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Xia S, Jiang Y, Guo X, Wang Y, Xu W. Effects of p-sulfonatocalixarene and p-sulfonatocalixarene/sulfobetaine surfactant complex on the activities of bromelain and polyphenol oxidase. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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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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3
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Deng D, Yang X, An J, Zhang K, Lin S, Dong X. Sulfonated calix[4]arene functionalized SiO 2@TiO 2 for recognition of lysine methylation. Talanta 2021; 224:121819. [PMID: 33379044 DOI: 10.1016/j.talanta.2020.121819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 11/18/2022]
Abstract
Lysine methylations are common protein post-translational modifications (PTMs), that play significant roles in regulating gene activities. Studies of their functions and connections with diseases have important values. However, due to the small variations from their native structures and very low component proportions, it is very difficult to extract methylated peptides from biological mixtures. In this research, a new material that utilizes sulfonated calix[4]arene (SC4A) as the recognition unit and silica coated with TiO2 as carrier, denoted as SiO2@TiO2@SC4A, was synthesized. The equilibrium binding experiments demonstrated that SiO2@TiO2@SC4A can identify lysine and arginine methylation and peptides with these methylated residues. The maximum isotherm binding capacities are 70.0, 55.9, 31.4 and 24.8 μmol g-1 for Lys(Me3), Lys(Me)2, Lys(Me) and Lys, respectively. It demonstrated that the higher the degree of methylation, the stronger the interactions. In addition, the analyses of high performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) demonstrated that peptides with methylated lysine or arginine can be selectively extracted from spiked histone trypsin digestion. The recoveries for the spiked GGAK(Me)R, GGAKR(Me)2 and GGAK(Me)3R are 83%, 78%, and 84% respectively. The experiments from the nuclear extracts of HeLa cells also illustrated that SiO2@TiO2@SC4A holds a potential in the enrichment and identification of lysine methylations.
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Affiliation(s)
- Dandan Deng
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xu Yang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Jinying An
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Shen Lin
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - XiangChao Dong
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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4
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Shaurya A, Garnett GAE, Starke MJ, Grasdal MC, Dewar CC, Kliuchynskyi AY, Hof F. An easily accessible, lower rim substituted calix[4]arene selectively binds N, N-dimethyllysine. Org Biomol Chem 2021; 19:4691-4696. [PMID: 33978657 DOI: 10.1039/d1ob00524c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Post-translational modifications (PTMs) are critical controllers of protein functions. One set of important PTMs are N-methylated side chains of lysine and arginine, which exist in several functionally distinct forms. Multiple groups have demonstrated the selective binding of the most hydrophobic family member, trimethyllysine (Kme3), using various macrocyclic hosts, but the selective binding of lower methylation states remains challenging. Herein we report that the installation of a sulfonate ester on the lower rim phenol of p-sulfonatocalix[4]arene efficiently generates a potent, N,N-dimethyllysine (Kme2)-selective host in one step from commercially available starting materials. We characterize its binding behaviors in solution, and examine the relationship between its unusual conformational dynamics and its guest-binding properties.
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Affiliation(s)
- Alok Shaurya
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Graham A E Garnett
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Melissa J Starke
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Mark C Grasdal
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Charlotte C Dewar
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Anton Y Kliuchynskyi
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Fraser Hof
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
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5
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Pan Y, Hu X, Guo D. Biomedizinische Anwendungen von Calixarenen: Stand der Wissenschaft und Perspektiven. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Xin‐Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Dong‐Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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6
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Pan Y, Hu X, Guo D. Biomedical Applications of Calixarenes: State of the Art and Perspectives. Angew Chem Int Ed Engl 2020; 60:2768-2794. [DOI: 10.1002/anie.201916380] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Xin‐Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Dong‐Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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7
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Distinctive spectroscopic properties and adsorption behaviors of p-sulfonatocalixarene-cetyltrimethylammonium bromide supra-amphiphilic systems. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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Li L, Liu M, Yue L, Wang R, Zhang N, Liang Y, Zhang L, Cheng L, Xia J, Wang R. Host-Guest Protein Assembly for Affinity Purification of Methyllysine Proteomes. Anal Chem 2020; 92:9322-9329. [PMID: 32510198 DOI: 10.1021/acs.analchem.0c01643] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions drive self-assembly of biomacromolecules and thus enable important physiological functions at a cellular level. Supramolecular chemists have developed artificial host-guest interactions that are similar with, yet distinct from and orthogonal to, the natural protein-protein interactions. For instance, cucurbit[n]urils are synthetic receptors that can specifically recognize proteins with N-terminal aromatic residues with high affinities, yet this interaction can be reversed by the competition of small molecules such as amantadine. Herein, we develop a site-specific, oriented protein-display method by combining the host-guest interaction based on cucurbit[7]uril and a covalent protein-peptide reaction. A methyllysine-binding protein HP1β chromodomain (CD) is immobilized via host-guest interactions and used as the "bait" to capture methyllysine proteomes from cancer cells. The captured "fish"-methyllysine-containing proteins-can be released via competitive displacement by amantadine in a nondenaturing and traceless manner. This affinity purification method found 73 novel methyllysine sites from 101 identified sites among 66 methylated proteins from 255 HP1β CD-binding proteins in cancer cells via subsequent mass spectrometric analysis. This work thereby presents a new strategy of artificial host-guest protein assembly in affinity purification of methyllysine proteins in coupling to mass spectrometry.
