV-induced cross-linking leads to the identification of 12 cross-links that are in agreement with the published three-dimensional structures. The accessibility of milligram amounts of pLeu-labeled proteins at low costs will be highly useful to address structural biology questions.
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Affiliation(s)
- Bastian Kohl
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Mitchell Brüderlin
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Danilo Ritz
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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8
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Wahab RA, Elias N, Abdullah F, Ghoshal SK. On the taught new tricks of enzymes immobilization: An all-inclusive overview. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104613] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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10
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Mao C, Lee MY, Jhan JR, Halpern AR, Woodworth MA, Glaser AK, Chozinski TJ, Shin L, Pippin JW, Shankland SJ, Liu JT, Vaughan JC. Feature-rich covalent stains for super-resolution and cleared tissue fluorescence microscopy. SCIENCE ADVANCES 2020; 6:eaba4542. [PMID: 32518827 PMCID: PMC7253160 DOI: 10.1126/sciadv.aba4542] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/11/2020] [Indexed: 05/02/2023]
Abstract
Fluorescence microscopy is a workhorse tool in biomedical imaging but often poses substantial challenges to practitioners in achieving bright or uniform labeling. In addition, while antibodies are effective specific labels, their reproducibility is often inconsistent, and they are difficult to use when staining thick specimens. We report the use of conventional, commercially available fluorescent dyes for rapid and intense covalent labeling of proteins and carbohydrates in super-resolution (expansion) microscopy and cleared tissue microscopy. This approach, which we refer to as Fluorescent Labeling of Abundant Reactive Entities (FLARE), produces simple and robust stains that are modern equivalents of classic small-molecule histology stains. It efficiently reveals a wealth of key landmarks in cells and tissues under different fixation or sample processing conditions and is compatible with immunolabeling of proteins and in situ hybridization labeling of nucleic acids.
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Affiliation(s)
- Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jing-Ru Jhan
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Leonard Shin
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jeffrey W. Pippin
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Stuart J. Shankland
- Department of Medicine, Division of Nephrology, University of Washington, Seattle, Washington, USA
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
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11
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Esch P, Fischer M, Heiles S, Schäfer M. Olefinic reagents tested for peptide derivatization with switchable properties: Stable upon collision induced dissociation and cleavable by in-source Paternò-Büchi reactions. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:976-986. [PMID: 31729095 DOI: 10.1002/jms.4474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
This contribution is part of our ongoing efforts to develop innovative cross-linking (XL) reagents and protocols for facilitated peptide mixture analysis and efficient assignment of cross-linked peptide products. In this report, we combine in-source Paternò-Büchi (PB) photo-chemistry with a tandem mass spectrometry approach to selectively address the fragmentation of a tailor-made cross-linking reagent. The PB photochemistry, so far exclusively used for the identification of unsaturation sites in lipids and in lipidomics, is now introduced to the field of chemical cross-linking. Based on trans-3-hexenedioic acid, an olefinic homo bifunctional amine reactive XL reagent was designed and synthesized for this proof-of-principle study. Condensation products of the olefinic reagent with a set of exemplary peptides are used to test the feasibility of the concept. Benzophenone is photochemically reacted in the nano-electrospray ion source and forms oxetane PB reaction products. Subsequent CID-MS triggered retro-PB reaction of the respective isobaric oxetane molecular ions and delivers reliably and predictably two sets of characteristic fragment ions of the cross-linker. Based on these signature ion sets, a straightforward identification of covalently interconnected peptides in complex digests is proposed. Furthermore, CID-MSn experiments of the retro-PB reaction products deliver peptide backbone characteristic fragment ions. Additionally, the olefinic XL reagents exhibit a pronounced robustness upon CID-activation, without previous UV-excitation. These experiments document that a complete backbone fragmentation is possible, while the linker-moiety remains intact. This feature renders the new olefinic linkers switchable between a stable, noncleavable cross-linking mode and an in-source PB cleavable mode.
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Affiliation(s)
- Patrick Esch
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich Buff Ring 17, D-35392 Giessen, Germany
| | - Moritz Fischer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, D-50939, Cologne, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich Buff Ring 17, D-35392 Giessen, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, D-50939, Cologne, Germany
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12
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Selective Derivatization of Hexahistidine-Tagged Recombinant Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31347051 DOI: 10.1007/978-3-030-15950-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Covalent modification of proteins is extensively used in research and industry for biosensing, medical diagnostics, targeted drug delivery, and many other practical applications. The conventional method for production of protein conjugates has changed little in the last 20 years mostly relying on reactions of side chains of cysteine and lysine residues. Due to the presence of large numbers of similar reactive amino acid residues in proteins, common synthetic methods generally produce complex mixtures of products, which are difficult to separate. An emerging alternative technology for covalent modification of proteins involves formation of a covalent bond with a hexahistidine affinity tag present in a majority of recombinant proteins without interfering with other amino acid residues. The approach is based on formation of a ternary complex of the hexahistidine sequence with a bivalent metal cation chelated by ligand bearing an electrophilic Baylis-Hillman ester group capable of subsequent formation of a covalent bond with one of the histidine residues of the tag. The reaction proceeds under mild reaction conditions in neutral aqueous solutions under high dilutions (10-5 to 10-4 M) providing a stable covalent bond between the label and an imidazole residue in a hexahistidine tag at either C- or N-terminus. Because hexahistidine affinity tag methodology is a de-facto standard for preparation of recombinant proteins our approach can be easily implemented for selective derivatization of these proteins with fluorescent groups, alkynyl groups for "click" reactions, or biotinylation.
