1
|
Grelich-Mucha M, Bachelart T, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Amyloid engineering - how terminal capping modifies morphology and secondary structure of supramolecular peptide aggregates. Biomater Sci 2024; 12:1590-1602. [PMID: 38323504 DOI: 10.1039/d3bm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The effects of peptide N- and C-termini on aggregation behavior have been scarcely studied. Herein, we examine (105-115) peptide fragments of transthyretin (TTR) containing various functional groups at both termini and study their impact on the morphology and the secondary structure. We synthesized TTR(105-115) peptides functionalized with α-amino (H-), N-acetyl-α-amino (Ac-) or N,N-dimethyl-α-amino (DiMe-) groups at the N-terminus, and with amide (-NH2) or carboxyl (-OH) functions at the C-terminus. We also investigated quasi-racemic mixtures by mixing the L-enantiomers with the D-enantiomer capped by H- and -NH2 groups. We observed that fibril formation is promoted by the sufficient number of hydrogen bonds at peptides' termini. Moreover, the final morphology of the aggregates can be controlled by the functional groups at the N-terminus. Remarkably, all quasi-racemic mixtures resulted in the robust formation of fibrils. Overall, this work illustrates how modifications of peptide termini may help to engineer supramolecular aggregates with a predicted morphology.
Collapse
Affiliation(s)
- Manuela Grelich-Mucha
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| |
Collapse
|
2
|
Sinnaeve D, Ben Bouzayene A, Ottoy E, Hofman GJ, Erdmann E, Linclau B, Kuprov I, Martins J, Torbeev V, Kieffer B. Fluorine NMR study of proline-rich sequences using fluoroprolines. Magn Reson (Gott) 2021; 2:795-813. [PMID: 37905223 PMCID: PMC10539733 DOI: 10.5194/mr-2-795-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/28/2021] [Indexed: 11/01/2023]
Abstract
Proline homopolymer motifs are found in many proteins; their peculiar conformational and dynamic properties are often directly involved in those proteins' functions. However, the dynamics of proline homopolymers is hard to study by NMR due to a lack of amide protons and small chemical shift dispersion. Exploiting the spectroscopic properties of fluorinated prolines opens interesting perspectives to address these issues. Fluorinated prolines are already widely used in protein structure engineering - they introduce conformational and dynamical biases - but their use as 19 F NMR reporters of proline conformation has not yet been explored. In this work, we look at model peptides where Cγ -fluorinated prolines with opposite configurations of the chiral Cγ centre have been introduced at two positions in distinct polyproline segments. By looking at the effects of swapping these (4R )-fluoroproline and (4S )-fluoroproline within the polyproline segments, we were able to separate the intrinsic conformational properties of the polyproline sequence from the conformational alterations instilled by fluorination. We assess the fluoroproline 19 F relaxation properties, and we exploit the latter in elucidating binding kinetics to the SH3 (Src homology 3) domain.
Collapse
Affiliation(s)
- Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 – Risk Factors and Molecular Determinants of
Aging-Related Diseases (RID-AGE), 59000 Lille, France
- CNRS, ERL9002 – Integrative Structural Biology, 59000 Lille, France
| | - Abir Ben Bouzayene
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Gert-Jan Hofman
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Eva Erdmann
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - José C. Martins
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS),
International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg,
CNRS UMR 7006, 67000 Strasbourg, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| |
Collapse
|
3
|
Grelich-Mucha M, Garcia AM, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Autofluorescence of Amyloids Determined by Enantiomeric Composition of Peptides. J Phys Chem B 2021; 125:5502-5510. [PMID: 34008978 PMCID: PMC8182742 DOI: 10.1021/acs.jpcb.1c00808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Amyloid fibrils are
peptide or protein aggregates possessing a
cross-β-sheet structure. They possess intrinsic fluorescence
property, which is still not fully understood. Herein, we compare
structural and optical properties of fibrils formed from L- and D-enantiomers
of the (105–115) fragment of transthyretin (TTR) and from their
racemic mixture. Our results show that autofluorescence of fibrils
obtained from enantiomers differs from that of fibrils from the racemic
mixture. In order to elucidate the origin of observed differences,
we analyzed the structure and morphology of fibrils and showed how
variations in β-sheet organization influence optical properties
of fibrils. We clarified the contribution of aromatic rings and the
amyloid backbone to the final blue-green emission of fibrils. This
work demonstrates how enantiomeric composition of amino acids allows
us to modulate the self-assembly and final morphology of well-defined
fibrillar bionanostructures with optical properties controlled by
supramolecular organization.
