1
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He M, Yao Y, Yang Z, Li B, Wang J, Wang Y, Kong Y, Zhou Z, Zhao W, Yang XJ, Tang J, Wu B. Biomimetic Charge-Neutral Anion Receptors for Reversible Binding and Release of Highly Hydrated Phosphate in Water. Angew Chem Int Ed Engl 2024; 63:e202406946. [PMID: 38802316 DOI: 10.1002/anie.202406946] [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: 04/12/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
Control of phosphate capture and release is vital in environmental, biological, and pharmaceutical contexts. However, the binding of trivalent phosphate (PO4 3-) in water is exceptionally difficult due to its high hydration energy. Based on the anion coordination chemistry of phosphate, in this study, four charge-neutral tripodal hexaurea receptors (L1-L4), which were equipped with morpholine and polyethylene glycol terminal groups to enhance their solubility in water, were synthesized to enable the pH-triggered phosphate binding and release in aqueous solutions. Encouragingly, the receptors were found to bind PO4 3- anion in a 1 : 1 ratio via hydrogen bonds in 100 % water solutions, with L1 exhibiting the highest binding constant (1.2×103 M-1). These represent the first neutral anion ligands to bind phosphate in 100 % water and demonstrate the potential for phosphate capture and release in water through pH-triggered mechanisms, mimicking native phosphate binding proteins. Furthermore, L1 can also bind multiple bioavailable phosphate species, which may serve as model systems for probing and modulating phosphate homeostasis in biological and biomedical researches.
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Affiliation(s)
- Maolin He
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yuhang Yao
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zihe Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Boyang Li
- College of Chemistry & Pharmacy, Northwest A&F University, Xian Yang Shi, Yangling, 712100, China
| | - Ji Wang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yanchao Wang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Yu Kong
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Zihan Zhou
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Xiao-Juan Yang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Juan Tang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
| | - Biao Wu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, China
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2
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Paoletti F. ATP binding to Nerve Growth Factor (NGF) and pro-Nerve Growth Factor (proNGF): an endogenous molecular switch modulating neurotrophins activity. Biochem Soc Trans 2024; 52:1293-1304. [PMID: 38716884 DOI: 10.1042/bst20231089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
ATP has recently been reconsidered as a molecule with functional properties which go beyond its recognized role of the energetic driver of the cell. ATP has been described as an allosteric modulator as well as a biological hydrotrope with anti-aggregation properties in the crowded cellular environment. The role of ATP as a modulator of the homeostasis of the neurotrophins (NTs), a growth factor protein family whose most known member is the nerve growth factor (NGF), has been investigated. The modulation of NTs by small endogenous ligands is still a scarcely described area, with few papers reporting on the topic, and very few reports on the molecular determinants of these interactions. However, a detailed atomistic description of the NTs interaction landscape is of urgent need, aiming at the identification of novel molecules as potential therapeutics and considering the wide range of potential pharmacological applications for NGF and its family members. This mini-review will focus on the unique cartography casting the interactions of the endogenous ligand ATP, in the interaction with NGF as well as with its precursor proNGF. These interactions revealed interesting features of the ATP binding and distinct differences in the binding mode between the highly structured mature NGF and its precursor, proNGF, which is characterized by an intrinsically unstructured domain. The overview on the recent available data will be presented, together with the future perspectives on the field.
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Affiliation(s)
- Francesca Paoletti
- Institute of Crystallography - C.N.R. - Trieste Outstation, Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
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3
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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [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: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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4
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Marshall LK, Fahrenbach AC, Thordarson P. RNA-Binding Peptides Inspired by the RNA Recognition Motif. ACS Chem Biol 2024; 19:243-248. [PMID: 38314708 DOI: 10.1021/acschembio.3c00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
β-Hairpin peptides with RNA-binding sequences mimicking the central two β-strands of the RNA recognition motif (RRM) protein domain have been observed to bind in a 2:1 fashion to a series of RNA homooligonucleotides in aqueous solution (PBS buffer, pH 7.40) with binding energies (-27 to -35 kJ mol-1) similar to those of full-size protein RRMs. The peptides display mild selectivities with respect to the binding of the different homooligomers. Binding studies in 500 mM magnesium chloride suggest that the complex formation is not predominantly driven by Coulombic attraction. These peptides represent a starting point for further studies of non-Coulombic binding of RNA by peptides and proteins, which is important in the context of contemporary biology, potential therapeutic applications, and prebiotic peptide-RNA interactions.
