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Bartocci A, Dumont E. Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations. J Chem Phys 2024; 160:105101. [PMID: 38465686 DOI: 10.1063/5.0198522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
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Affiliation(s)
- Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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2
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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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3
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Meskers SCJ. Circular Polarization of Luminescence as a Tool To Study Molecular Dynamical Processes. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stefan C. J. Meskers
- Molecular Materials and Nanosystems and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. box 513 (STW 4.37) NL 5600 MB Eindhoven Netherlands
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4
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Bagchi A. Latest trends in structure based drug design with protein targets. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:1-23. [PMID: 32312418 DOI: 10.1016/bs.apcsb.2019.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to determine their binding efficacies with protein target. However, the entire process is very lengthy and above all highly expensive. With the advent of supercomputers and increasing computational powers, the search process for finding suitable ligand molecules against target proteins have become more streamlined and cost-effective. Now the entire ligand search process is performed in-silico with the help of the techniques of virtual screening, molecular docking simulations and molecular dynamics studies. In the present chapter, a brief overview of the computational techniques involved in structure based drug designing is presented with a special emphasis on the thermodynamic principles behind the molecular interactions.
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Affiliation(s)
- Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
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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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6
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Ma FH, Wang X, Chen JL, Wen X, Sun H, Su XC. Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects. Chemistry 2017; 23:926-934. [DOI: 10.1002/chem.201604393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Fei-He Ma
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Han Sun
- Department of Structural Biology; Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
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Balogh CM, Veyre L, Pilet G, Charles C, Viriot L, Andraud C, Thieuleux C, Riobé F, Maury O. Two-Color Three-State Luminescent Lanthanide Core-Shell Crystals. Chemistry 2017; 23:1784-1788. [PMID: 27973734 DOI: 10.1002/chem.201605728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 01/09/2023]
Abstract
Luminescent core-shell crystals based on lanthanide tris-dipicolinate complexes were obtained from the successive growing of two different lanthanide complex layers. Selective or simultaneous emission of each part of the crystal can be achieved by a careful choice of the excitation wavelength.
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Affiliation(s)
- Cristina M Balogh
- Univ. Lyon, Ens Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5182, Laboratoire de Chimie, F69342, Lyon, France.,Univ. Lyon, ICL, UMR 5265 CNRS-ESCPE Lyon-UCBL, Laboratory of Chemistry, Catalysis, Polymers and processus (C2P2), ESCPE Lyon 43 Bvd du 11 Novembre 1918, 69616, Villeurbanne cedex, France
| | - Laurent Veyre
- Univ. Lyon, ICL, UMR 5265 CNRS-ESCPE Lyon-UCBL, Laboratory of Chemistry, Catalysis, Polymers and processus (C2P2), ESCPE Lyon 43 Bvd du 11 Novembre 1918, 69616, Villeurbanne cedex, France
| | - Guillaume Pilet
- Univ. Lyon, Laboratoire des Multimatériaux et Interfaces (LMI), UMR 5615, CNRS-Université Claude Bernard Lyon 1, Bâtiment Chevreul, Avenue du 11 Novembre 1918, 69622, Villeurbanne cedex, France
| | - Cyril Charles
- Univ Lyon, Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon, France
| | - Laurent Viriot
- Univ Lyon, Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon, France
| | - Chantal Andraud
- Univ. Lyon, Ens Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5182, Laboratoire de Chimie, F69342, Lyon, France
| | - Chloé Thieuleux
- Univ. Lyon, ICL, UMR 5265 CNRS-ESCPE Lyon-UCBL, Laboratory of Chemistry, Catalysis, Polymers and processus (C2P2), ESCPE Lyon 43 Bvd du 11 Novembre 1918, 69616, Villeurbanne cedex, France
| | - François Riobé
- Univ. Lyon, Ens Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5182, Laboratoire de Chimie, F69342, Lyon, France
| | - Olivier Maury
- Univ. Lyon, Ens Lyon, CNRS, Université Claude Bernard Lyon 1, UMR 5182, Laboratoire de Chimie, F69342, Lyon, France
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8
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Denis-Quanquin S, Riobé F, Delsuc MA, Maury O, Giraud N. Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins. Chemistry 2016; 22:18123-18131. [DOI: 10.1002/chem.201603460] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Sandrine Denis-Quanquin
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - François Riobé
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); UMR 7104; 1 rue Laurent Fries, BP 10142 67404 Illkirch cedex France
| | - Olivier Maury
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - Nicolas Giraud
- Equipe RMN en milieu orienté, ICMMO, UMR CNRS 8182, Univ Paris Sud; Université Paris-Saclay; 91405 Orsay cedex France
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Xu Q, Li Z, Li H. Water-Soluble Luminescent Hybrid Composites Consisting of Oligosilsesquioxanes and Lanthanide Complexes and their Sensing Ability for Cu2+. Chemistry 2016; 22:3037-43. [DOI: 10.1002/chem.201504300] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Qianqian Xu
- School of Chemical Engineering and Technology; Hebei University of Technology; GuangRong Dao 8, Hongqiao District Tianjin 300130 P. R. China
| | - Zhiqiang Li
- School of Chemical Engineering and Technology; Hebei University of Technology; GuangRong Dao 8, Hongqiao District Tianjin 300130 P. R. China
| | - Huanrong Li
- School of Chemical Engineering and Technology; Hebei University of Technology; GuangRong Dao 8, Hongqiao District Tianjin 300130 P. R. China
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10
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Lewis FW, Harwood LM, Hudson MJ, Distler P, John J, Stamberg K, Núñez A, Galán H, Espartero AG. Synthesis and Evaluation of Lipophilic BTBP Ligands for An/Ln Separation in Nuclear Waste Treatment: The Effect of Alkyl Substitution on Extraction Properties and Implications for Ligand Design. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101576] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Gregoliński J, Wieczorek R, Lisowski J. Formation of Chiral Heteronuclear Ln
III
Assemblies by Ion Pair Formation. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Janusz Gregoliński
- Department of Chemistry, University of Wrocław, 14 F. Joliot‐Curie, 50‐383 Wrocław, Poland, Fax: +48‐71‐3282348
| | - Robert Wieczorek
- Department of Chemistry, University of Wrocław, 14 F. Joliot‐Curie, 50‐383 Wrocław, Poland, Fax: +48‐71‐3282348
| | - Jerzy Lisowski
- Department of Chemistry, University of Wrocław, 14 F. Joliot‐Curie, 50‐383 Wrocław, Poland, Fax: +48‐71‐3282348
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12
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Rutten L, Wieczorek B, Mannie JP, Kruithof C, Dijkstra H, Egmond M, Lutz M, Klein Gebbink R, Gros P, van Koten G. Solid-State Structural Characterization of Cutinase-ECE-Pincer-Metal Hybrids. Chemistry 2009; 15:4270-80. [DOI: 10.1002/chem.200801995] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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