Collapse
Affiliation(s)
- Manuela Grelich-Mucha
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ana M Garcia
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Vladimir Torbeev
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| |
Collapse
|
4
|
Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
Collapse
Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| |
Collapse
|
5
|
Bauer V, Schmidtgall B, Gógl G, Dolenc J, Osz J, Nominé Y, Kostmann C, Cousido-Siah A, Mitschler A, Rochel N, Travé G, Kieffer B, Torbeev V. Conformational editing of intrinsically disordered protein by α-methylation. Chem Sci 2020; 12:1080-1089. [PMID: 34163874 PMCID: PMC8178997 DOI: 10.1039/d0sc04482b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) constitute a large portion of “Dark Proteome” – difficult to characterize or yet to be discovered protein structures. Here we used conformationally constrained α-methylated amino acids to bias the conformational ensemble in the free unstructured activation domain of transcriptional coactivator ACTR. Different sites and patterns of substitutions were enabled by chemical protein synthesis and led to distinct populations of α-helices. A specific substitution pattern resulted in a substantially higher binding affinity to nuclear coactivator binding domain (NCBD) of CREB-binding protein, a natural binding partner of ACTR. The first X-ray structure of the modified ACTR domain - NCBD complex visualized a unique conformation of ACTR and confirmed that the key α-methylated amino acids are localized within α-helices in the bound state. This study demonstrates a strategy for characterization of individual conformational states of IDPs. Control of protein conformation was achieved for intrinsically disordered protein by incorporation of α-methylated amino acids.![]()
Collapse
Affiliation(s)
- Valentin Bauer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS, UMR 7006 Strasbourg France
| | - Boris Schmidtgall
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS, UMR 7006 Strasbourg France
| | - Gergő Gógl
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - Jozica Dolenc
- Chemistry
- Biology
- Pharmacy Information Center, ETH Zurich Zurich Switzerland
| | - Judit Osz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France
| | - Yves Nominé
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - Camille Kostmann
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - Alexandra Cousido-Siah
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - André Mitschler
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - Natacha Rochel
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France
| | - Gilles Travé
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France.,Équipe Labellisée Ligue contre le cancer France
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM (U1258), University of Strasbourg, CNRS, UMR 7104 Illkirch France
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS, UMR 7006 Strasbourg France
| |
Collapse
|
6
|
Garcia AM, Giorgiutti C, El Khoury Y, Bauer V, Spiegelhalter C, Leize‐Wagner E, Hellwig P, Potier N, Torbeev V. Frontispiece: Aggregation and Amyloidogenicity of the Nuclear Coactivator Binding Domain of CREB‐Binding Protein. Chemistry 2020. [DOI: 10.1002/chem.202084471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ana Maria Garcia
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and icFRC (International Center for Frontier Research in Chemistry) University of Strasbourg CNRS—UMR 7006 8 allée Gaspard Monge 67083 Strasbourg France
| | - Christophe Giorgiutti
- Laboratory of Mass-Spectrometry of Interactions and Systems University of Strasbourg CNRS—UMR 7140 1 rue Blaise Pascal 67070 Strasbourg France
| | - Youssef El Khoury
- Laboratory of Bioelectrochemistry and Spectroscopy University of Strasbourg CNRS—UMR 7140 1 rue Blaise Pascal 67070 Strasbourg France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and icFRC (International Center for Frontier Research in Chemistry) University of Strasbourg CNRS—UMR 7006 8 allée Gaspard Monge 67083 Strasbourg France
| | - Coralie Spiegelhalter
- Imaging Center, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) INSERM-U964, University of Strasbourg CNRS—UMR 7104 1 rue Laurent Fries 67404 Illkirch France
| | - Emmanuelle Leize‐Wagner
- Laboratory of Mass-Spectrometry of Interactions and Systems University of Strasbourg CNRS—UMR 7140 1 rue Blaise Pascal 67070 Strasbourg France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy University of Strasbourg CNRS—UMR 7140 1 rue Blaise Pascal 67070 Strasbourg France
- Institute for Advanced Study USIAS University of Strasbourg 5 allée du Général Rouvillois 67083 Strasbourg France