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5
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Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024:S0006-3495(24)00070-5. [PMID: 38297834 DOI: 10.1016/j.bpj.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
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Affiliation(s)
- Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Gemechis D Degaga
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Wei Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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6
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Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
β-Sheet motifs such as the WW domain are increasingly being explored as building blocks for synthetic biological applications. Since the sequence-structure relationships of β-sheet motifs are generally complex compared to the well-studied α-helical coiled coil (CC), other approaches such as combinatorial screening should be included to vary the function of the peptide. In this study, we present a combinatorial approach to identify novel functional mini-proteins based on the WW-domain scaffold, which takes advantage of the successful reconstitution of the fragmented WW domain of hPin1 (hPin1WW) by CC association. Fragmentation of hPin1WW was performed in both loop 1 (CC-hPin1WW-L1) and loop 2 (CC-hPin1WW-L2), and the respective fragments were linked to the strands of an antiparallel heterodimeric CC. Structural analysis by CD and NMR spectroscopy revealed structural reconstitution of the WW-domain scaffold only in CC-hPin1WW-L1, but not in CC-hPin1WW-L2. Furthermore, by using 1H-15N HSQC NMR, fluorescence and CD spectroscopy, we demonstrated that binding properties of fragmented hPin1WW in CC-hPin1WW-L1 were fully restored by CC association. To demonstrate the power of this approach as a combinatorial screening platform, we synthesized a four-by-six library of N- and C-terminal hPin1WW-CC peptide fragments that was screened for a WW domain that preferentially binds to ATP over cAMP, phophocholine, or IP6. Using this screening platform, we identified one WW domain, which specifically binds ATP, and a phosphorylcholine-specific WW-based mini-receptor, both having binding dissociation constants in the lower micromolar range.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg Am Hubland Würzburg 97074 Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen Tammannstr. 2 Göttingen 37077 Germany
| | - Florian R Häge
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz Universitätsstraße 10 Konstanz 78457 Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
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7
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The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin. Molecules 2022; 27:molecules27134172. [PMID: 35807421 PMCID: PMC9268152 DOI: 10.3390/molecules27134172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/02/2023] Open
Abstract
The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.
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8
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Stanojlovic V, Müller A, Moazzam A, Hinterholzer A, Ożga K, Berlicki Ł, Schubert M, Cabrele C. A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. Chembiochem 2022; 23:e202100604. [PMID: 34856053 PMCID: PMC9299858 DOI: 10.1002/cbic.202100604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Indexed: 11/09/2022]
Abstract
The β-hairpin is a structural element of native proteins, but it is also a useful artificial scaffold for finding lead compounds to convert into peptidomimetics or non-peptide structures for drug discovery. Since linear peptides are synthetically more easily accessible than cyclic ones, but are structurally less well-defined, we propose XWXWXpPXK(/R)X(R) as an acyclic but still rigid β-hairpin scaffold that is robust enough to accommodate different types of side chains, regardless of the secondary-structure propensity of the X residues. The high conformational stability of the scaffold results from tight contacts between cross-strand cationic and aromatic side chains, combined with the strong tendency of the d-Pro-l-Pro dipeptide to induce a type II' β-turn. To demonstrate the robustness of the scaffold, we elucidated the NMR structures and performed molecular dynamics (MD) simulations of a series of peptides displaying mainly non-β-branched, poorly β-sheet-prone residues at the X positions. Both the NMR and MD data confirm that our acyclic β-hairpin scaffold is highly versatile as regards the amino-acid composition of the β-sheet face opposite to the cationic-aromatic one.
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Affiliation(s)
- Vesna Stanojlovic
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Anna Müller
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Ali Moazzam
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
- School of ChemistryCollege of ScienceUniversity of TehranP.O. Box 14155–6619TehranIran
| | - Arthur Hinterholzer
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Katarzyna Ożga
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Łukasz Berlicki
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Mario Schubert
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Chiara Cabrele
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
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9
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Martinent R, Tawffik S, López-Andarias J, Moreau D, Laurent Q, Matile S. Dithiolane quartets: thiol-mediated uptake enables cytosolic delivery in deep tissue. Chem Sci 2021; 12:13922-13929. [PMID: 34760179 PMCID: PMC8549803 DOI: 10.1039/d1sc04828g] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
The cytosolic delivery of various substrates in 3D multicellular spheroids by thiol-mediated uptake is reported. This is important because most orthodox systems, including polycationic cell-penetrating peptides, fail to deliver efficiently into deep tissue. The grand principles of supramolecular chemistry, that is the pH dependence of dynamic covalent disulfide exchange with known thiols on the transferrin receptor, are proposed to account for transcytosis into deep tissue, while the known but elusive exchange cascades along the same or other partners assure cytosolic delivery in kinetic competition. For quantitative detection in the cytosol, the 2D chloroalkane penetration assay (CAPA) is translated to 3D deep tissue. The targeted delivery of quantum dots, otherwise already troublesome in 2D culture, and the controlled release of mechanophores are realized to exemplify the power of thiol-mediated uptake into spheroids. As transporters, dithiolane quartets on streptavidin templates are introduced as modular motifs. Built from two amino acids only, the varied stereochemistry and peptide sequence are shown to cover maximal functional space with minimal structural change, i.e., constitutional isomers. Reviving a classic in peptide chemistry, this templated assembly of β quartets promises to expand streptavidin biotechnology in new directions, while the discovery of general cytosolic delivery in deep tissue as an intrinsic advantage further enhances the significance and usefulness of thiol-mediated uptake.
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Affiliation(s)
- Rémi Martinent
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Salman Tawffik
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Javier López-Andarias
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Dimitri Moreau
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Quentin Laurent
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva Geneva Switzerland https://www.unige.ch/sciences/chiorg/matile/ +41 22 379 6523
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10
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Fadler RE, Al Ouahabi A, Qiao B, Carta V, König NF, Gao X, Zhao W, Zhang Y, Lutz JF, Flood AH. Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes. J Org Chem 2021; 86:4532-4546. [PMID: 33636075 PMCID: PMC8063573 DOI: 10.1021/acs.joc.0c02887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.
