1
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Tran TH, Prusty P, Ricciardi M, Travis CR, Waters ML, Gibb BC. Probing the non-covalent forces key to the thermodynamics of β-hairpin unfolding. Chem Sci 2024; 15:d4sc03464c. [PMID: 39239483 PMCID: PMC11369966 DOI: 10.1039/d4sc03464c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/24/2024] [Indexed: 09/07/2024] Open
Abstract
Although it is well understood that the graph of the free energy of unfolding (ΔG) of a globular protein with temperature approximates to a negative parabola, there is as yet no link between this global (G) ΔG G(T) function and the individual structural elements-residue type and the non-covalent forces between groups-contributing to it. As such, there is little understanding of how each structural element contributes to the globally assessed changes of enthalpy (ΔH G), entropy (ΔS G), and heat capacity (ΔC p(G)) of unfolding calculated from the ΔG G(T) function. To address this situation, we consider here an alternative approach to examining fold stability. Specifically, we examine the local (L) reporting of the thermodynamics of unfolding provided by each residue. By using 1H NMR spectroscopy to monitor the response of the individual mainchain amide N-H groups of β-hairpin peptides with temperature, we generate local ΔG L(T) functions, using these to calculate the local enthalpy (ΔH L), entropy (ΔS L), and heat capacity (ΔC p(L)) of unfolding. Mapping the thermodynamic changes in this way, for specific point-mutations, provides new information about how specific residues, non-covalent forces, and secondary structure type, contribute to folding. This type of information provides new details of the factors contributing to the typically measured global ΔG G(T) function.
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Affiliation(s)
- Thien H Tran
- Department of Chemistry, Tulane University School of Science and Engineering New Orleans LA 70118 USA
| | - Priyanka Prusty
- Department of Chemistry, Tulane University School of Science and Engineering New Orleans LA 70118 USA
| | - Meghan Ricciardi
- Department of Chemistry, University of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Christopher R Travis
- 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
| | - Bruce C Gibb
- Department of Chemistry, Tulane University School of Science and Engineering New Orleans LA 70118 USA
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2
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Selinger AJ, Hof F. Adaptive Supramolecular Networks: Emergent Sensing from Complex Systems. Angew Chem Int Ed Engl 2023; 62:e202312407. [PMID: 37699200 DOI: 10.1002/anie.202312407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Molecular differentiation by supramolecular sensors is typically achieved through sensor arrays, relying on the pattern recognition responses of large panels of isolated sensing elements. Here we report a new one-pot systems chemistry approach to differential sensing in biological solutions. We constructed an adaptive network of three cross-assembling sensor elements with diverse analyte-binding and photophysical properties. This robust sensing approach exploits complex interconnected sensor-sensor and sensor-analyte equilibria, producing emergent supramolecular and photophysical responses unique to each analyte. We characterize the basic mechanisms by which an adaptive network responds to analytes. The inherently data-rich responses of an adaptive network discriminate among very closely related proteins and protein mixtures without relying on designed protein recognition elements. We show that a single adaptive sensing solution provides better analyte discrimination using fewer response observations than a sensor array built from the same components. We also show the network's ability to adapt and respond to changing biological solutions over time.
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Affiliation(s)
- Allison J Selinger
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, 3800 Finnerty Rd., Victoria, BC V8W 2Y2, Canada
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3
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Xiong Y, Li M, Cao Y, Li Z, Chang Y, Zhao X, Qing G. Nanofluidic Device for Detection of Lysine Methylpeptides and Sensing of Lysine Methylation. Anal Chem 2023; 95:7761-7769. [PMID: 37140051 DOI: 10.1021/acs.analchem.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein methylation is the smallest possible yet vitally important post-translational modification (PTM). This small and chemically inert addition in proteins makes the analysis of methylation more challenging, thus calling for an efficient tool for the sake of recognition and detection. Herein, we present a nanofluidic electric sensing device based on a functionalized nanochannel that was constructed by introducing monotriazole-containing p-sulfonatocalix[4]arene (TSC) into a single asymmetric polymeric nanochannel via click chemistry. The device can selectively detect lysine methylpeptides with subpicomole sensitivity, distinguish between different lysine methylation states, and monitor the lysine methylation process by methyltransferase at the peptide level in real time. The introduced TSC molecule, with its confined asymmetric configuration, presents the remarkable ability to selectively bind to lysine methylpeptides, which, coupled with the release of the complexed Cu ions, allows the device to transform the molecular-level recognition to the discernible change in ionic current of the nanofluidic electric device, thus enabling detection. This work could serve as a stepping stone to the development of a new methyltransferase assay and the chemical that specifically targets lysine methylation in PTM proteomics.