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Affiliation(s)
- Linting Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Min Liu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ludan Yue
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518000, P. R. China
| | - Ning Zhang
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Yujie Liang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
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Lee J, Chen J, Sarkar P, Xue M, Hooley RJ, Zhong W. Monitoring the crosstalk between methylation and phosphorylation on histone peptides with host-assisted capillary electrophoresis. Anal Bioanal Chem 2020; 412:6189-6198. [PMID: 32064571 DOI: 10.1007/s00216-020-02486-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and regulate their functions by changing the structures, properties, and molecular interactions of proteins. In peptide regions with high density of PTMs, PTMs can influence modification on residues in proximity or even at distal positions, adding another layer of regulation. Methods that can monitor the activities of PTM enzymes on peptides carrying multiple modifications are valuable tools for better understanding of PTM crosstalk. Herein, we developed a host-assisted capillary electrophoresis (CE) method to separate histone peptides with methylation and phosphorylation and applied it to monitor the crosstalk between serine phosphorylation and lysine methylation when they were added by Aurora B kinase and G9a lysine methyltransferase, respectively. A synthetic receptor molecule, 4-hexasulfonatocalix[6]arene (CX6), was included in the CE buffer to improve the resolution of the corresponding substrates and products. A linear polyacrylamide-coated capillary was employed to effectively reduce wall adsorption of the cationic histone peptides. The peptide substrates were labeled with fluorescein to enhance their detectability during CE separation. Our method successfully revealed that the activity of G9a methyltransferase was completely inhibited by the adjacent phosphorylation, while 25% reduction in the activity of Aurora B kinase was observed with the presence of dimethylation on the nearby residue. The PTM crosstalk was examined not only using a pure peptide substrate, but also in a competitive reaction environment, in which the modified and unmodified peptides were mixed and the enzyme actions on both peptides were monitored simultaneously. Our work demonstrates that host-assisted CE is an effective method for study of PTM crosstalk, which could offer the advantages of fast separation, high resolution, and low sample consumption. Graphical abstract.
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Affiliation(s)
- Jiwon Lee
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Junyi Chen
- Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Priyanka Sarkar
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Biochemistry and Molecular Biology, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA. .,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA.
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10
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Screening of inhibitors against histone demethylation jumonji domain-containing protein 3 by capillary electrophoresis. J Chromatogr A 2019; 1613:460625. [PMID: 31668999 DOI: 10.1016/j.chroma.2019.460625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/21/2022]
Abstract
Jumonji domain-containing proteins (JMJDs) play an important role in the epigenetic regulation of gene expression. Aberrant regulation of histone modification has been observed in the progression of a variety of diseases, such as neurological disorders and cancer. Therefore, discovery of selective modulators of JMJDs is very attractive in new drug discovery. Herein, a simple capillary electrophoresis (CE) method was developed for screening of inhibitors against JMJD3. A known JMJD3 inhibitor GSK-J1, 5-carboxyfluorescein labeled substrate peptide with an amino acid sequence of KAPRKQLATKAARK(me3)SAPATGG (truncated from histone H3), as well as a small chemical library composed of 37 purified natural compounds and 30 natural extracts were used for method development and validation. The separation of substrate from its demethylated product was achieved by addition of polycation hexadimethrine bromide (HDB) in the running buffer. The enzyme activity was thus assayed accurately through separating the demethylated product from the substrate and then measuring the peak area of the product. The enzyme inhibition can be read out by comparing the peak area of the demethylated product obtained in the present of inhibitors and that of the negative control in the absence of any inhibitor. The merit of the method is proved by discovering two new JMJD3 inhibitors: salvianic acid A and puerarin 6''-O-xyloside.