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Affiliation(s)
- Rachel E Fadler
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Bo Qiao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Veronica Carta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Niklas F König
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Xinfeng Gao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yankai Zhang
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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11
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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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12
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Abstract
The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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13
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Jeong WJ, Bu J, Han Y, Drelich AJ, Nair A, Král P, Hong S. Nanoparticle Conjugation Stabilizes and Multimerizes β-Hairpin Peptides To Effectively Target PD-1/PD-L1 β-Sheet-Rich Interfaces. J Am Chem Soc 2020; 142:1832-1837. [DOI: 10.1021/jacs.9b10160] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | | | | | | | | | | | - Seungpyo Hong
- Yonsei Frontier Lab, Department of Pharmacy, Yonsei University, Seoul 03722, Republic of Korea
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14
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Joshi S, Sharma P, Siddiqui R, Kaushal K, Sharma S, Verma G, Saini A. A review on peptide functionalized graphene derivatives as nanotools for biosensing. Mikrochim Acta 2019; 187:27. [PMID: 31811393 DOI: 10.1007/s00604-019-3989-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022]
Abstract
Peptides exhibit unique binding behavior with graphene and its derivatives by forming bonds on its edges and planes. This makes them useful for sensing and imaging applications. This review with (155 refs.) summarizes the advances made in the last decade in the field of peptide-GO bioconjugation, and the use of these conjugates in analytical sciences and imaging. The introduction emphasizes the need for understanding the biotic-abiotic interactions in order to construct controllable peptide-functionalized graphitic material-based nanotools. The next section covers covalent and non-covalent interactions between peptide and oxidized graphene derivatives along with a discussion of the adsorption events during interfacing. We then describe applications of peptide-graphene conjugates in bioassays, with subsections on (a) detection of cancer cells, (b) monitoring protease activity, (c) determination of environmental pollutants and (d) determination of pathogenic microorganisms. The concluding section describes the current status of peptide functionalized graphitic bioconjugates and addresses future perspectives. Graphical abstractSchematic representation depicting biosensing applications of peptide functionalized graphene oxide.
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Affiliation(s)
- Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Pratibha Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Ruby Siddiqui
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Kanica Kaushal
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Shweta Sharma
- Institute of Forensic Science & Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Gaurav Verma
- Dr. S.S. Bhatnagar University Institute of Chemical Engineering & Technology (Dr.SSBUICET), Panjab University, Sector 14, Chandigarh, 160014, India
- Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India.
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15
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Kroiss D, Aramini JM, McPhee SA, Tuttle T, Ulijn RV. Unbiased Discovery of Dynamic Peptide‐ATP Complexes. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniela Kroiss
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New York 365 Fifth Avenue New York NY 10016 USA
- Department of ChemistryHunter College, City University of New York 695 Park Avenue New York NY 10065 USA
| | - James M. Aramini
- Structural Biology Initiative at ASRCThe Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
| | - Scott A. McPhee
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
| | - Tell Tuttle
- WestCHEM and Department of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Rein V. Ulijn
- Nanoscience Initiative at Advanced Science Research Center (ASRC)The Graduate Center of the City University of New York 85 St. Nicholas Terrace New York NY 10031 USA
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New York 365 Fifth Avenue New York NY 10016 USA
- Department of ChemistryHunter College, City University of New York 695 Park Avenue New York NY 10065 USA
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16
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Wang J, Zhang L, Yang J, Yan H, Li X, Wang C, Wang D, Sun Y, Xu H. Platinum-Ion-Mediated Self-Assembly of Hairpin Peptides and Synthesis of Platinum Nanostructures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5617-5625. [PMID: 30942585 DOI: 10.1021/acs.langmuir.9b00265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanostructures and nanomaterials based on peptide self-assembly have attracted tremendous interests due to the functionalities of peptide molecules. Furthermore, the self-assembled peptide nanostructures are also adopted to fabricate nanomaterials and nanodevices. In this work, the intramolecular folding and self-assembly of a β-hairpin peptide CBHH were first studied under the regulation of platinum ion. And then, platinum nanostructures were synthesized through the reduction of platinum ions templated with peptide self-assemblies. The results of circular dichroism spectroscopy, UV-vis spectroscopy, isothermal titration calorimetry, and atomic force microscopy observation showed that platinum ions could promote the conversion of peptide CBHH secondary structure from a random coil to a β-sheet through coordination with histidine residues. Platinum nanostructures including nanorods and one dimensionally aligned nanorods were synthesized through in situ reduction with CBHH self-assembled nanofiber as the templates. And the synthesized platinum nanostructures showed excellent electrocatalytic activities.
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Affiliation(s)
- Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Liyan Zhang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Jingge Yang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Hongyu Yan
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Xiran Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Chengdong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology , China University of Petroleum (East China) , 66 Changjiang West Road , Qingdao 266580 , China
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17
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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18
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Roca C, Martinez-González L, Daniel-Mozo M, Sastre J, Infantes L, Mansilla A, Chaves-Sanjuan A, González-Rubio JM, Gil C, Cañada FJ, Martinez A, Sanchez-Barrena MJ, Campillo NE. Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators. J Med Chem 2018; 61:5910-5921. [DOI: 10.1021/acs.jmedchem.8b00088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Miguel Daniel-Mozo
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Javier Sastre
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano-CSIC, Serrano 119, 28006 Madrid, Spain
| | - Alicia Mansilla
- Fundación para la Investigación Biomédica, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, Km. 9, 28034 Madrid, Spain
| | | | | | - Carmen Gil
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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19
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Wang H, Feng Z, Qin Y, Wang J, Xu B. Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018; 57:4931-4935. [PMID: 29451962 PMCID: PMC6014697 DOI: 10.1002/anie.201712834] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Herein, we report that assemblies of nucleopeptides selectively sequester ATP in complex conditions (for example, serum and cytosol). We developed assemblies of nucleopeptides that selectively sequester ATP over ADP. Counteracting enzymes interconvert ATP and ADP to modulate the nanostructures formed by the nucleopeptides and the nucleotides. The nucleopeptides, sequestering ATP effectively in cells, slow down efflux pumps in multidrug-resistant cancer cells, thus boosting the efficacy of doxorubicin, an anticancer drug. Investigation of 11 nucleopeptides (including d- and l-enantiomers) yields five more nucleopeptides that differentiate ATP and ADP through either precipitation or gelation. As the first example of assemblies of nucleopeptides that interact with ATP and disrupt intracellular ATP dynamics, this work illustrates the use of supramolecular assemblies to interact with small and essential biological molecules for controlling cell behavior.