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Affiliation(s)
- Yuting Xiong
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
| | - Minmin Li
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yongxin Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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4
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Abstract
ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystallization and X-ray structure determination as well as by solution state methods, NMR spectroscopy, isothermal titration calorimetry (ITC), and light scattering. Much of this work benefitted from collaboration, highlighted here. Our first breakthrough was the cocrystallization of cationic cytochrome c with sulfonato-calix[4]arene leading to a crystal structure defining three binding sites. Together with NMR studies, a dynamic complexation was deduced in which the calixarene explores the protein surface. Other cationic proteins were similarly amenable to cocrystallization with sulfonato-calix[4]arene, confirming calixarene-arginine/lysine encapsulation and consequent protein assembly. Calixarenes bearing anionic substituents such as sulfonate or phosphonate, but not carboxylate, have proven useful.Studies with larger calix[n]arenes (n = 6, 8) demonstrated the bigger better binder phenomenon with increased affinities and more interesting assemblies, including solution-state oligomerization and porous frameworks. While the calix[4]arene cavity accommodates a single cationic side chain, the larger macrocycles adopt different conformations, molding to the protein surface and accommodating several residues (hydrophobic, polar, and/or charged) in small cavities. In addition to accommodating protein features, the calixarene can bind exogenous components such as polyethylene glycol (PEG), metal ions, buffer, and additives. Ternary cocrystallization of cytochrome c, sulfonato-calix[8]arene, and spermine resulted in altered framework fabrication due to calixarene encapsulation of the tetraamine. Besides host-guest chemistry with exogenous components, the calixarene can also self-assemble, with numerous instances of macrocycle dimers.Calixarene complexation enables protein encapsulation, not merely side chain encapsulation. Cocrystal structures of sulfonato-calix[8]arene with cytochrome c or Ralstonia solanacearum lectin (RSL) provide evidence of encapsulation, with multiple calixarenes masking the same protein. NMR studies of cytochrome c and sulfonato-calix[8]arene are also consistent with multisite binding. In the case of RSL, a C3 symmetric trimer, up to six calixarenes bind the protein yielding a cubic framework mediated by calixarene dimers. Biomolecular calixarene complexation has evolved from molecular recognition to framework construction. This latter development contributes to the challenge in design and preparation of porous molecular materials. Cytochrome c and sulfonato-calix[8]arene form frameworks with >60% solvent in which the degree of porosity depends on the protein:calixarene ratio and the crystallization conditions. Recent developments with RSL led to three frameworks with varying porosity depending on the crystallization conditions, particularly the pH. NMR studies indicate a pH-triggered assembly in which two acidic residues appear to play key roles. The field of supramolecular protein chemistry is growing, and this Account aims to encourage new developments at the interface between biomolecular and synthetic/supramolecular chemistry.
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Affiliation(s)
- Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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5
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Zhou X, Shi M, Wang X, Xu D. Exploring the Binding Mechanism of a Supramolecular Tweezer CLR01 to 14-3-3σ Protein via Well-Tempered Metadynamics. Front Chem 2022; 10:921695. [PMID: 35646830 PMCID: PMC9133541 DOI: 10.3389/fchem.2022.921695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Using supramolecules for protein function regulation is an effective strategy in chemical biology and drug discovery. However, due to the presence of multiple binding sites on protein surfaces, protein function regulation via selective binding of supramolecules is challenging. Recently, the functions of 14-3-3 proteins, which play an important role in regulating intracellular signaling pathways via protein–protein interactions, have been modulated using a supramolecular tweezer, CLR01. However, the binding mechanisms of the tweezer molecule to 14-3-3 proteins are still unclear, which has hindered the development of novel supramolecules targeting the 14-3-3 proteins. Herein, the binding mechanisms of the tweezer to the lysine residues on 14-3-3σ (an isoform in 14-3-3 protein family) were explored by well-tempered metadynamics. The results indicated that the inclusion complex formed between the protein and supramolecule is affected by both kinetic and thermodynamic factors. In particular, simulations confirmed that K214 could form a strong binding complex with the tweezer; the binding free energy was calculated to be −10.5 kcal·mol−1 with an association barrier height of 3.7 kcal·mol−1. In addition, several other lysine residues on 14-3-3σ were identified as being well-recognized by the tweezer, which agrees with experimental results, although only K214/tweezer was co-crystallized. Additionally, the binding mechanisms of the tweezer to all lysine residues were analyzed by exploring the representative conformations during the formation of the inclusion complex. This could be helpful for the development of new inhibitors based on tweezers with more functions against 14-3-3 proteins via modifications of CLR01. We also believe that the proposed computational strategies can be extended to understand the binding mechanism of multi-binding sites proteins with supramolecules and will, thus, be useful toward drug design.
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Affiliation(s)
- Xin Zhou
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu, China
- *Correspondence: Xin Wang, ; Dingguo Xu,
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6
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Zhong W, Hooley RJ. Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts. Acc Chem Res 2022; 55:1035-1046. [PMID: 35302733 DOI: 10.1021/acs.accounts.2c00026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe3+ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe3+ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.
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7
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Guillory X, Hadrović I, de Vink PJ, Sowislok A, Brunsveld L, Schrader T, Ottmann C. Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand. J Am Chem Soc 2021; 143:13495-13500. [PMID: 34427424 DOI: 10.1021/jacs.1c07095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.
