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Flood R, Mockler NM, Thureau A, Malinska M, Crowley PB. Supramolecular Synthons in Protein-Ligand Frameworks. CRYSTAL GROWTH & DESIGN 2024; 24:2149-2156. [PMID: 38463617 PMCID: PMC10921380 DOI: 10.1021/acs.cgd.3c01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Supramolecular synthons, defined as reproducible intermolecular structural units, have greatly aided small molecule crystal engineering. In this paper, we propose that supramolecular synthons guide ligand-mediated protein crystallization. The protein RSL and the macrocycle sulfonato-calix[8]arene cocrystallize in at least four ways. One of these cocrystals is a highly porous cube comprising protein nodes connected by calixarene dimers. We show that mutating an aspartic acid to an asparagine results in two new cubic assemblies that depend also on the crystallization method. One of the new cubic arrangements is mediated by calixarene trimers and has a ∼30% increased cell volume relative to the original crystal with calixarene dimers. Crystals of the sulfonato-calix[8]arene sodium salt were obtained from buffered conditions similar to those used to grow the protein-calix[8]arene cocrystals. X-ray analysis reveals a coordination polymer of the anionic calix[8]arene and sodium cation in which the macrocycle is arranged as staggered stacks of the pleated loop conformation. Remarkably, the calixarene packing arrangement is the same in the simple salt as in the protein cocrystal. With the pleated loop conformation, the calixarene presents an extended surface for binding other calixarenes (oligomerization) as well as binding to a protein patch (biomolecular complexation). Small-angle X-ray scattering data suggest pH-dependent calixarene assembly in solution. Therefore, the calix[8]arene-calix[8]arene structural unit may be regarded as a supramolecular synthon that directs at least two types of protein assembly, suggesting applications in protein crystal engineering.
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Affiliation(s)
- Ronan
J. Flood
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Niamh M. Mockler
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
| | - Aurélien Thureau
- Synchrotron
SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, Cedex, Gif-sur-Yvette 91192, France
| | - Maura Malinska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Peter B. Crowley
- SSPC,
Science Foundation Ireland Research Centre for Pharmaceuticals, School
of Biological and Chemical Sciences, University
of Galway, University
Road, Galway H91 TK33, Ireland
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2
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Kravets K, Kravets M, Kędra K, Danylyuk O. P-Sulfonatocalix[8]arene coordinates sodium cations and forms host-guest complex with berberine: insight from crystal structure. Supramol Chem 2023. [DOI: 10.1080/10610278.2022.2161901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kateryna Kravets
- Institute of Physical Chemistry Polish Academy of Sciences, Warsaw, Poland
| | - Mykola Kravets
- Institute of Physical Chemistry Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Kędra
- Institute of Physical Chemistry Polish Academy of Sciences, Warsaw, Poland
| | - Oksana Danylyuk
- Institute of Physical Chemistry Polish Academy of Sciences, Warsaw, Poland
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3
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Bartocci A, Pereira G, Cecchini M, Dumont E. Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. J Chem Inf Model 2022; 62:6739-6748. [PMID: 36054284 DOI: 10.1021/acs.jcim.2c00483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Calix[n]arenes' selective recognition of protein surfaces covers a broad range of timely applications, from controlling protein assembly and crystallization to trapping partially disordered proteins. Here, the interaction of para-sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization of two binding sites in quantitative agreement with experimental evidence. Free energy calculations based on the MM-PBSA and the attach-pull-release (APR) methods highlight key residues implicated in the recognition process and provide binding free energy results in quantitative agreement with isothermal titration calorimetry. Our study emphasizes the role of MD simulations to capture and describe the "walk" of sulfonated calix-[4]-arenes on the cytochrome c surface, with the arginine R13 as a pivotal interacting residue. Our MD investigation allows, through the quasi-harmonic multibasin (QHMB) method, probing an allosteric reinforcement of several per-residue interactions upon calixarene binding, which suggests a more complex mode of action of these supramolecular auxiliaries.