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13
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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14
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Kwon Y, Ju S, Kaushal P, Lee JW, Lee C. Neutralizing the Detrimental Effect of an N-Hydroxysuccinimide Quenching Reagent on Phosphopeptide in Quantitative Proteomics. Anal Chem 2018; 90:3019-3023. [PMID: 29406695 DOI: 10.1021/acs.analchem.7b04678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most common chemistries used to label primary amines utilizes N-hydroxysuccinimide (NHS), which is also structurally incorporated in various quantitative proteomic reagents such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT). In this paper we report detrimental effect of hydroxylamine, a widely used quenching reagent for excess NHS, on phosphopeptides. We found an impairment in the degree of phosphopeptide identification when hydroxylamine-quenched TMT-labeled samples were vacuum-dried and desalted compared to the nondried (just diluted) and desalted ones prior to phosphoenrichment. We have also demonstrated that vacuum-drying in the presence of hydroxylamine promotes β-elimination of phosphate groups from phosphoserine and phosphothreonine while having a minimalistic effect on phosphotyrosine. Additionally, we herein report that this negative impact of hydroxylamine could be minimized by direct desalting after appropriate dilution of quenched samples. We also found a 1.6-fold increase in the number of phosphopeptide identifications after employing our optimized method. The above method was also successfully applied to human tumor tissues to quantify over 15000 phosphopeptides from 3 mg TMT 6-plex labeled-peptides.
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Affiliation(s)
- Yumi Kwon
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Shinyeong Ju
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Prashant Kaushal
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Cheolju Lee
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
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15
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Jacobsen MT, Fairhead M, Fogelstrand P, Howarth M. Amine Landscaping to Maximize Protein-Dye Fluorescence and Ultrastable Protein-Ligand Interaction. Cell Chem Biol 2017; 24:1040-1047.e4. [PMID: 28757182 PMCID: PMC5563079 DOI: 10.1016/j.chembiol.2017.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022]
Abstract
Chemical modification of proteins provides great opportunities to control and visualize living systems. The most common way to modify proteins is reaction of their abundant amines with N-hydroxysuccinimide (NHS) esters. Here we explore the impact of amine number and positioning on protein-conjugate behavior using streptavidin-biotin, a central research tool. Dye-NHS modification of streptavidin severely damaged ligand binding, necessitating development of a new streptavidin-retaining ultrastable binding after labeling. Exploring the ideal level of dye modification, we engineered a panel bearing 1–6 amines per subunit: “amine landscaping.” Surprisingly, brightness increased as amine number decreased, revealing extensive quenching following conventional labeling. We ultimately selected Flavidin (fluorophore-friendly streptavidin), combining ultrastable ligand binding with increased brightness after conjugation. Flavidin enhanced fluorescent imaging, allowing more sensitive and specific cell labeling in tissues. Flavidin should have wide application in molecular detection, providing a general insight into how to optimize simultaneously the behavior of the biomolecule and the chemical probe. Labeling of streptavidin with small-molecule dyes impairs ligand binding K121R mutation rescues ligand stability after dye labeling Landscaping of protein amines optimizes brightness Fluorophore-friendly streptavidin improves imaging specificity and sensitivity
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Affiliation(s)
- Michael T Jacobsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Per Fogelstrand
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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16
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Izquierdo-Serra M, Bautista-Barrufet A, Trapero A, Garrido-Charles A, Díaz-Tahoces A, Camarero N, Pittolo S, Valbuena S, Pérez-Jiménez A, Gay M, García-Moll A, Rodríguez-Escrich C, Lerma J, de la Villa P, Fernández E, Pericàs MÀ, Llebaria A, Gorostiza P. Optical control of endogenous receptors and cellular excitability using targeted covalent photoswitches. Nat Commun 2016; 7:12221. [PMID: 27436051 PMCID: PMC4961765 DOI: 10.1038/ncomms12221] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 06/10/2016] [Indexed: 12/15/2022] Open
Abstract
Light-regulated drugs allow remotely photoswitching biological activity and enable plausible therapies based on small molecules. However, only freely diffusible photochromic ligands have been shown to work directly in endogenous receptors and methods for covalent attachment depend on genetic manipulation. Here we introduce a chemical strategy to covalently conjugate and photoswitch the activity of endogenous proteins and demonstrate its application to the kainate receptor channel GluK1. The approach is based on photoswitchable ligands containing a short-lived, highly reactive anchoring group that is targeted at the protein of interest by ligand affinity. These targeted covalent photoswitches (TCPs) constitute a new class of light-regulated drugs and act as prosthetic molecules that photocontrol the activity of GluK1-expressing neurons, and restore photoresponses in degenerated retina. The modularity of TCPs enables the application to different ligands and opens the way to new therapeutic opportunities. Biological activity can be photoswitched by light-regulated drugs, but so far only diffusible ligands have been shown to work on endogenous receptors. Here the authors develop targeted covalent photoswitches that couple to a protein target by ligand affinity, and demonstrate photocontrol of GluK1-expressing neurons.
