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Harmon TW, Horne WS. Protein Backbone Alteration in Non-Hairpin β-Turns: Impacts on Tertiary Folded Structure and Folded Stability. Chembiochem 2023; 24:e202300113. [PMID: 36920327 PMCID: PMC10239330 DOI: 10.1002/cbic.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/16/2023]
Abstract
The importance of β-turns to protein folding has motivated extensive efforts to stabilize the motif with non-canonical backbone connectivity. Prior work has focused almost exclusively on turns between strands in a β-sheet (i. e., hairpins). Turns in other structural contexts are also common in nature and have distinct conformational preferences; however, design principles for their mimicry remain poorly understood. Here, we report strategies that stabilize non-hairpin β-turns through systematic evaluation of the impacts of backbone alteration on the high-resolution folded structure and folded stability of a helix-loop-helix prototype protein. Several well-established hairpin turn mimetics are shown detrimental to folded stability and/or hydrophobic core packing, while less-explored modification schemes that reinforce alternate turn types lead to improved stability and more faithful structural mimicry. Collectively, these results have implications in control over protein folding through chemical modification as well as the design of protein mimetics.
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Affiliation(s)
- Thomas W Harmon
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
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2
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Bucci R, Foschi F, Loro C, Erba E, Gelmi ML, Pellegrino S. Fishing in the Toolbox of Cyclic Turn Mimics: a Literature Overview of the Last Decade. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Raffaella Bucci
- Dipartimento di Scienze farmaceutiche,DISFARM Università degli Studi di Milano Via Venezian 21 Milano 20133 Italy
| | - Francesca Foschi
- Dipartimento di Scienze e Alta Tecnologie,DiSAT Università degli Studi dell'Insubria Via Valleggio 9 Como 20100 Italy
| | - Camilla Loro
- Dipartimento di Scienze e Alta Tecnologie,DiSAT Università degli Studi dell'Insubria Via Valleggio 9 Como 20100 Italy
| | - Emanuela Erba
- Dipartimento di Scienze farmaceutiche,DISFARM Università degli Studi di Milano Via Venezian 21 Milano 20133 Italy
| | - Maria Luisa Gelmi
- Dipartimento di Scienze farmaceutiche,DISFARM Università degli Studi di Milano Via Venezian 21 Milano 20133 Italy
| | - Sara Pellegrino
- Dipartimento di Scienze farmaceutiche,DISFARM Università degli Studi di Milano Via Venezian 21 Milano 20133 Italy
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3
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Martínez-Crespo L, Escudero-Adán EC, Costa A, Rotger C. The Role of N
-Methyl Squaramides in a Hydrogen-Bonding Strategy to Fold Peptidomimetic Compounds. Chemistry 2018; 24:17802-17813. [DOI: 10.1002/chem.201803930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/18/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Luís Martínez-Crespo
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
| | - Eduardo C. Escudero-Adán
- Institute of Chemical Research of Catalonia (ICIQ); Av. Països Catalans 16 43007 Tarragona Spain
| | - Antonio Costa
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
| | - Carmen Rotger
- Department of Chemistry; University of Balearic Islands; Cra Valldemossa km 7.5 07122 Palma Spain
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4
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Affiliation(s)
- Christoph Priem
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
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6
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Grassi L, Regl C, Wildner S, Gadermaier G, Huber CG, Cabrele C, Schubert M. Complete NMR Assignment of Succinimide and Its Detection and Quantification in Peptides and Intact Proteins. Anal Chem 2017; 89:11962-11970. [PMID: 29058416 DOI: 10.1021/acs.analchem.7b01645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Detecting and quantifying post-translational modifications (PTMs) in full-length proteins is a challenge, especially in the case of spontaneously occurring, nonenzymatic PTMs. Such a PTM is the formation of succinimide (Snn) in a protein that occurs spontaneously in prone primary sequences and leads typically to an equilibrium between Snn and its hydrolysis products isoaspartate (isoAsp) and aspartate. In order to detect these modifications in proteins by NMR spectroscopy, chemical shift assignments of reference compounds are required. We used peptide synthesis and 2D NMR spectroscopy to assign all 1H and 13C chemical shifts of Snn and isoAsp and found characteristic chemical shift correlations. To provide chemical shift reference data suitable for comparison with data of denatured proteins, we repeated the assignment in 7 M urea (pH 2.3) and in DMSO. Most characteristic of Snn are the two downfield shifted carbonyl chemical shifts, the chemical shift correlations of Cβ-Hβ of Snn and Cα-Hα of the succeeding residue which are clearly distinct from random coil chemical shift correlations. The characteristic 2D NMR fingerprints of Snn were used to detect and quantify this PTM in the model protein lysozyme, the biotherapeutic filgrastim, and the Fc part of immunoglobulin G1. Mass spectrometry (MS) was applied as an additional independent method. The orthogonality of the NMR and MS techniques allows cross-validation, which is especially important to search for subtle PTMs in proteins. Studying PTMs by NMR spectroscopy is a promising method to analyze proteins and peptides from natural sources, recombinant expression, or chemical synthesis.