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Affiliation(s)
- Huaimin Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Zhaoqianqi Feng
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Yanan Qin
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Jiaqing Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
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20
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Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Patterns of cation binding to the aromatic amino acid R groups in Trp, Tyr, and Phe. Comput Biol Chem 2018; 72:11-15. [DOI: 10.1016/j.compbiolchem.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 11/24/2022]
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22
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Yu H, Zheng J, Yang S, Asiri AM, Alamry KA, Sun M, Zhang K, Wang S, Yang R. Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence. Talanta 2017; 178:282-286. [PMID: 29136823 DOI: 10.1016/j.talanta.2017.09.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/15/2017] [Accepted: 09/17/2017] [Indexed: 10/18/2022]
Abstract
We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.
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Affiliation(s)
- Huan Yu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Jing Zheng
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Sheng Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Abdullah M Asiri
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid A Alamry
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mingtai Sun
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Kui Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Suhua Wang
- School of Environment and Chemical Engineering, North China Electric Power University, Beijing 102206, China.
| | - Ronghua Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
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23
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Huang B, Geng Z, Yan S, Li Z, Cai J, Wang Z. Water-Soluble Conjugated Polymer as a Fluorescent Probe for Monitoring Adenosine Triphosphate Level Fluctuation in Cell Membranes during Cell Apoptosis and in Vivo. Anal Chem 2017; 89:8816-8821. [PMID: 28752761 DOI: 10.1021/acs.analchem.7b01212] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Adenosine triphosphate (ATP) is used as the energy source in cells and plays crucial roles in various cellular events. The cellular membrane is the protective barrier for the cytoplasm of living cells and involved in many essential biological processes. Many fluorescent probes for ATP have been successfully developed, but few of these probes were appropriate for visualizing ATP level fluctuation in cell membranes during the apoptotic cell death process. Herein, we report the synthesis of a new water-soluble cationic polythiophene derivative that can be utilized as a fluorescent sensor for detecting ATP in cell membranes. Poly((3-((4-methylthiophen-3-yl)oxy)propyl)triphenylphosphonium chloride) (PMTPP) exhibits high sensitivity and good selectivity to ATP, and the detection limit is 27 nM. The polymer shows low toxicity to live cells and excellent photostability in cell membranes. PMTPP was practically utilized for real-time monitoring of ATP levels in the cell membrane through fluorescence microscopy. We have demonstrated that the ATP levels in cell membranes increased during the apoptotic cell death process. The probe was also capable of imaging ATP levels in living mice.
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Affiliation(s)
- Binghuan Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhirong Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Shihai Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zan Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Jun Cai
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructure, Nanjing University , Nanjing, Jiangsu 210093, China
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24
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
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25
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017; 56:5904-5908. [PMID: 28440962 DOI: 10.1002/anie.201702472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 01/21/2023]
Abstract
The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or "heme cage" by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme-protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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26
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Mansilla A, Chaves-Sanjuan A, Campillo NE, Semelidou O, Martínez-González L, Infantes L, González-Rubio JM, Gil C, Conde S, Skoulakis EMC, Ferrús A, Martínez A, Sánchez-Barrena MJ. Interference of the complex between NCS-1 and Ric8a with phenothiazines regulates synaptic function and is an approach for fragile X syndrome. Proc Natl Acad Sci U S A 2017; 114:E999-E1008. [PMID: 28119500 PMCID: PMC5307446 DOI: 10.1073/pnas.1611089114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protein complex formed by the Ca2+ sensor neuronal calcium sensor 1 (NCS-1) and the guanine exchange factor protein Ric8a coregulates synapse number and probability of neurotransmitter release, emerging as a potential therapeutic target for diseases affecting synapses, such as fragile X syndrome (FXS), the most common heritable autism disorder. Using crystallographic data and the virtual screening of a chemical library, we identified a set of heterocyclic small molecules as potential inhibitors of the NCS-1/Ric8a interaction. The aminophenothiazine FD44 interferes with NCS-1/Ric8a binding, and it restores normal synapse number and associative learning in a Drosophila FXS model. The synaptic effects elicited by FD44 feeding are consistent with the genetic manipulation of NCS-1. The crystal structure of NCS-1 bound to FD44 and the structure-function studies performed with structurally close analogs explain the FD44 specificity and the mechanism of inhibition, in which the small molecule stabilizes a mobile C-terminal helix inside a hydrophobic crevice of NCS-1 to impede Ric8a interaction. Our study shows the drugability of the NCS-1/Ric8a interface and uncovers a suitable region in NCS-1 for development of additional drugs of potential use on FXS and related synaptic disorders.