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Affiliation(s)
- Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Inesa Hadrović
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Pim J de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Andrea Sowislok
- University Clinics Essen, Experimental Orthopedics and Trauma Surgery, 45147 Essen, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Thomas Schrader
- Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstraße 7, 45117 Essen, Germany
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8
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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9
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Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene. J Struct Biol 2021; 213:107711. [PMID: 33631304 DOI: 10.1016/j.jsb.2021.107711] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/14/2022]
Abstract
Controlled protein assembly holds great potential in the fabrication of biohybrid materials. However, the structural diversity and complexity of proteins present an obstacle to controlled assembly. Supramolecular chemistry is a possible solution as it offers tools to mediate self-assembly with molecular precision. This paper deals with the calixarene- and zinc-mediated assembly and crystallization of the histidine-rich Penicillium chrysogenum antifungal protein B (PAFB). We report crystal structures of pure PAFB, PAFB in complex with Zn2+, and the ternary complex of PAFB, Zn2+ and sulfonato-calix[8]arene (sclx8). A comparison of the three crystal structures revealed the structural plasticity of PAFB. While the flexible and highly anionic sclx8 resulted in large molecular weight aggregates of PAFB in solution, diffraction-quality crystals of PAFB-sclx8 were not obtained. We report crystals of PAFB-Zn2+-sclx8 in which a trinuclear zinc cluster occurred adjacent to a calixarene binding site. Interestingly, the combination of sclx8 complexation and zinc coordination resulted in a porous framework with channels of circa 2 nm diameter. Detailed analysis of the crystal structure highlighted novel molecular recognition features. This research enriches the set of supramolecular interactions available to promote protein assembly.
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10
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Ramberg KO, Engilberge S, Skorek T, Crowley PB. Facile Fabrication of Protein-Macrocycle Frameworks. J Am Chem Soc 2021; 143:1896-1907. [PMID: 33470808 PMCID: PMC8154523 DOI: 10.1021/jacs.0c10697] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Precisely defined protein aggregates,
as exemplified by crystals,
have applications in functional materials. Consequently, engineered
protein assembly is a rapidly growing field. Anionic calix[n]arenes
are useful scaffolds that can mold to cationic proteins and induce
oligomerization and assembly. Here, we describe protein-calixarene
composites obtained via cocrystallization of commercially available
sulfonato-calix[8]arene (sclx8) with the symmetric and “neutral” protein RSL. Cocrystallization
occurred across a wide range of conditions and protein charge states,
from pH 2.2–9.5, resulting in three crystal forms. Cationization
of the protein surface at pH ∼ 4 drives calixarene complexation
and yielded two types of porous frameworks with pore diameters >3
nm. Both types of framework provide evidence of protein encapsulation
by the calixarene. Calixarene-masked proteins act as nodes within
the frameworks, displaying octahedral-type coordination in one case.
The other framework formed millimeter-scale crystals within hours,
without the need for precipitants or specialized equipment. NMR experiments
revealed macrocycle-modulated side chain pKa values and suggested a mechanism for pH-triggered assembly.
The same low pH framework was generated at high pH with a permanently
cationic arginine-enriched RSL variant. Finally, in addition to protein
framework fabrication, sclx8 enables de novo structure determination.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Tomasz Skorek
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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11
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Manfredi N, Decavoli C, Boldrini CL, Dolla TH, Faroldi F, Sansone F, Montini T, Baldini L, Fornasiero P, Abbotto A. Multibranched Calix[4]arene‐Based Sensitizers for Efficient Photocatalytic Hydrogen Production. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Norberto Manfredi
- Department of Materials Science and Solar Energy Research Center MIB-SOLAR University of Milano-Bicocca INSTM Milano-Bicocca Research Unit Via Cozzi 55 20125 Milano Italy
| | - Cristina Decavoli
- Department of Materials Science and Solar Energy Research Center MIB-SOLAR University of Milano-Bicocca INSTM Milano-Bicocca Research Unit Via Cozzi 55 20125 Milano Italy
| | - Chiara Liliana Boldrini
- Department of Materials Science and Solar Energy Research Center MIB-SOLAR University of Milano-Bicocca INSTM Milano-Bicocca Research Unit Via Cozzi 55 20125 Milano Italy
| | - Tarekegn Heliso Dolla
- Department of Chemical and Pharmaceutical Sciences INSTM Trieste Research Unit and ICCOM-CNR Trieste Research Unit University of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Federica Faroldi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Tiziano Montini
- Department of Chemical and Pharmaceutical Sciences INSTM Trieste Research Unit and ICCOM-CNR Trieste Research Unit University of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Laura Baldini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale Università di Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paolo Fornasiero
- Department of Chemical and Pharmaceutical Sciences INSTM Trieste Research Unit and ICCOM-CNR Trieste Research Unit University of Trieste Via L. Giorgieri 1 34127 Trieste Italy
| | - Alessandro Abbotto
- Department of Materials Science and Solar Energy Research Center MIB-SOLAR University of Milano-Bicocca INSTM Milano-Bicocca Research Unit Via Cozzi 55 20125 Milano Italy
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12
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein-protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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13
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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14
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Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
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Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
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15
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Baldini L, Casnati A, Sansone F. Multivalent and Multifunctional Calixarenes in Bionanotechnology. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Laura Baldini
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Alessandro Casnati
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Francesco Sansone
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
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16
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Dai L, Feng WX, Zheng SP, Jiang JJ, Wang D, van der Lee A, Dumitrescu D, Barboiu M. Progressive Folding and Adaptive Multivalent Recognition of Alkyl Amines and Amino Acids in p-Sulfonatocalix[4]arene Hosts: Solid-State and Solution Studies. Chempluschem 2020; 85:1623-1631. [PMID: 32286737 DOI: 10.1002/cplu.202000232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 01/15/2023]
Abstract
Calix[4]arenes have the ability to encapsulate biomimetic guests, offering interesting opportunities to explore their molecular recognition, very close to biological scenarios. In this study, p-sulfonatocalix[4]arene (C4 A) anions and hydrated alkali cations have been used for the in situ recognition of cationic 1,ω-diammonium-alkanes and 1,ω-amino-acids of variable lengths. NMR spectroscopy illustrates that these systems are stable in aqueous solution and the interaction process involves several binding states or stabilized conformations within the C4 A anion, depending of the nature of the guest. DOSY experiments showed that monomeric 1 : 1 host-guest species are present, while the cation does not influence their self-assembly in solution. The folded conformations observed in the solid-state X-ray single-crystal structures shed light on the constitutional adaptivity of flexible chains to environmental factors. Futhermore, a comprehensive screening of 30 single crystal structures helped to understand the in situ conformational fixation and accurate determination of the folded structures of the confined guest molecules, with a compression up to 40 % compared with their linear conformations.