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Affiliation(s)
| | - Antoni Bautista-Barrufet
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain
| | - Ana Trapero
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Institut de Química Avançada de Catalunya (IQAC-CSIC), Barcelona 08034, Spain
| | | | - Ariadna Díaz-Tahoces
- Instituto de Bioingeniería, Universidad Miguel Hernández (UMH), Elche 03202, Spain
| | - Nuria Camarero
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain
| | - Silvia Pittolo
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain
| | - Sergio Valbuena
- Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante 03550, Spain
| | | | - Marina Gay
- Institut de Recerca en Biomedicina (IRBB), Barcelona 08028, Spain
| | | | - Carles Rodríguez-Escrich
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain
| | - Juan Lerma
- Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante 03550, Spain
| | - Pedro de la Villa
- Universidad de Alcalá de Henares (UAH), Alcalá de Henares 28871, Spain
| | - Eduardo Fernández
- Instituto de Bioingeniería, Universidad Miguel Hernández (UMH), Elche 03202, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza 50018, Spain
| | - Miquel À Pericàs
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona 43007, Spain.,Departament de Química Inorgànica i Orgànica, Universitat de Barcelona (UB), Barcelona 08007, Spain
| | - Amadeu Llebaria
- Institut de Química Avançada de Catalunya (IQAC-CSIC), Barcelona 08034, Spain
| | - Pau Gorostiza
- Institut de Bioenginyeria de Catalunya (IBEC), Barcelona 08028, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Zaragoza 50018, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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17
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Abstract
The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.
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18
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Sinz A, Arlt C, Chorev D, Sharon M. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology. Protein Sci 2015; 24:1193-209. [PMID: 25970732 PMCID: PMC4534171 DOI: 10.1002/pro.2696] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/14/2015] [Accepted: 04/29/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.
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Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Dror Chorev
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
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19
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Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:99-116. [PMID: 24881459 DOI: 10.1255/ejms.1259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications.
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20
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Liu XX, Melman A. Templated alkylation of hexahistidine with Baylis-Hillman esters. Chem Commun (Camb) 2013; 49:9042-4. [PMID: 23985693 DOI: 10.1039/c3cc43271h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alkylation of one of the imidazole rings of hexahistidine with Baylis-Hillman esters tethered to nitrilotriacetate residue was achieved in aqueous solutions at neutral pH and at micromolar concentrations in the presence of Ni(2+), Cu(2+), or Zn(2+) cations. The utility of the approach for selective functionalization of His-tagged recombinant proteins was demonstrated by attachment of a fluorescent label to recombinant protein A with an alkynyl group followed by a "click" 1,3-dipolar cycloaddition reaction.
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Affiliation(s)
- Xing Xin Liu
- Clarkson University, Department of Chemistry & Biomolecular Science, Potsdam, New York, USA.
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21
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Chen F, Nielsen S, Zenobi R. Understanding chemical reactivity for homo- and heterobifunctional protein cross-linking agents. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:807-812. [PMID: 23832936 DOI: 10.1002/jms.3224] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/23/2013] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
Chemical cross-linking, combined with mass spectrometry, has been applied to map three-dimensional protein structures and protein-protein interactions. Proper choice of the cross-linking agent, including its reactive groups and spacer arm length, is of great importance. However, studies to understand the details of reactivity of the chemical cross-linkers with proteins are quite sparse. In this study, we investigated chemical cross-linking from the aspects of the protein structures and the cross-linking reagents involved, by using two structurally well-known proteins, glyceraldehyde 3-phosohate dehydrogenase and ribonuclease S. Chemical cross-linking reactivity was compared using a series of homo- and hetero-bifunctional cross-linkers, including bis(sulfosuccinimidyl) suberate, dissuccinimidyl suberate, bis(succinimidyl) penta (ethylene glycol), bis(succinimidyl) nona (ethylene glycol), m-maleimidobenzoyl-N-hydroxysulfosuccinimide ester, 2-pyridyldithiol-tetraoxaoctatriacontane-N-hydrosuccinimide and succinimidyl-[(N-maleimidopropionamido)-tetracosaethyleneglycol]ester. The protein structure itself, especially the distances between target amino acid residues, was found to be a determining factor for the cross-linking efficiency. Moreover, the reactive groups of the chemical cross-linker also play an important role; a higher cross-linking reaction efficiency was found for maleimides compared to 2-pyrimidyldithiols. The reaction between maleimides and sulfhydryl groups is more favorable than that between N-hydroxysuccinimide esters and amine groups, although cysteine residues are less abundant in proteins compared to lysine residues.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
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22
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Slósarczyk AT, Baltzer L. Efficient formation of heterodimers from peptides and proteins using unsymmetrical polyfluorophenyl esters of dicarboxylic acids. J Pept Sci 2012; 18:261-9. [PMID: 22392885 DOI: 10.1002/psc.2394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/12/2011] [Accepted: 12/14/2011] [Indexed: 11/09/2022]
Abstract
An efficient method for the heteroconjugation of biomolecules carrying free amino groups was reported previously, where mixed polyfluorophenyl diesters of dicarboxylic acids with varied aliphatic chain length were shown to be efficient reagents for the conjugation of a variety of model biomolecules. The concept was based on the differential reactivity of the esters towards amines. The concept has now been further optimized, and a 2,6-difluorophenyl-pentafluorophenyl diester combination has been demonstrated to be the most efficient, both with respect to selectivity and to reaction rate. A pentafluorophenyl ester reacts faster with an amino group and requires a weaker base than a 2,6-difluorophenyl ester that requires a stronger base and longer reaction time. With the use of this combination of esters, we obtained considerably shortened reaction times compared with those reported previously, yet still retaining the desired selectivity in heteroconjugation. The increased reactivity of the bifunctional reagent allowed the construction of sophisticated peptide heteroconjugates from peptides, carbohydrates and proteins, showing a wide scope of applicability in the field of assembling functional bioconjugates.