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Affiliation(s)
- Alicia Mansilla
- Departamento de Neurobiología del Desarrollo, Instituto Cajal, Spanish National Research Council, 28002 Madrid, Spain
| | - Antonio Chaves-Sanjuan
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, Spanish National Research Council, 28006 Madrid, Spain
| | - Nuria E Campillo
- Centro de Investigaciones Biológicas, Spanish National Research Council, 28040 Madrid, Spain
| | - Ourania Semelidou
- Division of Neuroscience, Biomedical Sciences Research Centre Alexander Fleming, 16672 Vari, Greece
| | | | - Lourdes Infantes
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, Spanish National Research Council, 28006 Madrid, Spain
| | - Juana María González-Rubio
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, Spanish National Research Council, 28006 Madrid, Spain
| | - Carmen Gil
- Centro de Investigaciones Biológicas, Spanish National Research Council, 28040 Madrid, Spain
| | - Santiago Conde
- Instituto de Química Médica, Spanish National Research Council, 28006 Madrid, Spain
| | - Efthimios M C Skoulakis
- Division of Neuroscience, Biomedical Sciences Research Centre Alexander Fleming, 16672 Vari, Greece
| | - Alberto Ferrús
- Departamento de Neurobiología del Desarrollo, Instituto Cajal, Spanish National Research Council, 28002 Madrid, Spain
| | - Ana Martínez
- Centro de Investigaciones Biológicas, Spanish National Research Council, 28040 Madrid, Spain
| | - María José Sánchez-Barrena
- Departamento de Cristalografía y Biología Estructural, Instituto de Química Física Rocasolano, Spanish National Research Council, 28006 Madrid, Spain;
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27
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Waters ML. From supramolecular chemistry to the nucleosome: studies in biomolecular recognition. Beilstein J Org Chem 2016; 12:1863-1869. [PMID: 27829892 PMCID: PMC5082656 DOI: 10.3762/bjoc.12.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/05/2016] [Indexed: 11/23/2022] Open
Abstract
This review highlights the author’s indirect path to research at the interface of supramolecular chemistry and chemical biology.
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Affiliation(s)
- Marcey L Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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28
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Stewart AL, Lorts AR, Seal EL, Takas NJ, Fortenberry RC. The role of sodium ions in the solubility of peptides. Struct Chem 2016. [DOI: 10.1007/s11224-016-0825-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Yu G, Zhou J, Shen J, Tang G, Huang F. Cationic pillar[6]arene/ATP host-guest recognition: selectivity, inhibition of ATP hydrolysis, and application in multidrug resistance treatment. Chem Sci 2016; 7:4073-4078. [PMID: 30155051 PMCID: PMC6013913 DOI: 10.1039/c6sc00531d] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/02/2016] [Indexed: 12/23/2022] Open
Abstract
Due to the differences in the cavity size of the hosts and the charge and length of the guests, a cationic water-soluble pillar[6]arene (WP6) selectively complexes with ATP to form a stable 1 : 1 inclusion complex WP6⊃ATP. This host-guest complexation was utilized to efficiently inhibit the hydrolysis of ATP, arising from the existence of the hydrophobic cavity of WP6. A folic acid functionalized diblock copolymer (FA-PEG-b-PAA) was employed to PEGylate WP6 to endow the polyion complex (PIC) micelles with specific targeting ability, preferentially delivering WP6 to folate receptor over-expressing KB cell. This host-guest complexation was further used to block the efflux pump to transport anticancer drugs out of cells by cutting off the energy source, which enhanced the efficacy of the cancer chemotherapy of DOX·HCl towards drug resistant MCF-7/ADR cell. This supramolecular method provides an extremely distinct strategy to potentially overcome multidrug resistance (MDR).
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Affiliation(s)
- Guocan Yu
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
| | - Jiong Zhou
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
| | - Jie Shen
- Department of Chemistry , Institute of Chemical Biology and Pharmaceutical Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Guping Tang
- Department of Chemistry , Institute of Chemical Biology and Pharmaceutical Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering , Center for Chemistry of High-Performance & Novel Materials , Department of Chemistry , Zhejiang University , Hangzhou 310027 , P. R. China . ; ; Tel: +86-571-8795-3189
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30
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Ng S, Lim HS, Ma Q, Gao Z. Optical Aptasensors for Adenosine Triphosphate. Theranostics 2016; 6:1683-702. [PMID: 27446501 PMCID: PMC4955066 DOI: 10.7150/thno.15850] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.
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Affiliation(s)
| | | | | | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore 117543
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31
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Huang BH, Geng ZR, Ma XY, Zhang C, Zhang ZY, Wang ZL. Lysosomal ATP imaging in living cells by a water-soluble cationic polythiophene derivative. Biosens Bioelectron 2016; 83:213-20. [PMID: 27131993 DOI: 10.1016/j.bios.2016.04.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 12/27/2022]
Abstract
Lysosomes in astrocytes and microglia can release ATP as the signaling molecule for the cells through ca(2+)-dependent exocytosis in response to various stimuli. At present, fluorescent probes that can detect ATP in lysosomes have not been reported. In this work, we have developed a new water-soluble cationic polythiophene derivative that can be specifically localized in lysosomes and can be utilized as a fluorescent probe to sense ATP in cells. PEMTEI exhibits high selectivity and sensitivity to ATP at physiological pH values and the detection limit of ATP is as low as 10(-11)M. The probe has low cytotoxicity, good permeability and high photostability in living cells and has been applied successfully to real-time monitoring of the change in concentrations of ATP in lysosomes though fluorescence microscopy. We also demonstrated that lysosomes in Hela cells can release ATP through Ca(2+)-dependent exocytosis in response to drug stimuli.