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Affiliation(s)
- Liya Dai
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Wei-Xu Feng
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shannxi, 710129, P. R. China
| | - Shao-Ping Zheng
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Ji-Jun Jiang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Dawei Wang
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Arie van der Lee
- Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, Place E. Bataillon CC047, 34095, Montpellier, France
| | - Dan Dumitrescu
- XRD2 beamline, Elettra - Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Mihail Barboiu
- Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.,Institut Europeen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM-CNRS, Place E. Bataillon CC047, 34095, Montpellier, France
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17
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Gorbunov A, Iskandarova A, Puchnin K, Nenajdenko V, Kovalev V, Vatsouro I. A route to virtually unlimited functionalization of water-soluble p-sulfonatocalix[4]arenes. Chem Commun (Camb) 2020; 56:4122-4125. [PMID: 32166302 DOI: 10.1039/d0cc01196g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The functionality of p-sulfonatocalix[4]arenes can be easily extended using the propargylation/CuAAC reaction sequence, which allows the introduction of up to four substituted triazole units to the narrow rims of the macrocycles while maintaining their cone shapes and water solubility and, thus, biomedical applicability.
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Affiliation(s)
- Alexander Gorbunov
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Anna Iskandarova
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Kirill Puchnin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Valentine Nenajdenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Vladimir Kovalev
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
| | - Ivan Vatsouro
- Department of Chemistry, M. V. Lomonosov Moscow State University, Lenin's Hills 1, 119991 Moscow, Russia.
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18
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Alex JM, Brancatelli G, Volpi S, Bonaccorso C, Casnati A, Geremia S, Crowley PB. Probing the determinants of porosity in protein frameworks: co-crystals of cytochrome c and an octa-anionic calix[4]arene. Org Biomol Chem 2020; 18:211-214. [DOI: 10.1039/c9ob02275a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to sulfonato-calix[4]arene (sclx4), which mediates close-packed assemblies, the higher charge carboxylate-containing sclx4mc induced a crystalline framework of cytochrome c.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
| | - Giovanna Brancatelli
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Carmela Bonaccorso
- Dipartimento di Scienze Chimiche
- Università degli Studi di Catania
- Catania
- Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- 34127 Trieste
- Italy
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- University Road
- Galway
- Ireland
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19
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Reddy PS, Langlois d'Estaintot B, Granier T, Mackereth CD, Fischer L, Huc I. Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas. Chemistry 2019; 25:11042-11047. [PMID: 31257622 DOI: 10.1002/chem.201902942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Indexed: 01/12/2023]
Abstract
The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.
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Affiliation(s)
- Post Sai Reddy
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Béatrice Langlois d'Estaintot
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Thierry Granier
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Cameron D Mackereth
- ARNA (U1212), Univ. Bordeaux-INSERM-CNRS, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Lucile Fischer
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,Department Pharmazie and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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20
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Wang J, Ding X, Guo X. Assembly behaviors of calixarene-based amphiphile and supra-amphiphile and the applications in drug delivery and protein recognition. Adv Colloid Interface Sci 2019; 269:187-202. [PMID: 31082545 DOI: 10.1016/j.cis.2019.04.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/10/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023]
Abstract
Calixarene is the third generation of supra-molecular compounds after crown ether and cyclodextrin. Amphiphilic calixarene can be obtained by modulation with both hydrophilic group and hydrophobic alkyl chain. Compared with conventional surfactant, amphiphilic calixarene has much lower critical micelle concentration and is much easier to self-assemble into different morphological aggregates. Calixarene-basedsupra-amphiphile can be designed via noncovalent bonds due to the capability of calixarene to recognize surfactant; the binding of a surfactant with calixarene can decrease the critical micelle concentration of surfactant by several times. The calixarene-surfactant complex can self-aggregate to form spherical micelles, vesicles, and spherical nanoparticles, and the aggregation behavior can be controlled by the structures and the molar ratio of surfactant to calixarene and environmental factors. Calixarene-based amphiphile and supra-amphiphile show low cytotoxicity. They can load drugs and assemble into nanocapsules with drugs. The structure of the calixarene-drug complex can respond to external stimuli, rendering the sustained release of the drug and suggesting its potential application as a drug delivery system. Recently, calixarene has also been found to selectively bind proteins, suggesting its prospect in disease diagnosis and intervention treatment in clinics. This review elaborates on the research progress in the self-assembly behaviors of calixarene-based amphiphile and supra-amphiphile and the applications of the calixarenes in drug delivery and protein recognition. The prospectives for the studies are also provided in this review.