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Affiliation(s)
- Luigi Grassi
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Sabrina Wildner
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Gabriele Gadermaier
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Christian G Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
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Ghosh D, Lahiri P, Verma H, Mukherjee S, Chatterjee J. Engineering β-sheets employing N-methylated heterochiral amino acids. Chem Sci 2016; 7:5212-5218. [PMID: 29449932 PMCID: PMC5784515 DOI: 10.1039/c6sc00518g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/19/2016] [Indexed: 01/01/2023] Open
Abstract
There is a lack of functional group diversity in the reverse turn motifs nucleating a β-sheet conformation in designed peptides, proteins and foldamers. The majority of these sequences consist of d-Pro-l-Pro, d-Pro-Gly or Asn-Gly as the turn inducing motif restricting their biological application and physicochemical modulation. In this report, for the first time we elucidate that N-methylation of heterochiral amino acids in linear peptides nucleates β-sheet conformation without the necessity of having a ring or covalent constraint at the reverse turn. Our results show that d-Pro can be conveniently substituted by any other N-methylated d-amino acid followed by an N-methylated l-amino acid or sarcosine to adopt a βII' turn inducing the β-sheet folding. Furthermore, we reveal that a single amino acid either at the i + 1 or i + 2 site of the reverse turn can modulate the right-handed twist, which eventually dictates the extent of the foldedness of the β-hairpin.
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Affiliation(s)
- Dipan Ghosh
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Somnath Mukherjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
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8
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Fischer SN, Geyer A. Assembly of synthetic Aβ miniamyloids on polyol templates. Beilstein J Org Chem 2016; 11:2646-53. [PMID: 26734110 PMCID: PMC4685884 DOI: 10.3762/bjoc.11.284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/28/2015] [Indexed: 12/22/2022] Open
Abstract
Covalent dynamic chemistry is used to mimic the first steps of the highly cooperative fibril formation of Aβ peptides. For that purpose, Aβ peptide pentapeptide boronic acids 1 and 2 were synthesized by solid-phase peptide synthesis and studied in esterification experiments with polyhydroxylated templates. The bis-hydroxylated dipeptide Hot=Tap serves as a template of adjustable degree of oligomerization which spontaneously forms boronic esters with peptides of type 1 and 2. Nuclear magnetic resonance can differentiate between regioisomeric boronic esters and identifies preferred sites of esterification on the dimeric template 9. 2-Formylphenylboronic acid (14) is used to link the parent pentapeptide Leu-Val-Phe-Phe-Ala to the template 16 to obtain threefold boronic ester 17. The miniamyloid 17 assembles from seven components by imine and boronic ester bonds between the peptides and the template. The relative orientation and spacing of the peptides mimic the assembly of peptides in Alzheimer β-amyloids.
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Affiliation(s)
- Sebastian Nils Fischer
- Faculty of Chemistry, Philipps University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Armin Geyer
- Faculty of Chemistry, Philipps University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
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Martínez L, Martorell G, Sampedro Á, Ballester P, Costa A, Rotger C. Hydrogen Bonded Squaramide-Based Foldable Module Induces Both β- and α-Turns in Hairpin Structures of α-Peptides in Water. Org Lett 2015; 17:2980-3. [DOI: 10.1021/acs.orglett.5b01268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | - Pablo Ballester
- Institut of Chemical Research of Catalonia (ICIQ), Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig Lluís Compays 23, 08010 Barcelona, Spain
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