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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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12
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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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13
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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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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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15
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16
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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: 52] [Impact Index Per Article: 7.4] [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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Liu Y, Perez L, Mettry M, Gill AD, Byers SR, Easley CJ, Bardeen CJ, Zhong W, Hooley RJ. Site selective reading of epigenetic markers by a dual-mode synthetic receptor array. Chem Sci 2017; 8:3960-3970. [PMID: 28553538 PMCID: PMC5433514 DOI: 10.1039/c7sc00865a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022] Open
Abstract
Variably functionalized self-folding deep cavitands form an arrayed, fluorescent indicator displacement assay system for the detection of post-translationally modified (PTM) histone peptides. The hosts bind trimethyllysine (KMe3) groups, and use secondary upper rim interactions to provide more sensitive discrimination between targets with identical KMe3 binding handles. The sensor array uses multiple different recognition modes to distinguish between miniscule differences in target, such as identical lysine modifications at different sites of histone peptides. In addition, the sensor is affected by global changes in structure, so it is capable of discriminating between identical PTMs, at identical positions on amino acid fragments that vary only in peptide backbone length, and can be applied to detect non-methylation modifications such as acetylation and phosphorylations located multiple residues away from the targeted binding site. The synergistic application of multiple variables allows dual-mode deep cavitands to approach levels of recognition selectivity usually only seen with antibodies.
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Affiliation(s)
- Yang Liu
- Environmental Toxicology Program , University of California - Riverside , Riverside , CA 92521 , USA
| | - Lizeth Perez
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Magi Mettry
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Adam D Gill
- Department of Biochemistry and Molecular Biology , University of California - Riverside , Riverside , CA 92521 , USA
| | - Samantha R Byers
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Connor J Easley
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Christopher J Bardeen
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
| | - Wenwan Zhong
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
- Environmental Toxicology Program , University of California - Riverside , Riverside , CA 92521 , USA
| | - Richard J Hooley
- Department of Chemistry , University of California - Riverside , Riverside , CA 92521 , USA . ;
- Department of Biochemistry and Molecular Biology , University of California - Riverside , Riverside , CA 92521 , USA
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18
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Kisley L, Patil U, Dhamane S, Kourentzi K, Tauzin LJ, Willson RC, Landes CF. Competitive multicomponent anion exchange adsorption of proteins at the single molecule level. Analyst 2017; 142:3127-3131. [DOI: 10.1039/c7an00701a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging of multicomponent, competitive adsorption demonstrates that competitors block certain ligands from the analyte without changing analyte adsorption kinetics.
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry
- Rice University
- Houston
- USA
| | - Ujwal Patil
- Department of Biology & Biochemistry
- University of Houston
- Houston
- USA
| | - Sagar Dhamane
- Department of Biology & Biochemistry
- University of Houston
- Houston
- USA
| | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering
- University of Houston
- Houston
- USA
| | | | - Richard C. Willson
- Department of Chemical & Biomolecular Engineering
- University of Houston
- Houston
- USA
- Department of Biology & Biochemistry
| | - Christy F. Landes
- Department of Chemistry
- Rice University
- Houston
- USA
- Department of Electrical and Computer Engineering
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19
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Gober IN, Waters ML. Optimization of a synthetic receptor for dimethyllysine using a biphenyl-2,6-dicarboxylic acid scaffold: insights into selective recognition of hydrophilic guests in water. Org Biomol Chem 2017; 15:7789-7795. [DOI: 10.1039/c7ob01921a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction of an endo-carboxylate in a building block for dynamic combinatorial chemistry resulted in amplification of a new host with a Kd of 200 nM for dimethyllysine, a biologically important post-translational modification.
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Affiliation(s)
- Isaiah N. Gober
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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20
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Structural aspects of small-molecule inhibition of methyllysine reader proteins. Future Med Chem 2016; 8:1681-702. [PMID: 27577975 DOI: 10.4155/fmc-2016-0082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Methyl reader proteins recognize and bind to post-translationally methylated residues. They execute the commands issued by protein methyltransferases and play functional roles in diverse cellular processes including gene regulation, development and oncogenesis. Efforts to inhibit these proteins are relatively new. Only a small number of methyl reader proteins belonging to the chromodomain, malignant brain tumor domain, plant homeodomain finger and Tudor domain families have been targeted by chemical inhibitors. This review summarizes inhibitors that have been reported to date, and provides a perspective for future progress. Structural determinants for methyl reader inhibition will be presented, along with an analysis of the molecular interactions that control potency and selectivity for inhibitors of each family.
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21
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Hof F. Host–guest chemistry that directly targets lysine methylation: synthetic host molecules as alternatives to bio-reagents. Chem Commun (Camb) 2016; 52:10093-108. [DOI: 10.1039/c6cc04771h] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Post-translational methylation regulates the function of hundreds of proteins in profound ways, and is the target of many efforts to use host–guest chemistry to solve biochemical and biological problems.
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Affiliation(s)
- Fraser Hof
- Department of Chemistry
- University of Victoria
- V8W3V6 Canada
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