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21
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Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, Crowley PB. Calixarene-mediated assembly of a small antifungal protein. IUCRJ 2019; 6:238-247. [PMID: 30867921 PMCID: PMC6400181 DOI: 10.1107/s2052252519000411] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/08/2019] [Indexed: 05/24/2023]
Abstract
Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Gábor Lehoczki
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Hajdu Dorottya
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Ádám Fizil
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Gyula Batta
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
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22
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Jeamet E, Septavaux J, Héloin A, Donnier-Maréchal M, Dumartin M, Ourri B, Mandal P, Huc I, Bignon E, Dumont E, Morell C, Francoia JP, Perret F, Vial L, Leclaire J. Wetting the lock and key enthalpically favours polyelectrolyte binding. Chem Sci 2019; 10:277-283. [PMID: 30746081 PMCID: PMC6335637 DOI: 10.1039/c8sc02966k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/06/2018] [Indexed: 12/30/2022] Open
Abstract
By using a combination of readily accessible experimental and computational experiments in water, we explored the factors governing the association between polyanionic dyn[4]arene and a series of α,ω-alkyldiammonium ions of increasing chain length. We found that the lock-and-key concept based on the best match between the apolar and polar regions of the molecular partners failed to explain the observed selectivities. Instead, the dissection of the energetic and structural contributions demonstrated that the binding events were actually guided by two crucial solvent-related phenomena as the chain length of the guest increases: the expected decrease of the enthalpic cost of guest desolvation and the unexpected increase of the favourable enthalpy of complex solvation. By bringing to light the decisive enthalpic impact of complex solvation during the binding of polyelectrolytes by inclusion, this study may provide a missing piece to a puzzle that one day could display the global picture of molecular recognition in water.
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Affiliation(s)
- Emeric Jeamet
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Jean Septavaux
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Alexandre Héloin
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Marion Donnier-Maréchal
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Melissa Dumartin
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Benjamin Ourri
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Pradeep Mandal
- Institut de Chimie et Biologie des Membranes et des Nano-objets , UMR 5248 CNRS , Université de Bordeaux , IPB , 2 rue Escarpit , 33600 Pessac , France
| | - Ivan Huc
- Institut de Chimie et Biologie des Membranes et des Nano-objets , UMR 5248 CNRS , Université de Bordeaux , IPB , 2 rue Escarpit , 33600 Pessac , France
| | - Emmanuelle Bignon
- Laboratoire de Chimie , UMR 5182 CNRS , Ecole Normale Supérieure de Lyon , Université Claude Bernard Lyon 1 , 46 Allée d'Italie , 69364 Lyon Cedex 07 , France .
- Institut des Sciences Analytiques , UMR 5280 CNRS , Université Claude Bernard Lyon 1 , Ecole Nationale Supérieure de Lyon , 5, rue de la Doua , 69100 Villeurbanne , France
| | - Elise Dumont
- Laboratoire de Chimie , UMR 5182 CNRS , Ecole Normale Supérieure de Lyon , Université Claude Bernard Lyon 1 , 46 Allée d'Italie , 69364 Lyon Cedex 07 , France .
