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Hervø-Hansen S, Højgaard C, Johansson KE, Wang Y, Wahni K, Young D, Messens J, Teilum K, Lindorff-Larsen K, Winther JR. Charge Interactions in a Highly Charge-Depleted Protein. J Am Chem Soc 2021; 143:2500-2508. [PMID: 33529004 DOI: 10.1021/jacs.0c10789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Electrostatic forces are important for protein folding and are favored targets of protein engineering. However, interactions between charged residues are difficult to study because of the complex network of interactions found in most proteins. We have designed a purposely simple system to investigate this problem by systematically introducing individual and pairs of charged and titratable residues in a protein otherwise free of such residues. We used constant pH molecular dynamics simulations, NMR spectroscopy, and thermodynamic double mutant cycles to probe the structure and energetics of the interaction between the charged residues. We found that the partial burial of surface charges contributes to a shift in pKa value, causing an aspartate to titrate in the neutral pH range. Additionally, the interaction between pairs of residues was found to be highly context dependent, with some pairs having no apparent preferential interaction, while other pairs would engage in coupled titration forming a highly stabilized salt bridge. We find good agreement between experiments and simulations and use the simulations to rationalize our observations and to provide a detailed mechanistic understanding of the electrostatic interactions.
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Affiliation(s)
- Stefan Hervø-Hansen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE 221 00 Lund, Sweden
| | - Casper Højgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Yong Wang
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - David Young
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Kaare Teilum
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jakob Rahr Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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2
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Hadrup N, Knudsen KB, Berthing T, Wolff H, Bengtson S, Kofoed C, Espersen R, Højgaard C, Winther JR, Willemoës M, Wedin I, Nuopponen M, Alenius H, Norppa H, Wallin H, Vogel U. Pulmonary effects of nanofibrillated celluloses in mice suggest that carboxylation lowers the inflammatory and acute phase responses. Environ Toxicol Pharmacol 2019; 66:116-125. [PMID: 30665014 DOI: 10.1016/j.etap.2019.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
We studied if the pulmonary and systemic toxicity of nanofibrillated celluloses can be reduced by carboxylation. Nanofibrillated celluloses administered at 6 or 18 μg to mice by intratracheal instillation were: 1) FINE NFC, 2-20 μm in length, 2-15 nm in width, 2) AS (-COOH), carboxylated, 0.5-10 μm in length, 4-10 nm in width, containing the biocide BIM MC4901 and 3) BIOCID FINE NFC: as (1) but containing BIM MC4901. FINE NFC administration increased neutrophil influx in BAL and induced SAA3 in plasma. AS (-COOH) produced lower neutrophil influx and systemic SAA3 levels than FINE NFC. Results obtained with BIOCID FINE NFC suggested that BIM MC4901 biocide did not explain the lowered response. Increased DNA damage levels were observed across materials, doses and time points. In conclusion, carboxylation of nanofibrillated cellulose was associated with reduced pulmonary and systemic toxicity, suggesting involvement of OH groups in the inflammatory and acute phase responses.
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Affiliation(s)
- Niels Hadrup
- National Research Centre for the Working Environment (NFA), 105 Lersø Parkallé, Copenhagen Ø, Denmark.
| | - Kristina Bram Knudsen
- National Research Centre for the Working Environment (NFA), 105 Lersø Parkallé, Copenhagen Ø, Denmark.
| | - Trine Berthing
- National Research Centre for the Working Environment (NFA), 105 Lersø Parkallé, Copenhagen Ø, Denmark.
| | - Henrik Wolff
- Finnish Institute of Occupational Health (FIOH), P.O. Box 40, 00032, Työterveyslaitos, Helsinki, Finland.
| | - Stefan Bengtson
- National Research Centre for the Working Environment (NFA), 105 Lersø Parkallé, Copenhagen Ø, Denmark.
| | - Christian Kofoed
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Denmark.
| | - Roall Espersen
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Denmark.