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Affiliation(s)
- Adam T Slósarczyk
- Department of Biochemistry and Organic Chemistry, Uppsala University, PO Box 576, SE-751 23 Uppsala, Sweden
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23
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Link M, Schulze P, Belder D, Wolfbeis OS. New diode laser-excitable green fluorescent label and its application to detection of bovine serum albumin via microchip electrophoresis. Mikrochim Acta 2009. [DOI: 10.1007/s00604-009-0169-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Bae L, Vik SB. A more robust version of the Arginine 210-switched mutant in subunit a of the Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1129-34. [PMID: 19362069 DOI: 10.1016/j.bbabio.2009.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/30/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
Previous work has shown that the essential R210 of subunit a in the Escherichia coli ATP synthase can be switched with a conserved glutamine Q252 with retention of a moderate level of function, that a third mutation P204T enhances this function, and that the arginine Q252R can be replaced by lysine without total loss of activity. In this study, the roles of P204T and R210Q were examined. It was concluded that the threonine in P204T is not directly involved in function since its replacement by alanine did not significantly affect growth properties. Similarly, it was concluded that the glutamine in R210Q is not directly involved with function since replacement by glycine results in significantly enhanced function. Not only did the rate of ATP-driven proton translocation increase, but also the sensitivity of ATP hydrolysis to inhibition by N,N'-dicyclohexylcarbodiimide (DCCD) rose to more than 50%. Finally, mutations at position E219, a residue near the proton pathway, were used to test whether the Arginine-switched mutant uses the normal proton pathway. In a wild type background, the E219K mutant was confirmed to have greater function than the E219Q mutant, as has been shown previously. This same unusual result was observed in the triple mutant background, P204T/R210Q/Q252R, suggesting that the Arginine-switched mutants are using the normal proton pathway from the periplasm.
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Affiliation(s)
- Leon Bae
- Southern Methodist University, Department of Biological Sciences, Dallas, TX 75275-0376, USA
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25
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Mouradov D, King G, Ross IL, Forwood JK, Hume DA, Sinz A, Martin JL, Kobe B, Huber T. Protein structure determination using a combination of cross-linking, mass spectrometry, and molecular modeling. Methods Mol Biol 2008; 426:459-474. [PMID: 18542884 DOI: 10.1007/978-1-60327-058-8_31] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cross-linking in combination with mass spectrometry can be used as a tool for structural modeling of protein complexes and multidomain proteins. Although cross-links represent only weak structural constraints, the combination of a limited set of experimental cross-links with molecular docking/modeling is often sufficient to determine the structure of a protein complex or multidomain protein at low resolution.
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Affiliation(s)
- Dmitri Mouradov
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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26
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Ishmukhametov RR, Pond JB, Al-Huqail A, Galkin MA, Vik SB. ATP synthesis without R210 of subunit a in the Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1777:32-8. [PMID: 18068111 DOI: 10.1016/j.bbabio.2007.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 11/02/2007] [Accepted: 11/07/2007] [Indexed: 11/29/2022]
Abstract
Interactions between subunit a and oligomeric subunit c are essential for the coupling of proton translocation to rotary motion in the ATP synthase. A pair of previously described mutants, R210Q/Q252R and P204T/R210Q/Q252R [L.P. Hatch, G.B. Cox and S.M. Howitt, The essential arginine residue at position 210 in the a subunit of the Escherichia coli ATP synthase can be transferred to position 252 with partial retention of activity, J. Biol. Chem. 270 (1995) 29407-29412] has been constructed and further analyzed. These mutants, in which the essential arginine of subunit a, R210, was switched with a conserved glutamine residue, Q252, are shown here to be capable of both ATP synthesis by oxidative phosphorylation, and ATP-driven proton translocation. In addition, lysine can replace the arginine at position 252 with partial retention of both activities. The pH dependence of ATP-driven proton translocation was determined after purification of mutant enzymes, and reconstitution into liposomes. Proton translocation by the lysine mutant, and to a lesser extent the arginine mutant, dropped off sharply above pH 7.5, consistent with the requirement for a positive charge during function. Finally, the rates of ATP synthesis and of ATP-driven proton translocation were completely inhibited by treatment with DCCD (N,N'-dicyclohexylcarbodiimide), while rates of ATP hydrolysis by the mutants were not significantly affected, indicating that DCCD modification disrupts the F(1)-F(o) interface. The results suggest that minimal requirements for proton translocation by the ATP synthase include a positive charge in subunit a and a weak interface between subunit a and oligomeric subunit c.
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Affiliation(s)
- Robert R Ishmukhametov
- Department of Biological Sciences, Box 750376, Southern Methodist University, Dallas, TX 75275-0376, USA
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27
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Martinek K, Mozhaev VV. Immobilization of enzymes: an approach to fundamental studies in biochemistry. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 57:179-249. [PMID: 3898741 DOI: 10.1002/9780470123034.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Penefsky HS. Mitochondrial ATPase. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 49:223-80. [PMID: 162556 DOI: 10.1002/9780470122945.ch6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Considerable progress has been made in recent years in our understanding of the phosphorylating apparatus in mitochondria, chloroplasts, and bacteria. It has become clear that the structure and the function of the ATP synthesizing apparatus in these widely divergent organisms is similar if not virtually identical. The subunit composition of F1, its molecular architecture, the location and function of substrate binding sites, as well as putative control sites, understanding of the component parts of the oligomycin-sensitive ATPase complex, and the role of these components in the function of the complex all are under active investigation in many laboratories. The developing information and the new insights provided have begun to permit experimental approaches, at the molecular level, to the mode of action of the ATPase in electron-transport-coupled ATP synthesis.
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29
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Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. MASS SPECTROMETRY REVIEWS 2006; 25:663-82. [PMID: 16477643 DOI: 10.1002/mas.20082] [Citation(s) in RCA: 510] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.