| | - Christophe Morell
- Institut des Sciences Analytiques , UMR 5280 CNRS , Université Claude Bernard Lyon 1 , Ecole Nationale Supérieure de Lyon , 5, rue de la Doua , 69100 Villeurbanne , France
| | - Jean-Patrick Francoia
- Institut des Biomolécules Max Mousseron , UMR 5247 CNRS , Université de Montpellier , ENSCM , Place Eugène Bataillon , 34296 Montpellier Cedex 5 , France
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Laurent Vial
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
| | - Julien Leclaire
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires , UMR 5246 CNRS , Université Claude Bernard Lyon1 , CPE Lyon , 43 Boulevard du 11 Novembre 1918 , 69622 Villeurbanne Cedex , France . ;
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23
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Zhang J, Chen H, Cao Y, Feng C, Zhu X, Li G. Design Nanoprobe Based on Its Binding with Amino Acid Residues on Cell Surface and Its Application to Electrochemical Analysis of Cells. Anal Chem 2018; 91:1005-1010. [DOI: 10.1021/acs.analchem.8b04247] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Chang Feng
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
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24
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Mummidivarapu VVS, Rennie ML, Doolan AM, Crowley PB. Noncovalent PEGylation via Sulfonatocalix[4]arene–A Crystallographic Proof. Bioconjug Chem 2018; 29:3999-4003. [DOI: 10.1021/acs.bioconjchem.8b00769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
| | - Aishling M. Doolan
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
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25
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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26
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Esmaielzade Rostami M, Gorji B, Zadmard R. Calix[4]arene-based Multifunctional Ligand as Potent Protein Binding Agent. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Banafsheh Gorji
- Department of Chemistry, South Tehran Branch; Islamic Azad University; Tehran Iran
| | - Reza Zadmard
- Department of Organic Chemistry; Chemistry and Chemical Engineering Research Center of Iran (CCERCI); Post Office Box 14335-186 Tehran Iran
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27
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Beatty MA, Busmann JA, Fagen NG, Garnett GAE, Hof F. A clip-like host that undergoes self-assembly and competitive guest-induced disassembly in water. Supramol Chem 2018. [DOI: 10.1080/10610278.2018.1494275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Meagan A. Beatty
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Jil A. Busmann
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Noah G. Fagen
- Department of Chemistry, University of Victoria, Victoria, Canada
| | | | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, Canada
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28
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Engilberge S, Riobé F, Wagner T, Di Pietro S, Breyton C, Franzetti B, Shima S, Girard E, Dumont E, Maury O. Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Chemistry 2018; 24:9739-9746. [DOI: 10.1002/chem.201802172] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/18/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - François Riobé
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Tristan Wagner
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Sebastiano Di Pietro
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Cécile Breyton
- Univ Grenoble Alpes; CEA; CNRS, IBS; 38000 Grenoble France
| | | | - Seigo Shima
- Microbial Protein Structure Group; Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Eric Girard
- Univ Grenoble Alpes; CEA; CNRS, IBS; 38000 Grenoble France
| | - Elise Dumont
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
| | - Olivier Maury
- Université de Lyon; École Normale Supérieure de Lyon; CNRS, Université Claude Bernard Lyon 1; Laboratoire de Chimie UMR 518; F-69342 Lyon France
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29
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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30
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018; 57:7126-7130. [DOI: 10.1002/anie.201803232] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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31
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Hewitt SH, Wilson AJ. Generation of Dynamic Combinatorial Libraries Using Hydrazone-Functionalized Surface Mimetics. European J Org Chem 2018; 2018:1872-1879. [PMID: 29780280 PMCID: PMC5947633 DOI: 10.1002/ejoc.201800022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 01/01/2023]
Abstract
Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
| | - Andrew J Wilson
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
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32
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Abstract
A key challenge in chemical biology is to identify small molecule regulators for every single protein. However, protein surfaces are notoriously difficult to recognise with synthetic molecules, often having large flat surfaces that are poorly matched to traditional small molecules. In the surface mimetic approach, a supramolecular scaffold is used to project recognition groups in such a manner as to make multivalent non-covalent contacts over a large area of protein surface. Metal based supramolecular scaffolds offer unique advantages over conventional organic molecules for protein binding, including greater stereochemical and geometrical diversity conferred through the metal centre and the potential for direct assessment of binding properties and even visualisation in cells without recourse to further functionalisation. This feature article will highlight the current state of the art in protein surface recognition using metal complexes as surface mimetics.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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33
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Lee J, Perez L, Liu Y, Wang H, Hooley RJ, Zhong W. Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis. Anal Chem 2018; 90:1881-1888. [PMID: 29286640 DOI: 10.1021/acs.analchem.7b03969] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.
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Affiliation(s)
| | | | | | - Hua Wang
- Instrument Analysis Center, Yancheng Teachers University , Yancheng, Jiangsu 224007, China
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34
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Doolan AM, Rennie ML, Crowley PB. Protein Recognition by Functionalized Sulfonatocalix[4]arenes. Chemistry 2017; 24:984-991. [PMID: 29125201 DOI: 10.1002/chem.201704931] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/31/2022]
Abstract
The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.
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Affiliation(s)
- Aishling M Doolan
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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35
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Hogeweg A, Sowislok A, Schrader T, Beuck C. Eine NMR-Methode zur Bestimmung der Bindungsreihenfolge supramolekularer Liganden an basische Reste in Proteinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Anna Hogeweg
- Bayer Pharma AG; Aprather Weg 18a 42096 Wuppertal Deutschland
| | - Andrea Sowislok
- Universität Duisburg-Essen; Organische Chemie; Universitätsstraße 2-5 45144 Essen Deutschland
| | - Thomas Schrader
- Universität Duisburg-Essen; Organische Chemie; Universitätsstraße 2-5 45144 Essen Deutschland
| | - Christine Beuck
- Universität Duisburg-Essen; Strukturelle und Medizinische Biochemie; Universitätsstraße 2-5 45144 Essen Deutschland
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36
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Hogeweg A, Sowislok A, Schrader T, Beuck C. An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins. Angew Chem Int Ed Engl 2017; 56:14758-14762. [PMID: 28877391 DOI: 10.1002/anie.201707950] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 01/14/2023]
Abstract
Targeting protein surfaces involved in protein-protein interactions by using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand-binding sites with single-residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We herein employed Lys- and Arg-specific H2(C)N NMR experiments to directly observe the side-chain atoms in close contact with the ligand, for which the largest changes in the NMR signals are expected. The binding of Lys- and Arg-specific supramolecular tweezers and a calixarene to two model proteins was studied. The H2(C)N spectra track the terminal CH2 groups of all Lys and Arg residues, revealing significant differences in their binding kinetics and chemical shift perturbation, and can be used to clearly pinpoint the order of ligand binding.