| | - Casper Højgaard
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Denmark.
| | - Jakob Rahr Winther
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Denmark.
| | - Martin Willemoës
- Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Denmark.
| | | | | | - Harri Alenius
- Department of Bacteriology and Immunology, University of Helsinki, Finland; Institute of Environmental Medicine (IMM), Karolinska Institutet, Sweden.
| | - Hannu Norppa
- Finnish Institute of Occupational Health (FIOH), P.O. Box 40, 00032, Työterveyslaitos, Helsinki, Finland.
| | - Håkan Wallin
- National Institute of Occupational Health, Oslo, Norway.
| | - Ulla Vogel
- National Research Centre for the Working Environment (NFA), 105 Lersø Parkallé, Copenhagen Ø, Denmark; Department of Micro- and Nanotechnology, Danish Technical University (DTU), DK-2800, Kgs., Lyngby, Denmark.
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3
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Højgaard C, Sørensen HV, Pedersen JS, Winther JR, Otzen DE. Can a Charged Surfactant Unfold an Uncharged Protein? Biophys J 2018; 115:2081-2086. [PMID: 30447995 DOI: 10.1016/j.bpj.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/05/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022] Open
Abstract
Does sodium dodecyl sulfate (SDS) denature proteins through electrostatic SDS-protein interactions? We show that a protein completely lacking charged side chains is unfolded by SDS in a manner similar to charged proteins, revealing that formal protein charges are not required for SDS-induced protein unfolding or binding.
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Affiliation(s)
- Casper Højgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jan Skov Pedersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jakob Rahr Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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4
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Ilves M, Vilske S, Aimonen K, Lindberg HK, Pesonen S, Wedin I, Nuopponen M, Vanhala E, Højgaard C, Winther JR, Willemoës M, Vogel U, Wolff H, Norppa H, Savolainen K, Alenius H. Nanofibrillated cellulose causes acute pulmonary inflammation that subsides within a month. Nanotoxicology 2018; 12:729-746. [DOI: 10.1080/17435390.2018.1472312] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Marit Ilves
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sara Vilske
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Kukka Aimonen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | | | - Saila Pesonen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | | | | | - Esa Vanhala
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Casper Højgaard
- Liderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob R. Winther
- Liderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Willemoës
- Liderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Henrik Wolff
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Hannu Norppa
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Kai Savolainen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Harri Alenius
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Virkkunen S, Wolff H, Haglund C, Højgaard C, Winther JR, Willemoës M, Vogel U, Hagström J. Positive staining for cellulose in oral pulse granuloma. Oral Surg Oral Med Oral Pathol Oral Radiol 2017; 123:464-467. [DOI: 10.1016/j.oooo.2016.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 10/20/2022]
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Catalán J, Rydman E, Aimonen K, Hannukainen KS, Suhonen S, Vanhala E, Moreno C, Meyer V, Perez DDS, Sneck A, Forsström U, Højgaard C, Willemoes M, Winther JR, Vogel U, Wolff H, Alenius H, Savolainen KM, Norppa H. Genotoxic and inflammatory effects of nanofibrillated cellulose in murine lungs. Mutagenesis 2016; 32:23-31. [DOI: 10.1093/mutage/gew035] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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7
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Højgaard C, Kofoed C, Espersen R, Johansson KE, Villa M, Willemoës M, Lindorff-Larsen K, Teilum K, Winther JR. A Soluble, Folded Protein without Charged Amino Acid Residues. Biochemistry 2016; 55:3949-56. [PMID: 27307139 DOI: 10.1021/acs.biochem.6b00269] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable side chains can maintain solubility, stability, and function. As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. We find that the protein shows a surprising resilience toward extremes of pH, demonstrating stability and function (cellulose binding) in the pH range from 2 to 11. To ask whether the four charged residues present were required for these properties of this protein, we altered them to nontitratable ones. Remarkably, this chargeless protein is produced reasonably well in Escherichia coli, retains its stable three-dimensional structure, and is still capable of strong cellulose binding. To further deprive this protein of charges, we removed the N-terminal charge by acetylation and studied the protein at pH 2, where the C-terminus is effectively protonated. Under these conditions, the protein retains its function and proved to be both soluble and have a reversible folding-unfolding transition. To the best of our knowledge, this is the first time a soluble, functional protein with no titratable side chains has been produced.