| | - Noelle Potier
- Laboratory of Mass-Spectrometry of Interactions and Systems University of Strasbourg CNRS—UMR 7140 1 rue Blaise Pascal 67070 Strasbourg France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and icFRC (International Center for Frontier Research in Chemistry) University of Strasbourg CNRS—UMR 7006 8 allée Gaspard Monge 67083 Strasbourg France
| |
Collapse
|
7
|
Garcia AM, Giorgiutti C, El Khoury Y, Bauer V, Spiegelhalter C, Leize-Wagner E, Hellwig P, Potier N, Torbeev V. Aggregation and Amyloidogenicity of the Nuclear Coactivator Binding Domain of CREB-Binding Protein. Chemistry 2020; 26:9889-9899. [PMID: 32364648 DOI: 10.1002/chem.202001847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/30/2020] [Indexed: 12/28/2022]
Abstract
The nuclear coactivator binding domain (NCBD) of transcriptional co-regulator CREB-binding protein (CBP) is an example of conformationally malleable proteins that can bind to structurally unrelated protein targets and adopt distinct folds in the respective protein complexes. Here, we show that the folding landscape of NCBD contains an alternative pathway that results in protein aggregation and self-assembly into amyloid fibers. The initial steps of such protein misfolding are driven by intermolecular interactions of its N-terminal α-helix bringing multiple NCBD molecules into contact. These oligomers then undergo slow but progressive interconversion into β-sheet-containing aggregates. To reveal the concealed aggregation potential of NCBD we used a chemically synthesized mirror-image d-NCBD form. The addition of d-NCBD promoted self-assembly into amyloid precipitates presumably due to formation of thermodynamically more stable racemic β-sheet structures. The unexpected aggregation of NCBD needs to be taken into consideration given the multitude of protein-protein interactions and resulting biological functions mediated by CBP.
Collapse
Affiliation(s)
- Ana Maria Garcia
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Christophe Giorgiutti
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Youssef El Khoury
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Coralie Spiegelhalter
- Imaging Center, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Emmanuelle Leize-Wagner
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
- Institute for Advanced Study, USIAS University of Strasbourg, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Noelle Potier
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| |
Collapse
|
8
|
Torbeev V, Kent SBH. Chemical Synthesis of an Enzyme Containing an Artificial Catalytic Apparatus. Aust J Chem 2020. [DOI: 10.1071/ch19460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
With the goal of investigating electronic aspects of the catalysis of peptide bond hydrolysis, an analogue of HIV-1 protease was designed in which a non-peptide hydroxy-isoquinolinone artificial catalytic apparatus replaced the conserved Asp25–Thr26–Gly27 sequence in each 99-residue polypeptide chain of the homodimeric enzyme molecule. The enzyme analogue was prepared by total chemical synthesis and had detectable catalytic activity on known HIV-1 protease peptide substrates. Compared with uncatalyzed hydrolysis, the analogue enzyme increased the rate of peptide bond hydrolysis by ∼108-fold. Extensions of this unique approach to the study of enzyme catalysis in HIV-1 protease are discussed.
Collapse
|
9
|
Vergauwe RMA, Thomas A, Nagarajan K, Shalabney A, George J, Chervy T, Seidel M, Devaux E, Torbeev V, Ebbesen TW. Modification of Enzyme Activity by Vibrational Strong Coupling of Water. Angew Chem Int Ed Engl 2019; 58:15324-15328. [PMID: 31449707 PMCID: PMC6856831 DOI: 10.1002/anie.201908876] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/23/2019] [Indexed: 01/06/2023]
Abstract
Vibrational strong coupling (VSC) has recently emerged as a completely new tool for influencing chemical reactivity. It harnesses electromagnetic vacuum fluctuations through the creation of hybrid states of light and matter, called polaritonic states, in an optical cavity resonant to a molecular absorption band. Here, we investigate the effect of vibrational strong coupling of water on the enzymatic activity of pepsin, where a water molecule is directly involved in the enzyme's chemical mechanism. We observe an approximately 4.5-fold decrease of the apparent second-order rate constant kcat /Km when coupling the water stretching vibration, whereas no effect was detected for the strong coupling of the bending vibration. The possibility of modifying enzymatic activity by coupling water demonstrates the potential of VSC as a new tool to study biochemical reactivity.