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Affiliation(s)
- Anna Hogeweg
- Current address: Bayer Pharma AG, Aprather Weg 18a, 42096, Wuppertal, Germany
| | - Andrea Sowislok
- University of Duisburg-Essen, Organic Chemistry, Universitätsstrasse 2-5, 45144, Essen, Germany
| | - Thomas Schrader
- University of Duisburg-Essen, Organic Chemistry, Universitätsstrasse 2-5, 45144, Essen, Germany
| | - Christine Beuck
- University of Duisburg-Essen, Structural and Medicinal Biochemistry, Universitätsstrasse 2-5, 45144, Essen, Germany
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37
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van Dun S, Ottmann C, Milroy LG, Brunsveld L. Supramolecular Chemistry Targeting Proteins. J Am Chem Soc 2017; 139:13960-13968. [PMID: 28926241 PMCID: PMC5639466 DOI: 10.1021/jacs.7b01979] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.
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Affiliation(s)
- Sam van Dun
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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38
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Liu Y, Perez L, Gill AD, Mettry M, Li L, Wang Y, Hooley RJ, Zhong W. Site-Selective Sensing of Histone Methylation Enzyme Activity via an Arrayed Supramolecular Tandem Assay. J Am Chem Soc 2017; 139:10964-10967. [PMID: 28777546 DOI: 10.1021/jacs.7b05002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Arrayed deep cavitands can be coupled to a fluorescence-based supramolecular tandem assay that allows site-selective in situ monitoring of post-translational modifications catalyzed by the lysine methyltransferase PRDM9 or the lysine demethylase JMJD2E. An arrayed sensor system containing only three cavitand components can detect the specific substrates of enzyme modification, in the presence of other histone peptides in the enzyme assay, enabling investigation of cross-reactivity over multiple methylation sites and interference from nonsubstrate peptides.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Lizeth Perez
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Adam D Gill
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Magi Mettry
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Lin Li
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Yinsheng Wang
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Richard J Hooley
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, ‡Environmental Toxicology Program, §Department of Biochemistry and Molecular Biology, University of California-Riverside , Riverside, California 92521, United States
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39
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Carmali S, Murata H, Amemiya E, Matyjaszewski K, Russell AJ. Tertiary Structure-Based Prediction of How ATRP Initiators React with Proteins. ACS Biomater Sci Eng 2017; 3:2086-2097. [DOI: 10.1021/acsbiomaterials.7b00281] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Sheiliza Carmali
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Hironobu Murata
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Erika Amemiya
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Alan J. Russell
- Center
for Polymer-Based Protein Engineering and ‡Department of Chemical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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40
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Bontempi N, Biavardi E, Bordiga D, Candiani G, Alessandri I, Bergese P, Dalcanale E. Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator. NANOSCALE 2017; 9:8639-8646. [PMID: 28608884 DOI: 10.1039/c7nr02491f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Binder and effector molecules that allow studying and manipulating epigenetic processes are of biological relevance and pose severe technical challenges. We report the first example of a synthetic receptor able to recognize mono-methylated lysines in a histone H3 tail peptide, which has relevant functions in epigenetic regulation. Recognition is robust and specific regardless of the position and the number of mono-methylated lysines along the polypeptide chain. The peptide is first captured in solution by a tetraphosphonate cavitand (Tiiii) that selectively binds its Lys-NMe+ moieties. Separation from solution and detection of the peptide-Tiiii complexes is then enabled in one single step by an all dielectric SiO2-TiO2 core-shell resonator (T-rex), which captures the complex and operates fully reproducible signal transduction by non-plasmonic surface enhanced Raman scattering (SERS) without degrading the complex. The realized abiotic probe is able to distinguish multiple mono-methylated peptides from the single mono-methylated ones.
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Affiliation(s)
- N Bontempi
- Department of Mechanical and Industrial Engineering, Chemistry for Technologies Laboratory, University of Brescia and INSTM UdR Brescia, Via Branze 38, 25123 Brescia, Italy.
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41
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Rennie ML, Doolan AM, Raston CL, Crowley PB. Protein Dimerization on a Phosphonated Calix[6]arene Disc. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Aishling M. Doolan
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Colin L. Raston
- Centre for Nanoscale Science and Technology; School of Chemical and Physical Sciences; Flinders University; GPO Box 2100 Adelaide Australia
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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42
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Rennie ML, Doolan AM, Raston CL, Crowley PB. Protein Dimerization on a Phosphonated Calix[6]arene Disc. Angew Chem Int Ed Engl 2017; 56:5517-5521. [DOI: 10.1002/anie.201701500] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Aishling M. Doolan
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Colin L. Raston
- Centre for Nanoscale Science and Technology; School of Chemical and Physical Sciences; Flinders University; GPO Box 2100 Adelaide Australia
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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43
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Hanauer T, Hopkinson RJ, Patel K, Li Y, Correddu D, Kawamura A, Sarojini V, Leung IKH, Gruber T. Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor. Org Biomol Chem 2017; 15:1100-1105. [PMID: 28091667 DOI: 10.1039/c6ob02616h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Chemical tools that recognise post-translational modifications have promising applications in biochemistry and in therapy. We report a simple carboxycalixarene that selectively binds molecules containing di/trimethylammonium moieties in isolation, in cell lysates and when incorporated in histone peptides. Our findings reveal the potential of using carboxycalixarene-based receptors to study epigenetic regulation.