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Affiliation(s)
- Alessio Bartocci
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Gilberto Pereira
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France.,Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Elise Dumont
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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Gassoumi B, Ben Mohamed F, Castro M, Melendez F, Karayel A, Nouar L, Madi F, Ghalla H, Özkınalı S, Kovalenko V, Ben Chaabane R, Ben Ouada H. In silico exploration of O-H…X2+ (X = Cu, Ag, Hg) interaction, targeted adsorption zone, charge density iso-surface, O-H proton analysis and topographic parameters theory for calix[6]arene and calix[8]arene as model. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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5
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Applications of reticular diversity in metal–organic frameworks: An ever-evolving state of the art. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213655] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Gaeta M, Rodolico E, Fragalà ME, Pappalardo A, Pisagatti I, Gattuso G, Notti A, Parisi MF, Purrello R, D’Urso A. Self-Assembly of Discrete Porphyrin/Calix[4]tube Complexes Promoted by Potassium Ion Encapsulation. Molecules 2021; 26:molecules26030704. [PMID: 33572895 PMCID: PMC7866244 DOI: 10.3390/molecules26030704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/14/2021] [Accepted: 01/23/2021] [Indexed: 11/25/2022] Open
Abstract
The pivotal role played by potassium ions in the noncovalent synthesis of discrete porphyrin-calixarene nanostructures has been examined. The flattened-cone conformation adopted by the two cavities of octa-cationic calix[4]tube C4T was found to prevent the formation of complexes with well-defined stoichiometry between this novel water-soluble calixarene and the tetra-anionic phenylsulfonate porphyrin CuTPPS. Conversely, preorganization of C4T into a C4v-symmetrical scaffold, triggered by potassium ion encapsulation (C4T@K+), allowed us to carry out an efficient hierarchical self-assembly process leading to 2D and 3D nanostructures. The stepwise formation of discrete CuTPPS/C4T@K+ noncovalent assemblies, containing up to 33 molecular elements, was conveniently monitored by UV/vis spectroscopy by following the absorbance of the porphyrin Soret band.
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Affiliation(s)
- Massimiliano Gaeta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
| | - Elisabetta Rodolico
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
| | - Maria E. Fragalà
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
| | - Andrea Pappalardo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
| | - Ilenia Pisagatti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy; (I.P.); (G.G.)
| | - Giuseppe Gattuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy; (I.P.); (G.G.)
| | - Anna Notti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy; (I.P.); (G.G.)
- Correspondence: (A.N.); (M.F.P.); (R.P.); (A.D.)
| | - Melchiorre F. Parisi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università degli Studi di Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy; (I.P.); (G.G.)
- Correspondence: (A.N.); (M.F.P.); (R.P.); (A.D.)
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
- Correspondence: (A.N.); (M.F.P.); (R.P.); (A.D.)
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (M.G.); (E.R.); (M.E.F.); (A.P.)
- Correspondence: (A.N.); (M.F.P.); (R.P.); (A.D.)
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Wang FF, Li JH, Liu HY, Deng SP, Liu YY, Ma JF. Functionalized resorcin[4]arene-based coordination polymers as heterogeneous catalysts for click reactions. NEW J CHEM 2021. [DOI: 10.1039/d0nj06051h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One Cu(i) and two Cd(ii) coordination polymers have been achieved using a 4-mercaptopyridine-functionalized resorcin[4]arene. 1 exhibits predominant efficiency and excellent recyclability for the synthesis of 1,2,3-triazoles and β-OH-1,2,3-triazoles.
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Affiliation(s)
- Fei-Fei Wang
- Key Lab of Polyoxometalate Science
- Department of Chemistry
- Northeast Normal University
- Changchun 130024
- China
| | - Jia-Hui Li
- Key Lab of Polyoxometalate Science
- Department of Chemistry
- Northeast Normal University
- Changchun 130024
- China
| | - Hai-Yan Liu
- Key Lab of Chemical Additive Synthesis and Separation
- Department of Chemical and Environmental Engineering, Yingkou Institute of Technology
- Yingkou 115014
- China
| | - Shu-Ping Deng
- Key Lab of Chemical Additive Synthesis and Separation
- Department of Chemical and Environmental Engineering, Yingkou Institute of Technology
- Yingkou 115014
- China
| | - Ying-Ying Liu
- Key Lab of Polyoxometalate Science
- Department of Chemistry
- Northeast Normal University
- Changchun 130024
- China
| | - Jian-Fang Ma
- Key Lab of Polyoxometalate Science
- Department of Chemistry
- Northeast Normal University
- Changchun 130024
- China
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