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Affiliation(s)
- Bing-Huan Huang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Rong Geng
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China.
| | - Xiao-Yan Ma
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Cui Zhang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Yang Zhang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China
| | - Zhi-Lin Wang
- State key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, PR China.
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32
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Zhao T, Lin C, Yao Q, Chen X. A label-free electrochemiluminescent sensor for ATP detection based on ATP-dependent ligation. Talanta 2016; 154:492-7. [PMID: 27154705 DOI: 10.1016/j.talanta.2016.03.091] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/21/2016] [Accepted: 03/28/2016] [Indexed: 11/26/2022]
Abstract
In this work, we describe a new label-free, sensitive and highly selective strategy for the electrochemiluminescent (ECL) detection of ATP at the picomolar level via ATP-induced ligation. The molecular-beacon like DNA probes (P12 complex) are self-assembled on a gold electrode. The presence of ATP leads to the ligation of P12 complex which blocks the digestion by Exonuclease III (Exo III). The protected P12 complex causes the intercalation of numerous ECL indicators (Ru(phen)3(2+)) into the duplex DNA grooves, resulting in significantly amplified ECL signal output. Since the ligating site of T4 DNA ligase and the nicking site of Exo III are the same, it involves no long time of incubation for conformation change. The proposed strategy combines the amplification power of enzyme and the inherent high sensitivity of the ECL technique and enables picomolar detection of ATP. The developed strategy also shows high selectivity against ATP analogs, which makes our new label-free and highly sensitive ligation-based method a useful addition to the amplified ATP detection arena.
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Affiliation(s)
| | - Chunshui Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Qiuhong Yao
- Xiamen Huaxia University, Xiamen 361024, China
| | - Xi Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
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33
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Zhang Y, Liu J, Zhang CY. Real-time monitoring of small biological molecules by ligation-mediated polymerase chain reaction. Chem Commun (Camb) 2016; 51:12270-3. [PMID: 26139082 DOI: 10.1039/c5cc04269k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a ligation-mediated polymerase chain reaction (PCR) for real-time detection of small biological molecules in a high-throughput format. This method is extremely sensitive with a detection limit of as low as 18.8 fM for ATP and 17.3 fM for NAD(+), and it can discriminate target molecules from their analogues as well.
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Affiliation(s)
- Yan Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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34
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Kumar A, Pandey R, Kumar A, Gupta RK, Dubey M, Mohammed A, Mobin SM, Pandey DS. Self-assembled copper(II) metallacycles derived from asymmetric Schiff base ligands: efficient hosts for ADP/ATP in phosphate buffer. Dalton Trans 2015; 44:17152-65. [PMID: 26373609 DOI: 10.1039/c5dt01433f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Novel asymmetric Schiff base ligands 2-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-phenol (H2L(1)) and 1-{[3-(3-hydroxy-1-methyl-but-2-enylideneamino)-2,4,6-trimethylphenylimino]-methyl}-naphthalen-2-ol (H2L(2)) possessing dissimilar N,O-chelating sites and copper(ii) metallacycles (CuL(1))4 (1) and (CuL(2))4 (2) based on these ligands have been described. The ligands and complexes have been thoroughly characterized by satisfactory elemental analyses, and spectral (IR, (1)H, (13)C NMR, ESI-MS, UV/vis) and electrochemical studies. Structures of H2L(2) and 1 have been unambiguously determined by X-ray single crystal analyses. The crystal structure of H2L(2) revealed the presence of two distinct N,O-chelating sites on dissimilar cores (naphthalene and β-ketoaminato groups) offering a diverse coordination environment. Metallacycles 1 and 2 having a cavity created by four Cu(ii) centres coordinated in a homo- and heteroleptic fashion with respective ligands act as efficient hosts for adenosine-5'-diphosphate (ADP) and adenosine-5'-triphosphate (ATP) respectively, over other nucleoside polyphosphates (NPPs). The disparate sensitivity of these metallacycles toward ADP and ATP has been attributed to the size of the ligands assuming diverse dimensions and spatial orientations. These are attuned for π-π stacking and electrostatic interactions suitable for different guest molecules under analogous conditions, metallacycle 1 offers better orientation for ADP, while 2 for ATP. The mechanism of the host-guest interaction has been investigated by spectral and electrochemical studies and supported by molecular docking studies.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry, Faculty of Science, Banaras Hindu University, Varanasi-221 005, India.
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35
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Xu L, Chou S, Wang J, Shao C, Li W, Zhu X, Shan A. Antimicrobial activity and membrane-active mechanism of tryptophan zipper-like β-hairpin antimicrobial peptides. Amino Acids 2015; 47:2385-97. [PMID: 26088720 DOI: 10.1007/s00726-015-2029-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022]
Abstract
Antimicrobial peptides (AMPs) with amphipathic β-hairpin structures have been demonstrated to possess potent antimicrobial activities and great cell selectivities. However, our understanding of β-hairpin antimicrobial peptides lags behind that of α-helices, mainly because it is difficult for short peptides to form robust β-hairpin structures. Tryptophan zipper (trpzip) peptides are among the most stable β-hairpin peptides known to fold spontaneously without requiring covalent disulfide constraint or metal binding. To develop model β-hairpin AMPs with small size and remarkable stability, a series of amphiphilic linear peptides were designed based on the trpzip motif. The sequence of designed peptides is (WK) n (D) PG(KW) n -NH2 (n = 1, 2, 3, 4, 5), and the antimicrobial activity and membrane interaction mechanism of the peptides were evaluated. The results showed that these peptides readily fold into β-hairpin structures in aqueous and membrane-mimicking environments and exhibit broad-spectrum antimicrobial activities against both gram-positive and gram-negative bacteria. The antibacterial potency of the peptides initially increased and then decreased with increasing chain length. WK3, a 14-residue peptide, displayed excellent antimicrobial activity with minimal hemolytic activity and cytotoxicity, suggesting that it possesses great cell selectivity. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), fluorescence spectroscopy, and flow cytometry indicated that representative peptides WK3 and WK4 exert their activities by permeabilizing the microbial membrane and damaging cell membrane integrity. This study reveals the application potential of the designed peptides as promising antimicrobial agents for the control of infectious diseases, and it also provides new insights into the design and optimization of highly stable β-hairpin AMPs with great antimicrobial activities and cell selectivities.
