1
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Leong SX, Kao YC, Han X, Poh ZW, Chen JRT, Tan EX, Leong YX, Lee YH, Teo WX, Yip GW, Lam Y, Ling XY. Achieving Molecular Recognition of Structural Analogues in Surface-Enhanced Raman Spectroscopy: Inducing Charge and Geometry Complementarity to Mimic Molecular Docking. Angew Chem Int Ed Engl 2023; 62:e202309610. [PMID: 37675645 DOI: 10.1002/anie.202309610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Molecular recognition of complex isomeric biomolecules remains challenging in surface-enhanced Raman scattering (SERS) spectroscopy due to their small Raman cross-sections and/or poor surface affinities. To date, the use of molecular probes has achieved excellent molecular sensitivities but still suffers from poor spectral specificity. Here, we induce "charge and geometry complementarity" between probe and analyte as a key strategy to achieve high spectral specificity for effective SERS molecular recognition of structural analogues. We employ 4-mercaptopyridine (MPY) as the probe, and chondroitin sulfate (CS) disaccharides with isomeric sulfation patterns as our proof-of-concept study. Our experimental and in silico studies reveal that "charge and geometry complementarity" between MPY's binding pocket and the CS sulfation patterns drives the formation of site-specific, multidentate interactions at the respective CS isomerism sites, which "locks" each CS in its analogue-specific complex geometry, akin to molecular docking events. Leveraging the resultant spectral fingerprints, we achieve > 97 % classification accuracy for 4 CSs and 5 potential structural interferences, as well as attain multiplex CS quantification with < 3 % prediction error. These insights could enable practical SERS differentiation of biologically important isomers to meet the burgeoning demand for fast-responding applications across various fields such as biodiagnostics, food and environmental surveillance.
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Affiliation(s)
- Shi Xuan Leong
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Ya-Chuan Kao
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Xuemei Han
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Zhong Wei Poh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Jaslyn Ru Ting Chen
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Emily Xi Tan
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yong Xiang Leong
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yih Hong Lee
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Wei Xuan Teo
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore
| | - George W Yip
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, 117594, Singapore
| | - Yulin Lam
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Xing Yi Ling
- Division of Chemistry and Biological Chemistry, School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
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2
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Franco-Ulloa S, Cesari A, Riccardi L, De Biasi F, Rosa-Gastaldo D, Mancin F, De Vivo M, Rastrelli F. Molecular Mechanisms Underlying Detection Sensitivity in Nanoparticle-Assisted NMR Chemosensing. J Phys Chem Lett 2023; 14:6912-6918. [PMID: 37498189 PMCID: PMC10405269 DOI: 10.1021/acs.jpclett.3c01005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
Nanoparticle-assisted nuclear magnetic resonance (NMR) chemosensing exploits monolayer-protected nanoparticles as supramolecular hosts to detect small molecules in complex mixtures via nuclear Overhauser effect experiments with detection limits down to the micromolar range. Still, the structure-sensitivity relationships at the basis of such detection limits are little understood. In this work, we integrate NMR spectroscopy and atomistic molecular dynamics simulations to examine the covariates that affect the sensitivity of different NMR chemosensing experiments [saturation transfer difference (STD), water STD, and high-power water-mediated STD]. Our results show that the intensity of the observed signals correlates with the number and duration of the spin-spin interactions between the analytes and the nanoparticles and/or between the analytes and the nanoparticles' solvation molecules. In turn, these parameters depend on the location and dynamics of each analyte inside the monolayer. This insight will eventually facilitate the tailoring of experimental and computational setups to the analyte's chemistry, making NMR chemosensing an even more effective technique in practical use.
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Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Expert
Analytics, Møllergata
8, 0179 Oslo, Norway
| | - Andrea Cesari
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Laura Riccardi
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Federico De Biasi
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Daniele Rosa-Gastaldo
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Marco De Vivo
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Federico Rastrelli
- Department
of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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3
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Franco-Ulloa S, Riccardi L, Rimembrana F, Grottin E, Pini M, De Vivo M. NanoModeler CG: A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution. J Chem Theory Comput 2023; 19:1582-1591. [PMID: 36795071 PMCID: PMC10018737 DOI: 10.1021/acs.jctc.2c01029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Functionalized metal nanoparticles (NPs) are macromolecular assemblies with a tunable physicochemical profile that makes them interesting for biotechnology, materials science, and energy conversion. In this regard, molecular simulations offer a way to scrutinize the structural and dynamical features of monolayer-protected NPs and their interactions with relevant matrices. Previously, we developed NanoModeler, a webserver that automates the preparation of functionalized gold NPs for atomistic molecular dynamics (MD) simulations. Here, we present NanoModeler CG (www.nanomodeler.it), a new release of NanoModeler that now also allows the building and parametrizing of monolayer-protected metal NPs at a coarse-grained (CG) resolution. This new version extends our original methodology to NPs of eight different core shapes, conformed by up to 800,000 beads and coated by eight different monolayer morphologies. The resulting topologies are compatible with the Martini force field but are easily extendable to any other set of parameters parsed by the user. Finally, we demonstrate NanoModeler CG's capabilities by reproducing experimental structural features of alkylthiolated NPs and rationalizing the brush-to-mushroom phase transition of PEGylated anionic NPs. By automating the construction and parametrization of functionalized NPs, the NanoModeler series offers a standardized way to computationally model monolayer-protected nanosized systems.