Collapse
Affiliation(s)
| | - Anoop Thomas
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Kalaivanan Nagarajan
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | | | - Jino George
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
- Present address: Department of Chemical SciencesIndian Institute of Science Education and Research MohaliKnowledge city, Sector 81, SAS Nagar, ManauliPO 140306MohaliIndia
| | - Thibault Chervy
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
- Present address: Institute for Quantum ElectronicsETH ZurichOtto-Stern-Weg 18093ZurichSwitzerland
| | - Marcus Seidel
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Eloïse Devaux
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Vladimir Torbeev
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| | - Thomas W. Ebbesen
- University of StrasbourgCNRSISIS & icFRC8 allée Gaspard Monge67000StrasbourgFrance
| |
Collapse
|
10
|
Affiliation(s)
- Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires, International Center for Frontier Research in Chemistry, University of Strasbourg and CNRS (UMR 7006), Strasbourg, France.
| |
Collapse
|
11
|
Vergauwe RMA, Thomas A, Nagarajan K, Shalabney A, George J, Chervy T, Seidel M, Devaux E, Torbeev V, Ebbesen TW. Modification of Enzyme Activity by Vibrational Strong Coupling of Water. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908876] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Anoop Thomas
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Kalaivanan Nagarajan
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | | | - Jino George
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
- Present address: Department of Chemical Sciences Indian Institute of Science Education and Research Mohali Knowledge city, Sector 81, SAS Nagar, Manauli PO 140306 Mohali India
| | - Thibault Chervy
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
- Present address: Institute for Quantum Electronics ETH Zurich Otto-Stern-Weg 1 8093 Zurich Switzerland
| | - Marcus Seidel
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Eloïse Devaux
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Vladimir Torbeev
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| | - Thomas W. Ebbesen
- University of Strasbourg CNRS ISIS & icFRC 8 allée Gaspard Monge 67000 Strasbourg France
| |
Collapse
|
12
|
Baral A, Asokan A, Bauer V, Kieffer B, Torbeev V. Chemical synthesis of transactivation domain (TAD) of tumor suppressor protein p53 by native chemical ligation of three peptide segments. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.11.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Boehringer R, Kieffer B, Torbeev V. Total chemical synthesis and biophysical properties of a designed soluble 24 kDa amyloid analogue. Chem Sci 2018; 9:5594-5599. [PMID: 30061991 PMCID: PMC6049524 DOI: 10.1039/c8sc01790e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/24/2018] [Indexed: 12/02/2022] Open
Abstract
A soluble amyloid analogue was designed and prepared by total chemical synthesis using native chemical ligation.
Discovering molecular probes that specifically recognize distinct amyloid structures is highly important for physiological studies of protein-misfolding diseases as well as for the development of diagnostic reagents and inhibitors of amyloid self-assembly. Here, we demonstrate an approach that allows for identification of N-methylated peptides that are specific binders for a particular amyloid fiber subtype (or polymorph). Protein design and chemical synthesis were used to produce covalently tethered amyloid analogues with molecular masses approaching 24 kDa and containing nine copies of an amyloidogenic peptide. Such engineered constructs served as a molecular testing platform to evaluate the aggregation properties and solubility as a function of N-methylation pattern. An advantage of the method is the possibility of biophysical characterization of amyloid constructs in solution.