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Affiliation(s)
- Lin Xu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.,Heilongjiang Polytechnic, 5 Xuefu Road, Harbin, 150080, China
| | - Shuli Chou
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Jiajun Wang
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Changxuan Shao
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Weizhong Li
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Xin Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.
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36
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Kataev EA, Shumilova TA. Investigation of structural mimetics of natural phosphate ion binding motifs. Molecules 2015; 20:3354-70. [PMID: 25690293 PMCID: PMC6272573 DOI: 10.3390/molecules20023354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 01/19/2015] [Accepted: 02/12/2015] [Indexed: 11/20/2022] Open
Abstract
Phosphates are ubiquitous in biology and nearly half of all proteins interact with their partners by means of recognition of phosphate residues. Therefore, a better understanding of the phosphate ion binding by peptidic structures is highly desirable. Two new receptors have been designed and synthesized and their anion binding properties in an acetonitrile solution have been determined. The structure of hosts mimics a part of the kinase active site that is responsible for the recognition of the phosphate residue. New hosts contain additional free amino groups with the aim to facilitate coordination of protonated anions, such as dihydrogen phosphate. According to spectrophotometric measurements, stepwise 1:1 and 1:2 binding modes have been observed for both receptors in the presence of acetate, hydrogen sulfate and dihydrogen phosphate. Compared with the acyclic receptor, the macrocyclic receptor has demonstrated a remarkably enhanced selectivity for dihydrogen phosphate over other anions. Fluorometric measurements have revealed different responses of the acyclic and macrocyclic receptors towards anions. However, in both cases, a 5–8 nm hypsochromic shift of fluorescence maximum has been observed upon interaction of acetate and dihydrogen phosphate with receptors.
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Affiliation(s)
- Evgeny A Kataev
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
| | - Tatiana A Shumilova
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
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37
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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38
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Lin C, Cai Z, Wang Y, Zhu Z, Yang CJ, Chen X. Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise. Anal Chem 2014; 86:6758-62. [PMID: 24983417 DOI: 10.1021/ac501730u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.
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Affiliation(s)
- Chunshui Lin
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen, Fujian 361005, China
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39
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Shi L, Hu P, Ren Y, Feng G. An unexpected highly selective mononuclear zinc complex for adenosine diphosphate (ADP). Chem Commun (Camb) 2014; 49:11704-6. [PMID: 24192643 DOI: 10.1039/c3cc47437b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A simple and readily available mononuclear zinc complex, which appends two anthracene groups, was unexpectedly found to show high selectivity for ADP with a unique increased fluorescence response in neutral aqueous solution.
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Affiliation(s)
- Lei Shi
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China.
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40
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Hu P, Yang S, Feng G. Discrimination of adenine nucleotides and pyrophosphate in water by a zinc complex of an anthracene-based cyclophane. Org Biomol Chem 2014; 12:3701-6. [PMID: 24777701 DOI: 10.1039/c4ob00184b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Combining metal-anion coordination and π-π stacking interactions, a zinc complex of a novel anthracene-based cyclophane was designed to recognise adenine nucleoside polyphosphates. This complex was found to show selective fluorescence enhancement for ATP, ADP, AMP and PPi in neutral aqueous solution. Among them, ADP induced the largest fluorescence change to the complex, while ATP showed the strongest binding affinity to the complex. This property was used to sense ATP in the presence of excess amounts of other phosphates such as ADP, AMP, PPi and Pi.
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Affiliation(s)
- Ping Hu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, P. R. China.
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41
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Ghosh K, Kar D, Joardar S, Samadder A, Khuda-Bukhsh AR. Azaindole-1,2,3-triazole conjugate in a tripod for selective sensing of Cl−, H2PO4− and ATP under different conditions. RSC Adv 2014. [DOI: 10.1039/c3ra45018j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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42
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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43
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Ma C, Tang Z, Wang K, Yang X, Tan W. A novel sensitive and selective ligation-based ATP assay using a molecular beacon. Analyst 2013; 138:3013-7. [PMID: 23563079 DOI: 10.1039/c3an00161j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, a novel, facile fluorometric ATP assay with high sensitivity and excellent selectivity has been reported. This approach utilizes a molecular beacon, T4 DNA ligase and two short oligonucleotides. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction and the ligation product restores the fluorescence of the molecular beacon. Owing to the high sensitivity of the molecular beacon and T4 DNA ligase's high substrate dependence, this novel ATP assay demonstrates exceptional selectivity and high sensitivity down to 0.14 nM in homogeneous solution. Cellular ATP concentrations in several cell lines have been determined by measuring the lysate sample containing 8.0 × 10(3) cells.
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Affiliation(s)
- Changbei Ma
- School of Biological Science and Technology, Central South University, Changsha 410013, P. R. China.