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Affiliation(s)
- Thomas Hanauer
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Kamal Patel
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Yu Li
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Danilo Correddu
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Tobias Gruber
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
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44
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Kejík Z, Kaplánek R, Havlík M, Bříza T, Jakubek M, Králová J, Mikula I, Martásek P, Král V. Optical probes and sensors as perspective tools in epigenetics. Bioorg Med Chem 2017; 25:2295-2306. [PMID: 28285925 DOI: 10.1016/j.bmc.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Modifications of DNA cytosine bases and histone posttranslational modifications play key roles in the control of gene expression and specification of cell states. Such modifications affect many important biological processes and changes to these important regulation mechanisms can initiate or significantly contribute to the development of many serious pathological states. Therefore, recognition and determination of chromatin modifications is an important goal in basic and clinical research. Two of the most promising tools for this purpose are optical probes and sensors, especially colourimetric and fluorescence devices. The use of optical probes and sensors is simple, without highly expensive instrumentation, and with excellent sensitivity and specificity for target structural motifs. Accordingly, the application of various probes and sensors in the recognition and determination of cytosine modifications and structure of histones and histone posttranslational modifications, are discussed in detail in this review.
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Affiliation(s)
- Zdeněk Kejík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Robert Kaplánek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Martin Havlík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Tomáš Bříza
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Milan Jakubek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Jarmila Králová
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Ivan Mikula
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Pavel Martásek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Vladimír Král
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic.
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Zadmard R, Darvishi S, Akbari-Moghaddam P. Synthesis and protein binding properties of novel highly functionalized Calix[4]arene. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0637-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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46
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Pinalli R, Brancatelli G, Pedrini A, Menozzi D, Hernández D, Ballester P, Geremia S, Dalcanale E. The Origin of Selectivity in the Complexation of N-Methyl Amino Acids by Tetraphosphonate Cavitands. J Am Chem Soc 2016; 138:8569-80. [PMID: 27310660 DOI: 10.1021/jacs.6b04372] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the eligibility of tetraphosphonate resorcinarene cavitands for the molecular recognition of amino acids. We determined the crystal structure of 13 complexes of the tetraphosphonate cavitand Tiiii[H, CH3, CH3] with amino acids. (1)H NMR and (31)P NMR experiments and ITC analysis were performed to probe the binding between cavitand Tiiii[C3H7, CH3, C2H5] or the water-soluble counterpart Tiiii[C3H6Py(+)Cl(-), CH3, C2H5] and a selection of representative amino acids. The reported studies and results allowed us (i) to highlight the noncovalent interactions involved in the binding event in each case; (ii) to investigate the ability of tetraphosphonate cavitand receptors to discriminate between the different amino acids; (iii) to calculate the Ka values of the different complexes formed and evaluate the thermodynamic parameters of the complexation process, dissecting the entropic and enthalpic contributions; and (iv) to determine the solvent influence on the complexation selectivity. By moving from methanol to water, the complexation changed from entropy driven to entropy opposed, leading to a drop of almost three orders in the magnitude of the Ka. However, this reduction in binding affinity is associated with a dramatic increase in selectivity, since in aqueous solutions only N-methylated amino acids are effectively recognized. The thermodynamic profile of the binding does not change in PBS solution. The pivotal role played by cation-π interactions is demonstrated by the linear correlation found between the log Ka in methanol solution and the depth of (+)N-CH3 cavity inclusion in the molecular structures. These findings are relevant for the potential use of phosphonate cavitands as synthetic receptors for the detection of epigenetic modifications of histones in physiological media.
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Affiliation(s)
- Roberta Pinalli
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Giovanna Brancatelli
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Alessandro Pedrini
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniela Menozzi
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniel Hernández
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Pablo Ballester
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16, 43007 Tarragona, Spain
| | - Silvano Geremia
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Enrico Dalcanale
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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Garnett GA, Starke MJ, Shaurya A, Li J, Hof F. Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics. Anal Chem 2016; 88:3697-703. [DOI: 10.1021/acs.analchem.5b04508] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Graham A.E. Garnett
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Melissa J. Starke
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Alok Shaurya
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Janessa Li
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
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48
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Abstract
A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.
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Affiliation(s)
- Joshua E. Beaver
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
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Mallon M, Dutt S, Schrader T, Crowley PB. Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin. Chembiochem 2016; 17:774-83. [PMID: 26818656 DOI: 10.1002/cbic.201500477] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Indexed: 11/11/2022]
Abstract
Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.
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Affiliation(s)
- Madeleine Mallon
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Som Dutt
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
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50
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Peacock H, Thinnes CC, Kawamura A, Hamilton AD. Tetracyanoresorcin[4]arene selectively recognises trimethyllysine and inhibits its enzyme-catalysed demethylation. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1140898] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Hayden Peacock
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew D. Hamilton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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