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Affiliation(s)
- Andrea Sinz
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany.
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30
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Galkin MA, Ishmukhametov RR, Vik SB. A functionally inactive, cold-stabilized form of the Escherichia coli F1Fo ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:206-14. [PMID: 16581013 PMCID: PMC1538965 DOI: 10.1016/j.bbabio.2006.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 02/15/2006] [Accepted: 02/20/2006] [Indexed: 11/16/2022]
Abstract
An unusual effect of temperature on the ATPase activity of E. coli F1Fo ATP synthase has been investigated. The rate of ATP hydrolysis by the isolated enzyme, previously kept on ice, showed a lag phase when measured at 15 degrees C, but not at 37 degrees C. A pre-incubation of the enzyme at room temperature for 5 min completely eliminated the lag phase, and resulted in a higher steady-state rate. Similar results were obtained using the isolated enzyme after incorporation into liposomes. The initial rates of ATP-dependent proton translocation, as measured by 9-amino-6-chloro-2-methoxyacridine (ACMA) fluorescence quenching, at 15 degrees C also varied according to the pre-incubation temperature. The relationship between this temperature-dependent pattern of enzyme activity, termed thermohysteresis, and pre-incubation with other agents was examined. Pre-incubation of membrane vesicles with azide and Mg2+, without exogenous ADP, resulted in almost complete inhibition of the initial rate of ATPase when assayed at 10 degrees C, but had little effect at 37 degrees C. Rates of ATP synthesis following this pre-incubation were not affected at any temperature. Azide inhibition of ATP hydrolysis by the isolated enzyme was reduced when an ATP-regenerating system was used. A gradual reactivation of azide-blocked enzyme was slowed down by the presence of phosphate in the reaction medium. The well-known Mg2+ inhibition of ATP hydrolysis was shown to be greatly enhanced at 15 degrees C relative to at 37 degrees C. The results suggest that thermohysteresis is a consequence of an inactive form of the enzyme that is stabilized by the binding of inhibitory Mg-ADP.
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Affiliation(s)
- Mikhail A Galkin
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
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31
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Vik SB, Ishmukhametov RR. Structure and Function of Subunit a of the ATP Synthase of Escherichia coli. J Bioenerg Biomembr 2005; 37:445-9. [PMID: 16691481 DOI: 10.1007/s10863-005-9488-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The structure of subunit a of the Escherichia coli ATP synthase has been probed by construction of more than one hundred monocysteine substitutions. Surface labeling with 3-N-maleimidyl-propionyl biocytin (MPB) has defined five transmembrane helices, the orientation of the protein in the membrane, and information about the relative exposure of the loops connecting these helices. Cross-linking studies using TFPAM-3 (N-(4-azido-2,3,5,6-tetrafluorobenzyl)-3-maleimido-propionamide) and benzophenone-4-maleimide have revealed which elements of subunit a are near subunits b and c. Use of a chemical protease reagent, 5-(-bromoacetamido)-1,10-phenanthroline-copper, has indicated that the periplasmic end of transmembrane helix 5 is near that of transmembrane helix 2.
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Affiliation(s)
- Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, USA.
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32
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Sinz A. Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:1225-1237. [PMID: 14696200 DOI: 10.1002/jms.559] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.
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Affiliation(s)
- Andrea Sinz
- Biotechnological-Biomedical Center, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany.
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Athlan ES, Mushynski WE. Heterodimeric associations between neuronal intermediate filament proteins. J Biol Chem 1997; 272:31073-8. [PMID: 9388258 DOI: 10.1074/jbc.272.49.31073] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Formation of protein dimers involving alpha-internexin, peripherin, and the neurofilament (NF) proteins NFH, NFM, and NFL was investigated by partial renaturation of various combinations of individually purified subunits in buffered 2 M urea. Oligomers that were formed were resolved by "blue" native electrophoresis (Schägger, H., Cramer, W. A., and von Jagow, G. (1994) Anal. Biochem. 217, 220-230) modified to include urea in the polyacrylamide gels. Combining this method with Western blot analysis, disulfide cross-linking, and SDS-polyacrylamide gel electrophoresis in the second dimension showed that NFL readily forms significant amounts of heterodimer with NFH, NFM, alpha-internexin, or peripherin in the presence of 2 M urea. alpha-Internexin and peripherin also formed heterodimers with NFH or NFM under these conditions. The modified version of blue native gel electrophoresis described here may be useful in monitoring the impact of post-translational modifications and mutations on the dimerization of intermediate filament proteins.
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Affiliation(s)
- E S Athlan
- Department of Biochemistry, McGill University, 3655 Drummond Street, Montreal, Quebec H3G 1Y6, Canada
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35
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Beharry S, Bragg PD. The bound adenine nucleotides of purified bovine mitochondrial ATP synthase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:165-72. [PMID: 8797850 DOI: 10.1111/j.1432-1033.1996.0165h.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The experiments in this study were directed towards defining the nucleotide content of purified beef-heart mitochondrial F1F0 ATP synthase during binding and hydrolysis of ATP. The purified, soluble synthase as prepared contained 2 mol ATP and 2 mol ADP/mol enzyme. Three of these four nucleotides were exchangeable on incubation with radiolabelled MgATP. Passage of the ATP synthase through a column of Sephadex G-50 readily removed 1 mol ADP/mol. The remaining bound nucleotides were not displaced by incubation with 1 mM GTP or 5 mM sodium sulfite, the latter an activator of the ATPase activity of the synthase. Incubation of the synthase with 250 microM MgATP in the presence of 3 mM sodium azide, an inhibitor of the ATPase, resulted in the transitory formation of a form of the enzyme in which 5-6 nucleotide-binding sites were loaded with ATP and/or ADP, thus showing that the ATP synthase, like the soluble F1 ATPase, contained a minimum of six nucleotide-binding sites. The presence of an ATP-regenerating system during incubation with MgATP resulted in the loading of 5-6 sites to yield a form of the enzyme containing 3-4 mol ATP and 2 mol ADP/mol synthase even after passage through a centrifuged column. Following hydrolysis of the medium MgATP, the enzyme reached a stable form containing 2 mol ATP and 2 mol ADP/mol synthase. Like the form of the enzyme originally prepared, 1 mol ADP/mol synthase was readily released. However, this ADP remained bound to the synthase in the presence of GTP if azide was present. These results are discussed in the context of current ideas about nucleotide-binding sites on the F1 ATPase portion of the F1F0 ATP synthase. It is concluded that the properties of the sites on the F1F0 synthase show some differences from those on the F1 ATPase.