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Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy.,Expert Analytics, Møllergata 8, Oslo 0179, Norway
| | - Laura Riccardi
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Federico Rimembrana
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Edwin Grottin
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Mattia Pini
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
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4
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Gabellini C, Şologan M, Pellizzoni E, Marson D, Daka M, Franchi P, Bignardi L, Franchi S, Posel Z, Baraldi A, Pengo P, Lucarini M, Pasquato L, Posocco P. Spotting Local Environments in Self-Assembled Monolayer-Protected Gold Nanoparticles. ACS NANO 2022; 16:20902-20914. [PMID: 36459668 PMCID: PMC9798909 DOI: 10.1021/acsnano.2c08467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Organic-inorganic (O-I) nanomaterials are versatile platforms for an incredible high number of applications, ranging from heterogeneous catalysis to molecular sensing, cell targeting, imaging, and cancer diagnosis and therapy, just to name a few. Much of their potential stems from the unique control of organic environments around inorganic sites within a single O-I nanomaterial, which allows for new properties that were inaccessible using purely organic or inorganic materials. Structural and mechanistic characterization plays a key role in understanding and rationally designing such hybrid nanoconstructs. Here, we introduce a general methodology to identify and classify local (supra)molecular environments in an archetypal class of O-I nanomaterials, i.e., self-assembled monolayer-protected gold nanoparticles (SAM-AuNPs). By using an atomistic machine-learning guided workflow based on the Smooth Overlap of Atomic Positions (SOAP) descriptor, we analyze a collection of chemically different SAM-AuNPs and detect and compare local environments in a way that is agnostic and automated, i.e., with no need of a priori information and minimal user intervention. In addition, the computational results coupled with experimental electron spin resonance measurements prove that is possible to have more than one local environment inside SAMs, being the thickness of the organic shell and solvation primary factors in the determining number and nature of multiple coexisting environments. These indications are extended to complex mixed hydrophilic-hydrophobic SAMs. This work demonstrates that it is possible to spot and compare local molecular environments in SAM-AuNPs exploiting atomistic machine-learning approaches, establishes ground rules to control them, and holds the potential for the rational design of O-I nanomaterials instructed from data.
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Affiliation(s)
- Cristian Gabellini
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
| | - Maria Şologan
- Department
of Chemical and Pharmaceutical Sciences and INSTM Trieste Research
Unit, University of Trieste, 34127 Trieste, Italy
| | - Elena Pellizzoni
- Department
of Chemical and Pharmaceutical Sciences and INSTM Trieste Research
Unit, University of Trieste, 34127 Trieste, Italy
| | - Domenico Marson
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
| | - Mario Daka
- Department
of Chemical and Pharmaceutical Sciences and INSTM Trieste Research
Unit, University of Trieste, 34127 Trieste, Italy
| | - Paola Franchi
- Department
of Chemistry “G. Ciamician”, University of Bologna, I-40126 Bologna, Italy
| | - Luca Bignardi
- Department
of Physics, University of Trieste, 34127 Trieste, Italy
| | - Stefano Franchi
- Elettra
Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - Zbyšek Posel
- Department
of Informatics, Jan Evangelista Purkyně
University, 400 96 Ústí nad Labem, Czech Republic
| | | | - Paolo Pengo
- Department
of Chemical and Pharmaceutical Sciences and INSTM Trieste Research
Unit, University of Trieste, 34127 Trieste, Italy
| | - Marco Lucarini
- Department
of Chemistry “G. Ciamician”, University of Bologna, I-40126 Bologna, Italy
| | - Lucia Pasquato
- Department
of Chemical and Pharmaceutical Sciences and INSTM Trieste Research
Unit, University of Trieste, 34127 Trieste, Italy
| | - Paola Posocco
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
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5
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Sun X, Guo F, Ye Q, Zhou J, Han J, Guo R. Fluorescent Sensing of Glutathione and Related Bio-Applications. BIOSENSORS 2022; 13:16. [PMID: 36671851 PMCID: PMC9855688 DOI: 10.3390/bios13010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Glutathione (GSH), as the most abundant low-molecular-weight biological thiol, plays significant roles in vivo. Abnormal GSH levels have been demonstrated to be related to the dysfunction of specific physiological activities and certain kinds of diseases. Therefore, the sensing of GSH is emerging as a critical issue. Cancer, with typical high morbidity and mortality, remains one of the most serious diseases to threaten public health. As it is clear that much more concentrated GSH is present at tumor sites than at normal sites, the in vivo sensing of GSH offers an option for the early diagnosis of cancer. Moreover, by monitoring the amounts of GSH in specific microenvironments, effective diagnosis of ROS levels, neurological diseases, or even stroke has been developed as well. In this review, we focus on the fluorescent methodologies for GSH detection, since they can be conveniently applied in living systems. First, the fluorescent sensing methods are introduced. Then, the principles for fluorescent sensing of GSH are discussed. In addition, the GSH-sensing-related biological applications are reviewed. Finally, the future opportunities in in the areas of fluorescent GSH sensing-in particular, fluorescent GSH-sensing-prompted disease diagnosis-are addressed.