Collapse
Affiliation(s)
- Régis Boehringer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) , International Center for Frontier Research in Chemistry (icFRC) , University of Strasbourg , CNRS (UMR 7006) , Strasbourg , France .
| | - Bruno Kieffer
- Department of Integrated Structural Biology , Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) , INSERM (U964) , University of Strasbourg , CNRS (UMR 7104) , Illkirch , France
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) , International Center for Frontier Research in Chemistry (icFRC) , University of Strasbourg , CNRS (UMR 7006) , Strasbourg , France .
| |
Collapse
|
14
|
Schmidtgall B, Chaloin O, Bauer V, Sumyk M, Birck C, Torbeev V. Dissecting mechanism of coupled folding and binding of an intrinsically disordered protein by chemical synthesis of conformationally constrained analogues. Chem Commun (Camb) 2017; 53:7369-7372. [DOI: 10.1039/c7cc02276j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Non-canonical α-methyl amino acids were incorporated at various sites in the sequence of intrinsically disordered activation domain from the p160 transcriptional co-activator (ACTR) to facilitate the formation of α-helical structures.
Collapse
Affiliation(s)
- Boris Schmidtgall
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) & icFRC (International Center for Frontier Research in Chemistry)
- University of Strasbourg and CNRS – UMR 7006
- Strasbourg
- France
| | - Olivier Chaloin
- IBMC (Institut de Biologie Moléculaire et Cellulaire)
- Immunopathologie et Chimie Thérapeutique
- CNRS – UPR 3572
- Strasbourg
- France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) & icFRC (International Center for Frontier Research in Chemistry)
- University of Strasbourg and CNRS – UMR 7006
- Strasbourg
- France
| | - Manuela Sumyk
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) & icFRC (International Center for Frontier Research in Chemistry)
- University of Strasbourg and CNRS – UMR 7006
- Strasbourg
- France
| | - Catherine Birck
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire)
- University of Strasbourg and CNRS – UMR 7104
- Illkirch
- France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) & icFRC (International Center for Frontier Research in Chemistry)
- University of Strasbourg and CNRS – UMR 7006
- Strasbourg
- France
| |
Collapse
|
15
|
Ruiz J, Boehringer R, Grogg M, Raya J, Schirer A, Crucifix C, Hellwig P, Schultz P, Torbeev V. Covalent Tethering and Residues with Bulky Hydrophobic Side Chains Enable Self-Assembly of Distinct Amyloid Structures. Chembiochem 2016; 17:2274-2285. [PMID: 27717158 DOI: 10.1002/cbic.201600440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Indexed: 11/10/2022]
Abstract
Polymorphism is a common property of amyloid fibers that complicates their detailed structural and functional studies. Here we report experiments illustrating the chemical principles that enable the formation of amyloid polymorphs with distinct stoichiometric composition. Using appropriate covalent tethering we programmed self-assembly of a model peptide corresponding to the [20-41] fragment of human β2-microglobulin into fibers with either trimeric or dimeric amyloid cores. Using a set of biophysical and biochemical methods we demonstrated their distinct structural, morphological, and templating properties. Furthermore, we showed that supramolecular approaches in which the peptide is modified with bulky substituents can also be applied to modulate the formation of different fiber polymorphs. Such strategies, when applied to disease-related peptides and proteins, will greatly help in the evaluation of the biological properties of structurally distinct amyloids.