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Affiliation(s)
- Casper Højgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Christian Kofoed
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Roall Espersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Mara Villa
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Jakob R Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
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8
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Knudsen KB, Kofoed C, Espersen R, Højgaard C, Winther JR, Willemoës M, Wedin I, Nuopponen M, Vilske S, Aimonen K, Weydahl IEK, Alenius H, Norppa H, Wolff H, Wallin H, Vogel U. Visualization of Nanofibrillar Cellulose in Biological Tissues Using a Biotinylated Carbohydrate Binding Module of β-1,4-Glycanase. Chem Res Toxicol 2015. [DOI: 10.1021/acs.chemrestox.5b00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kristina Bram Knudsen
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
| | - Christian Kofoed
- Section for Biomolecular Sciences, Department
of Biology, University of Copenhagen, Copenhagen, DK-2200 N, Denmark
| | - Roall Espersen
- Section for Biomolecular Sciences, Department
of Biology, University of Copenhagen, Copenhagen, DK-2200 N, Denmark
| | - Casper Højgaard
- Section for Biomolecular Sciences, Department
of Biology, University of Copenhagen, Copenhagen, DK-2200 N, Denmark
| | - Jakob Rahr Winther
- Section for Biomolecular Sciences, Department
of Biology, University of Copenhagen, Copenhagen, DK-2200 N, Denmark
| | - Martin Willemoës
- Section for Biomolecular Sciences, Department
of Biology, University of Copenhagen, Copenhagen, DK-2200 N, Denmark
| | | | | | - Sara Vilske
- Nanosafety Research Centre, Finnish Institute of Occupational Health, P.O. Box 40, FI-00250 Helsinki, Finland
| | - Kukka Aimonen
- Nanosafety Research Centre, Finnish Institute of Occupational Health, P.O. Box 40, FI-00250 Helsinki, Finland
| | | | - Harri Alenius
- Nanosafety Research Centre, Finnish Institute of Occupational Health, P.O. Box 40, FI-00250 Helsinki, Finland
| | - Hannu Norppa
- Nanosafety Research Centre, Finnish Institute of Occupational Health, P.O. Box 40, FI-00250 Helsinki, Finland
| | - Henrik Wolff
- Nanosafety Research Centre, Finnish Institute of Occupational Health, P.O. Box 40, FI-00250 Helsinki, Finland
| | - Håkan Wallin
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
- Institute
of Public Health, Copenhagen University, Øster Farimagsgade 5, Copenhagen K, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen Ø, Denmark
- Department
of Micro- and Nanotechnology, DTU, Kgs. Lyngby, Denmark
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9
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Engbaek HC, Heckscher T, Højgaard C, Larsen SO, Rasmussen KN, Vergmann B. Tuberculosis treated with rifampicin, ethambutol and isoniazid: Danish tuberculosis trial 1972-1974. Eur J Respir Dis 1982; 63:84-93. [PMID: 7040100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A total of 577 Danish patients with tuberculosis were observed for a period of 5 years. A primary phase of treatment with 300 mg Isoniazid (INH), 450 mg Rifampicin (RMP) and 1200 mg Ethambutol (EMB) daily for 3 months was followed by administration of either INH+RMP or INH+EMB for 12 or 18 months after conversion. During the initial period the number of bacteria decreased rapidly, even in patients with the most severe tuberculosis, and all patients became culture negative. There was no significant difference in efficacy of RMP and EMB in the secondary phase. One of the 577 patients again became positive during the follow-up period, but there were no bona fide cases of relapse among patients who completed the treatment.
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