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Affiliation(s)
- S Beharry
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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Santana M, Ionescu MS, Vertes A, Longin R, Kunst F, Danchin A, Glaser P. Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants. J Bacteriol 1994; 176:6802-11. [PMID: 7961438 PMCID: PMC197047 DOI: 10.1128/jb.176.22.6802-6811.1994] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We cloned and sequenced an operon of nine genes coding for the subunits of the Bacillus subtilis F0F1 ATP synthase. The arrangement of these genes in the operon is identical to that of the atp operon from Escherichia coli and from three other Bacillus species. The deduced amino acid sequences of the nine subunits are very similar to their counterparts from other organisms. We constructed two B. subtilis strains from which different parts of the atp operon were deleted. These B. subtilis atp mutants were unable to grow with succinate as the sole carbon and energy source. ATP was synthesized in these strains only by substrate-level phosphorylation. The two mutants had a decreased growth yield (43 and 56% of the wild-type level) and a decreased growth rate (61 and 66% of the wild-type level), correlating with a twofold decrease of the intracellular ATP/ADP ratio. In the absence of oxidative phosphorylation, B. subtilis increased ATP synthesis through substrate-level phosphorylation, as shown by the twofold increase of by-product formation (mainly acetate). The increased turnover of glycolysis in the mutant strain presumably led to increased synthesis of NADH, which would account for the observed stimulation of the respiration rate associated with an increase in the expression of genes coding for respiratory enzymes. It therefore appears that B. subtilis and E. coli respond in similar ways to the absence of oxidative phosphorylation.
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Affiliation(s)
- M Santana
- Unité de Régulation de l'Expression Génétique, Institut Pasteur, Paris, France
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37
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Xiao R, Penefsky H. Unisite catalysis and the delta subunit of F1-ATPase in Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32157-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Lagoni OR, von Meyenburg K, Michelsen O. Limited differential mRNA inactivation in the atp (unc) operon of Escherichia coli. J Bacteriol 1993; 175:5791-7. [PMID: 7690747 PMCID: PMC206657 DOI: 10.1128/jb.175.18.5791-5797.1993] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Individual subunits of ATP synthase, encoded by the eight genes of the atp operon (atpA through atpH), have been found to be synthesized at a 10-fold range in molar amounts (D.L. Foster and R.H. Fillingame, J. Biol. Chem. 257:2009-2015, 1982; K. von Meyenburg, B.B. Jorgensen, J. Nielsen, F.G. Hansen, and O. Michelsen. Tokai J. Exp. Clin. Med. 7:23-31, 1982). We have determined the functional half-lives at 30 degrees C of mRNAs transcribed from these genes either during constitutive expression in a partial diploid strain or after induced expression from a plasmid. Accurate decay kinetics of the relative mRNA levels were determined by monitoring the rates of synthesis of the individual ATP synthase subunits by radioactive pulse labeling at different times after blocking transcription initiation with rifampin. The mRNA transcribed from the atp operon was found to be inactivated about twice as fast as the bulk mRNA in E. coli. Exceptions are the mRNA from the promoter-proximal atpB gene, which was inactivated about three times as fast as the bulk mRNA, and atpC mRNA, the inactivation rate of which was comparable to that of the bulk mRNA. These moderate differences in the kinetics of functional decay explain only a minor part of the differences in expression levels of the atp genes. We conclude, therefore, that the individual atp mRNAs must be translated with widely different efficiencies. The present analysis further revealed that mRNA degradation is sensitive to heat shock; i.e., after incubation at 39 degrees C for 5 min followed by a shift back to 30 degrees C, the decay rate of the bulk mRNA was decreased by 30%.
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Affiliation(s)
- O R Lagoni
- Department of Microbiology, Technical University of Denmark, Lyngby
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39
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Beharry S, Bragg PD. Changes in the adenine nucleotide and inorganic phosphate content of Escherichia coli F1-ATPase during ATP synthesis in dimethyl sulphoxide. Biochem J 1992; 286 ( Pt 2):603-6. [PMID: 1388355 PMCID: PMC1132940 DOI: 10.1042/bj2860603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Escherichia coli F1-ATPase contained 2.9 +/- 0.1 mol of adenine nucleotide and 3.1 +/- 0.3 mol of Pi/mol of enzyme. After preincubation with ATP, the nucleotide and phosphate contents were 5.6 and 6.0 +/- 0.5 mol/mol of enzyme respectively. The F1-ATPase was induced to synthesize ATP in the presence of 30% (v/v) dimethyl sulphoxide (Me2SO). The ATP originated from endogenous bound ADP. The bound adenine nucleotide and Pi contents of the enzyme during the time course of ATP synthesis were investigated by using F1-ATPase which had been preincubated with ATP. We show that the process of ATP synthesis in Me2SO involves (i) an initial rapid loss of nucleotide from the enzyme, the process being facilitated by exogenous Pi, (ii) a rapid loss of Pi from the enzyme, at least in the absence of exogenous Pi, (iii) re-binding of a portion of the lost nucleotide, and (iv) synthesis of ATP from bound ADP and exogenous Pi. It is proposed that transfer of the F1-ATPase to the Me2SO medium induces a change in the conformation of the enzyme to a form favouring ATP synthesis.