Collapse
Affiliation(s)
- Jérémy Ruiz
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Régis Boehringer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Marcel Grogg
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Jésus Raya
- Membrane Biophysics and NMR, Institute of Chemistry, University of Strasbourg, CNRS-, UMR 7177, 4 rue Blaise Pascal, 67008, Strasbourg, France
| | - Alicia Schirer
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Corinne Crucifix
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-, UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Patrick Schultz
- Department of Integrated Structural Biology, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-, UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-, UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| |
Collapse
|
16
|
Torbeev V, Grogg M, Ruiz J, Boehringer R, Schirer A, Hellwig P, Jeschke G, Hilvert D. Chiral recognition in amyloid fiber growth. J Pept Sci 2016; 22:290-304. [DOI: 10.1002/psc.2861] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Jérémy Ruiz
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Régis Boehringer
- Institut de Science et d'Ingénierie Supramoléculaires; International Center for Frontier Research in Chemistry, UMR 7006, Université de Strasbourg; 8 allée Gaspard Monge 67000 Strasbourg France
| | - Alicia Schirer
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie; Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg-CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry; ETH Zurich, Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich; Vladimir-Prelog-Weg 1-5/10; Zürich CH-8093 Switzerland
| |
Collapse
|
17
|
Friedmann MP, Torbeev V, Zelenay V, Sobol A, Greenwald J, Riek R. Towards Prebiotic Catalytic Amyloids Using High Throughput Screening. PLoS One 2015; 10:e0143948. [PMID: 26650386 PMCID: PMC4674085 DOI: 10.1371/journal.pone.0143948] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
Enzymes are capable of directing complex stereospecific transformations and of accelerating reaction rates many orders of magnitude. As even the simplest known enzymes comprise thousands of atoms, the question arises as to how such exquisite catalysts evolved. A logical predecessor would be shorter peptides, but they lack the defined structure and size that are apparently necessary for enzyme functions. However, some very short peptides are able to assemble into amyloids, thereby forming a well-defined tertiary structure called the cross-β-sheet, which bestows unique properties upon the peptides. We have hypothesized that amyloids could have been the catalytically active precursor to modern enzymes. To test this hypothesis, we designed an amyloid peptide library that could be screened for catalytic activity. Our approach, amenable to high-throughput methodologies, allowed us to find several peptides and peptide mixtures that form amyloids with esterase activity. These results indicate that amyloids, with their stability in a wide range of conditions and their potential as catalysts with low sequence specificity, would indeed be fitting precursors to modern enzymes. Furthermore, our approach can be efficiently expanded upon in library size, screening conditions, and target activity to yield novel amyloid catalysts with potential applications in aqueous-organic mixtures, at high temperature and in other extreme conditions that could be advantageous for industrial applications.
Collapse
Affiliation(s)
- Michael P. Friedmann
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Vladimir Torbeev
- Laboratory of Organic Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Viviane Zelenay
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, Zurich, Switzerland
- * E-mail: (JG); (RR)
| |
Collapse
|
18
|
Torbeev V, Ebert MO, Dolenc J, Hilvert D. Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids. J Am Chem Soc 2015; 137:2524-35. [PMID: 25633201 DOI: 10.1021/ja510109p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Conversion of soluble folded proteins into insoluble amyloids generally proceeds in three distinct mechanistic stages: (1) initial protein misfolding into aggregation-competent conformers, (2) subsequent formation of oligomeric species and, finally, (3) self-assembly into extended amyloid fibrils. In the work reported herein, we interrogated the amyloidogenesis mechanism of human β2-microglobulin (β2m), which is thought to be triggered by a pivotal cis-trans isomerization of a proline residue at position 32 in the polypeptide, with nonstandard amino acids. Using chemical protein synthesis we prepared a β2m analogue in which Pro32 was replaced by the conformationally constrained amino acid α-methylproline (MePro). The strong propensity of MePro to adopt a trans prolyl bond led to enhanced population of a non-native [trans-MePro32]β2m protein conformer, which readily formed oligomers at neutral pH. In the presence of the antibiotic rifamycin SV, which inhibits amyloid growth of wild-type β2m, [MePro32]β2m was nearly quantitatively converted into different spherical oligomeric species. Self-assembly into amyloid fibrils was not observed in the absence of seeding, however, even at low pH (<3), where wild-type β2m spontaneously forms amyloids. Nevertheless, we found that aggregation-preorganized [MePro32]β2m can act in a prion-like fashion, templating misfolded conformations in a natively folded protein. Overall, these results provide detailed insight into the role of cis-trans isomerization of Pro32 and ensuing structural rearrangements that lead to initial β2m misfolding and aggregation. They corroborate the view that conformational protein dynamics enabled by reversible Pro32 cis-trans interconversion rather than simple population of the trans conformer is critical for both nucleation and subsequent growth of β2m amyloid structures.
Collapse
Affiliation(s)
- Vladimir Torbeev
- Laboratory of Organic Chemistry and ‡Laboratory of Physical Chemistry, ETH Zurich , Zurich CH-8093, Switzerland
| | | | | | | |
Collapse
|