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6
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Self-organized nanoreceptors-based fluorescent probe for quantitative detection of denatured glutathione. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Medves M, Toffoli D, Stener M, Sementa L, Fortunelli A. Coupling between Plasmonic and Molecular Excitations: TDDFT Investigation of an Ag-Nanorod/BODIPY-Dye Interaction. J Phys Chem A 2022; 126:5890-5899. [PMID: 36001802 DOI: 10.1021/acs.jpca.2c04168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A time-dependent density functional theory (TDDFT) computational approach is employed to study the optical coupling between a plasmonic system (a Ag50 nanorod) and a fluorescent dye (BODIPY). It is found that the BODIPY dye can interact with a plasmonic system in a rather different and selective way according to the mutual orientation of the fragments. Indeed, (i) the plasmon excitation turns out to be sensitive to the presence of the BODIPY transition and (ii) this can lead to amplify or suppress the resonance accordingly to the relative orientation of the corresponding transition dipoles. To understand the coupling mechanism, we analyze the shape of the induced density in real space and the Individual Component Map of the Oscillator Strength (ICM-OS) plots and achieve a simple rationalization and insight on the origin and features of the coupling. The resulting possibility of understanding plasmon/fluorophore interactions by simple qualitative arguments opens the way to a rational design of hybrid (plasmon + dye) systems with the desired optical behavior.
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Affiliation(s)
- Marco Medves
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Daniele Toffoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Luca Sementa
- CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, via G. Moruzzi 1, Pisa, 56124, Italy
| | - Alessandro Fortunelli
- CNR-ICCOM & IPCF, Consiglio Nazionale delle Ricerche, via G. Moruzzi 1, Pisa, 56124, Italy
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8
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Xu J, Gao T, Sheng L, Wang Y, Lou C, Wang H, Liu Y, Cao A. Conformationally engineering flexible peptides on silver nanoparticles. iScience 2022; 25:104324. [PMID: 35601913 PMCID: PMC9117549 DOI: 10.1016/j.isci.2022.104324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular conformational engineering is to engineer flexible non-functional molecules into unique conformations to create novel functions just like natural proteins fold. Obviously, it is a grand challenge with tremendous opportunities. Based on the facts that natural proteins are only marginally stable with a net stabilizing energy roughly equivalent to the energy of two hydrogen bonds, and the energy barriers for the adatom diffusion of some metals are within a similar range, we propose that metal nanoparticles can serve as a general replacement of protein scaffolds to conformationally engineer protein fragments on the surface of nanoparticles. To prove this hypothesis, herein, we successfully restore the antigen-recognizing function of the flexible peptide fragment of a natural anti-lysozyme antibody on the surface of silver nanoparticles, creating a silver nanoparticle-base artificial antibody (Silverbody). A plausible mechanism is proposed, and some general principles for conformational engineering are summarized to guide future studies in this area. A silver NP-based artificial antibody is created by conformational engineering Function emerges on NPs from non-functional peptide by mimicking the protein folding A general mechanism is proposed for the conformational engineering on metal NPs
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Affiliation(s)
- Jia Xu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Tiange Gao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Lingjie Sheng
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Yan Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Chenxi Lou
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
| | - Yuanfang Liu
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Aoneng Cao
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China
- Corresponding author
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9
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Peruffo N, Parolin G, Collini E, Corni S, Mancin F. Engineering the Aggregation of Dyes on Ligand-Shell Protected Gold Nanoparticles to Promote Plexcitons Formation. NANOMATERIALS 2022; 12:nano12071180. [PMID: 35407298 PMCID: PMC9000468 DOI: 10.3390/nano12071180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 12/10/2022]
Abstract
The ability to control the light–matter interaction in nanosystems is a major challenge in the field of innovative photonics applications. In this framework, plexcitons are promising hybrid light–matter states arising from the strong coupling between plasmonic and excitonic materials. However, strategies to precisely control the formation of plexcitons and to modulate the coupling between the plasmonic and molecular moieties are still poorly explored. In this work, the attention is focused on suspensions of hybrid nanosystems prepared by coupling cationic gold nanoparticles to tetraphenyl porphyrins in different aggregation states. The role of crucial parameters such as the dimension of nanoparticles, the pH of the solution, and the ratio between the nanoparticles and dye concentration was systematically investigated. A variety of structures and coupling regimes were obtained. The rationalization of the results allowed for the suggestion of important guidelines towards the control of plexcitonic systems.