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Affiliation(s)
- S Beharry
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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40
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Lindroth M, Bell PB, Fredriksson BA, Liu XD. Preservation and visualization of molecular structure in detergent-extracted whole mounts of cultured cells. Microsc Res Tech 1992; 22:130-50. [PMID: 1504345 DOI: 10.1002/jemt.1070220203] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Today's electron microscopes have a resolution sufficient to resolve supramolecular structures. However, the methods used to prepare biological samples for electron microscopy often limit our ability to achieve the resolution that is theoretically possible. We use whole mounts of detergent-extracted cells grown on Formvar-coated gold grids as a model system to evaluate various steps in the preparation of biological samples for high resolution scanning electron microscopy (SEM). Factors that are important in determining the structure and composition of detergent-extracted cells include the nature of the detergent and the composition of the extraction vehicle. Chelation of calcium is extremely important to stabilize and preserve the cytoskeletal filaments. We have also demonstrated both morphologically and by gel electrophoresis that treatment of cells with bifunctional protein crosslinkers before or during extraction with detergent can significantly enhance the preservation of both proteins and supramolecular structures. The methods used to dry samples are a major determinant of the quality of structural preservation. For cytoskeletons freeze-drying (FD) is superior to critical point-drying (CPD), one reason being that CPD samples have to be dehydrated, thereby causing more shrinkage as compared to FD samples. The high pressures to which samples are exposed during CPD may also cause increased shrinkage, and water contamination during CPD causes severe structural damage. We have obtained the best structural preservation of detergent-extracted and fixed cells by manually plunging them into liquid propane and drying over night in a freeze-dryer. The factor that most limits achievement of high resolution in SEM is the metal coat, which has to be very thin, uniform, and free of grain in order not to hide structures or to create artifactual ones. We have found that sputter-coating with 1-3 nm of tungsten (W) or niobium (Nb) gives extremely fine-grained films as well as satisfactory emission of secondary electrons. These samples can also be examined at high resolution by transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). The best preservation and visualization of supramolecular structures have been obtained using cryosputtering, in which the samples are freeze-dried and then sputter-coated within the freeze-dryer while still frozen.
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Affiliation(s)
- M Lindroth
- Department of Pathology II, Faculty of Health Sciences, Linköping University, Sweden
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Baracca A, Esposti MD, Castelli GP, Solaini G. Purification and characterization of adenosine triphosphatase from eel liver mitochondria. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0305-0491(92)90022-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Oda Y, Asakawa N, Abe S, Yoshida Y, Sato T. Avidin protein-conjugated column for direct injection analysis of drug enantiomers in plasma by high-performance liquid chromatography. JOURNAL OF CHROMATOGRAPHY 1991; 572:133-41. [PMID: 1818049 DOI: 10.1016/0378-4347(91)80478-u] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new concept in high-performance liquid chromatography supports is proposed for the direct injection analysis of drug enantiomers in plasma. The new supports are designed with disuccinimidyl suberate as a hydrophobic internal region, and avidin protein as a hydrophilic and bulky surface region. Plasma proteins are excluded by the avidin phase and are eluted immediately from the column, whereas low-molecular-mass analytes can penetrate the surface region and interact with disuccinimidyl suberate. Enantiomers interact differentially with avidin, and are thereby separated. This column was used in reversed-phase high-performance liquid chromatographic analysis to determine ketoprofen enantiomers in plasma by direct injection. The recovery of racemic drug from plasma was almost 100%.
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Affiliation(s)
- Y Oda
- Department of Physical and Analytical Chemistry, Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
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43
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Mendel-Hartvig J, Capaldi RA. Structure-function relationships of domains of the delta subunit in Escherichia coli adenosine triphosphatase. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1060:115-24. [PMID: 1655028 DOI: 10.1016/s0005-2728(05)80126-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The topology of the and subunit of the Escherichia coli adenosinetriphosphatase (ECF1) has been explored by proteinase digestion and chemical labeling methods. The delta subunit of ECF1 could be cleaved selectively by reaction of the enzyme complex with very low amounts of trypsin (1:5000, w/w). Cleavage of the delta subunit occurred serially from the C-terminus. The N-terminal fragments of the delta subunit remained bound to the core ECF1 complex through sucrose gradient centrifugation, indicating that part of the binding of this subunit involves the N-terminal segment. ECF1, in which around 20 amino acids had been removed from the C-terminus of delta, still bound to ECF0 but DCCD sensitivity of the ATPase activity was lost. When ECF1 was reacted with N-ethyl[14C]maleimide ([14C]NEM) in the native state, only one of the two Cys residues on the delta subunit was modified. This residue, Cys-140, was also labeled in ECF1F0. Cys-140 was shown to be involved in the disulfide bridge between alpha and delta subunits that is generated when ECF1 is treated with CuCl2. Thus, the C-terminal part of the delta subunit around Cys-140 can interact with the core ECF1 complex. These results suggest a model for the delta subunit in which the central part of polypeptide is a part of the stalk, with both N- and C-termini associated with ECF1.