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44
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Diez-García F, Pantoja-Uceda D, Jiménez MÁ, Chakrabartty A, Laurents DV. Structure of a simplified β-hairpin and its ATP complex. Arch Biochem Biophys 2013; 537:62-71. [PMID: 23811197 DOI: 10.1016/j.abb.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/13/2013] [Accepted: 06/16/2013] [Indexed: 11/29/2022]
Abstract
The capacity of three designed duodecamer peptides with the low diversity sequence: H1ϕ2I3K4I5D6G7K8ϕ9I10K11H12 where ϕ is His, Phe or Trp, to adopt a β-hairpin conformation was studied using NMR spectroscopy. Whereas KIAβH, the variant with His at positions two and nine, is disordered, KIAβF, the peptide with Phe at these positions, adopts a small population of β-hairpin. A high population of β-hairpin structure was detected for KIAβW, the variant with Trp. Utilizing NMR data, the structure of KIAβW was solved and it reveals a β-hairpin stabilized by hydrophobic interactions between Ile residues on one face and Trp-Trp and cation-π interactions on the opposite face. Upon adding ATP, these peptides show chemical shift changes indicative of ATP binding. The binding of ATP to KIAβW shows a KD ≈ 20 μM at pH 5, 5 °C and has a 1:1 stoichiometry. The KIAβW-ATP complex was determined using NMR spectroscopy and reveals the adenine ring sandwiched between the two Trp indole rings and that ATP binding induces important conformational changes in His1, Trp2, Lys4, Trp9 and Lys11 in the β-hairpin. The implications of these results for the hypothetic presence of β-hairpins and amyloids alongside RNAs on the prebiotic Earth are discussed.
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45
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Park JH, Waters ML. Positional effects of click cyclization on β-hairpin structure, stability, and function. Org Biomol Chem 2013; 11:69-77. [PMID: 23064223 DOI: 10.1039/c2ob26445e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The use of the copper(I)-assisted azide-alkyne cycloaddition (CuAAC, or "click" reaction) as a method of β-hairpin stabilization was investigated at several different positions to determine the impact on hairpin structure and function, including hydrogen bonded sites, non-hydrogen bonded sites, and at the peptide termini. The role of the turn sequence in the peptide and the chain length of the azide were also investigated. It was determined that the CuAAC reaction was a suitable method for locking in β-hairpin structure in peptides possessing either the type I' turn, VNGO and the type II' turn, VpGO. Moreover, all cyclic variants exhibited improved thermal stability and resistance to proteolysis as compared to the non-cyclic peptides, regardless of the position in the strand. Additionally, the function of the CuAAC cyclized peptides was not altered as exhibited by similar binding affinities for ATP as the WKWK peptide. These studies provide a comprehensive investigation of CuAAC cyclization of β-hairpin peptides, which could further be applied to the inhibition of protein-protein and protein-nucleic acid interactions.
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Affiliation(s)
- Jessica H Park
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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46
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Mi Y, Zhu W, Zhao J, Jiang J, Shen G, Yu R. A Ligation Triggered Label-Free Fluorescent Assay for Adenosine-Triphosphate Based on Nicking Endonuclease Signal Amplification and Ligand Responsive G-Quadruplex Formation. ANAL LETT 2013. [DOI: 10.1080/00032719.2012.749484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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47
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Mahajan M, Bhattacharjya S. β-Hairpin peptides: heme binding, catalysis, and structure in detergent micelles. Angew Chem Int Ed Engl 2013; 52:6430-4. [PMID: 23640811 DOI: 10.1002/anie.201300241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/25/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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48
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Mahajan M, Bhattacharjya S. β-Hairpin Peptides: Heme Binding, Catalysis, and Structure in Detergent Micelles. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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49
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Ray S, Takafuji M, Ihara H. Chromatographic evaluation of a newly designed peptide-silica stationary phase in reverse phase liquid chromatography and hydrophilic interaction liquid chromatography: Mixed mode behavior. J Chromatogr A 2012; 1266:43-52. [DOI: 10.1016/j.chroma.2012.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/17/2022]
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50
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Gorrea E, Pohl G, Nolis P, Celis S, Burusco KK, Branchadell V, Perczel A, Ortuño RM. Secondary structure of short β-peptides as the chiral expression of monomeric building units: a rational and predictive model. J Org Chem 2012; 77:9795-806. [PMID: 23030251 DOI: 10.1021/jo302034b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chirality of the monomeric residues controls and determines the prevalent folding of small oligopeptides (from di- to tetramers) composed of 2-aminocyclobutane-1-carboxylic acid (ACBA) derivatives with the same or different absolute and relative configuration. The cis-form of the monomeric ACBA gives rise to two conformers, namely, Z6 and Z8, while the trans-form manifests uniquely as an H8 structure. By combining these subunits in oligo- and polypeptides, their local structural preference remains, thus allowing the rational design of new short foldamers. A lego-type molecular architecture evolves; the overall look depends only on the conformational properties of the structural building units. A versatile and efficient method to predict the backbone folds of designed cyclobutane β-peptides is based on QM calculations. Predictions are corroborated by high-resolution NMR studies on selected stereoisomers, most of them being new foldamers that have been synthesized and characterized for the first time. Thus, the chiral expression of monomeric building units results in the defined secondary structures of small oligomers. As a result of this study, a new set of chirality controlled foldamers is provided to probe as biocompatible biopolymers.
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Affiliation(s)
- Esther Gorrea
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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