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Affiliation(s)
- J Mendel-Hartvig
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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44
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A topological analysis of subunit alpha from Escherichia coli F1F0-ATP synthase predicts eight transmembrane segments. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)86981-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Bragg PD, Hou C. Reaction of 2-azido-ATP with beta subunits in the F1-adenosine triphosphatase of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 974:24-9. [PMID: 2522320 DOI: 10.1016/s0005-2728(89)80161-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three beta subunits of the Escherichia coli F1-ATPase react independently with chemical reagents (Stan Lotter, H. and Bragg, P.D. (1986) Arch. Biochem. Biophys. 248, 116-120). Thus, one beta subunit is readily cross-linked to the epsilon subunit, another reacts with N,N'-dicyclohexylcarbodiimide (DCCD), and the third one is modified by 4-chloro-7-nitrobenzofurazan (NbfCl). The relationship of the binding site for 2-azido-ATP to the three types of beta subunit recognized by chemical labeling was examined. The binding site for 2-azido-ATP was not associated with a specific type of beta-subunit. There was no relationship between the site of nucleotide and the association of the epsilon subunit with a particular beta subunit. It is concluded that the presence of the epsilon subunit (possibly in association with the other minor subunits) does not determine the position of the catalytic site. The possibility that the lack of a specific relationship between the 2-azido-ATP binding site and a specific beta subunit was due to turnover of the enzyme, making each beta a catalytic site in turn, could not be entirely rejected. However, the rate of hydrolysis of 2-azido-ATP by the DCCD-modified ATPase was very low in the presence of EDTA, and was likely due to catalysis at single sites.
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Affiliation(s)
- P D Bragg
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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46
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Hermolin J, Fillingame RH. H+-ATPase activity of Escherichia coli F1F0 is blocked after reaction of dicyclohexylcarbodiimide with a single proteolipid (subunit c) of the F0 complex. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84937-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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47
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Hanley-Trawick S, Carpen ME, Dunaway-Mariano D, Pedersen PL, Hullihen J. Investigation of the substrate structure and metal cofactor requirements of the rat liver mitochondrial ATP synthase/ATPase complex. Arch Biochem Biophys 1989; 268:116-23. [PMID: 2521440 DOI: 10.1016/0003-9861(89)90571-7] [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] [Indexed: 01/01/2023]
Abstract
The F1 moiety of the rat liver mitochondrial ATP synthase/ATPase complex contains as isolated 2 mol Mg2+/mol F1, 1 mol of which is nonexchangeable and the other which is exchangeable (N. Williams, J. Hullihen, and P.L. Pedersen, (1987) Biochemistry 26, 162-169). In addition, the enzyme binds 1 mol ADP/mol F1 and 3 mol AMP.PNP, the latter of which can bind in complex formation with divalent cation and displace the Mg2+ at the exchangeable site. Thus, in terms of ligand binding sites the fully loaded rat liver F1 complex contains 3 mol MgAMP.PNP, 1 mol ADP, and 1 mol Mg2+. In this study we have used several metal ATP complexes or analogs thereof to gain further insight into the ligand binding domains of rat liver F1 and the mechanism by which it catalyzes ATP hydrolysis in soluble and membrane bound form. Studies with LaATP confirmed that MgATP is the most likely substrate for rat liver F1, and provided evidence that the enzyme may contain additional Mg2+ binding sites, undetected in previous studies of F1-ATPases, that are required for catalytic activity. Thus, F1 containing the thermodynamically stable LaATP complex in place of MgATP requires added Mg2+ to induce ATP hydrolysis. As Mg2+ cannot readily displace La2+ under these conditions there appears to be a catalytically important class of Mg2+ binding sites on rat liver F1, distinct from the nonexchangeable Mg2+ site and the sites involved in binding MgATP. Additional studies carried out with exchange inert metal-nucleotide complexes involving rhodium and the Mg2+ and Cd2+ complexes of ATP beta S and ATP alpha S imply that the rate-limiting step in the ATPase reaction pathway occurs subsequent to the P gamma-O-P beta bond cleavage steps, perhaps at the level of Mg(ADP)(Pi) hydrolysis or MgADP release. Evidence is presented that Mg2+ remains coordinated to the leaving group of the reaction, i.e., the beta phosphoryl group. Finally, in contrast to soluble F1, F1 bound to F0 in the inner mitochondrial membrane failed to discriminate between the Mg2+ complexes of the ATP beta S isomers. This indicates that a fundamental difference may exist between the catalytic or kinetic mechanism of F1 and the more physiologically intact F0F1 complex.
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Affiliation(s)
- S Hanley-Trawick
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742
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Mutagenesis of the alpha subunit of the F1Fo-ATPase from Escherichia coli. Mutations at Glu-196, Pro-190, and Ser-199. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68683-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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49
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Rao R, Al-Shawi MK, Senior AE. Trinitrophenyl-ATP and -ADP bind to a single nucleotide site on isolated beta-subunit of Escherichia coli F1-ATPase. In vitro assembly of F1-subunits requires occupancy of the nucleotide-binding site on beta-subunit by nucleoside triphosphate. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)60602-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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50
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Schneider E, Altendorf K. Bacterial adenosine 5'-triphosphate synthase (F1F0): purification and reconstitution of F0 complexes and biochemical and functional characterization of their subunits. Microbiol Rev 1987; 51:477-97. [PMID: 2893973 PMCID: PMC373128 DOI: 10.1128/mr.51.4.477-497.1987] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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