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Affiliation(s)
- Nicola Peruffo
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (N.P.); (G.P.)
| | - Giovanni Parolin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (N.P.); (G.P.)
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (N.P.); (G.P.)
- Padua Quantum Technologies Research Center, Via Gradenigo 6, 35131 Padova, Italy
- Correspondence: (E.C.); (S.C.); (F.M.)
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (N.P.); (G.P.)
- Correspondence: (E.C.); (S.C.); (F.M.)
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (N.P.); (G.P.)
- Correspondence: (E.C.); (S.C.); (F.M.)
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10
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Jeong Y, Jin S, Palanikumar L, Choi H, Shin E, Go EM, Keum C, Bang S, Kim D, Lee S, Kim M, Kim H, Lee KH, Jana B, Park MH, Kwak SK, Kim C, Ryu JH. Stimuli-Responsive Adaptive Nanotoxin to Directly Penetrate the Cellular Membrane by Molecular Folding and Unfolding. J Am Chem Soc 2022; 144:5503-5516. [PMID: 35235326 DOI: 10.1021/jacs.2c00084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological nanomachines, including proteins and nucleic acids whose function is activated by conformational changes, are involved in every biological process, in which their dynamic and responsive behaviors are controlled by supramolecular recognition. The development of artificial nanomachines that mimic the biological functions for potential application as therapeutics is emerging; however, it is still limited to the lower hierarchical level of the molecular components. In this work, we report a synthetic machinery nanostructure in which actuatable molecular components are integrated into a hierarchical nanomaterial in response to external stimuli to regulate biological functions. Two nanometers core-sized gold nanoparticles are covered with ligand layers as actuatable components, whose folding/unfolding motional response to the cellular environment enables the direct penetration of the nanoparticles across the cellular membrane to disrupt intracellular organelles. Furthermore, the pH-responsive conformational movements of the molecular components can induce the apoptosis of cancer cells. This strategy based on the mechanical motion of molecular components on a hierarchical nanocluster would be useful to design biomimetic nanotoxins.
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Affiliation(s)
- Youngdo Jeong
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Soyeong Jin
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - L Palanikumar
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Huyeon Choi
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eunhye Shin
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Eun Min Go
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Changjoon Keum
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seunghwan Bang
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Division of Bio-Medical Science & Technology, Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Dongkap Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seungho Lee
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Minsoo Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Department of Chemistry, School of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hojun Kim
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kwan Hyi Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Batakrishna Jana
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Myoung-Hwan Park
- Department of Chemistry & Life Science, Sahmyook University, Seoul 01795, Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Chaekyu Kim
- Fusion Biotechnology, Inc., Ulsan 44919, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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11
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Brancolini G, Rotello VM, Corni S. Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing. Int J Mol Sci 2022; 23:ijms23042368. [PMID: 35216496 PMCID: PMC8874478 DOI: 10.3390/ijms23042368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022] Open
Abstract
Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP–GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold–sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry.
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Affiliation(s)
- Giorgia Brancolini
- Institute of Nanoscience, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy;
- Correspondence: ; Tel.: +39-059-2055333
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA;
| | - Stefano Corni
- Institute of Nanoscience, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy;
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
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12
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Pellizzoni E, Şologan M, Daka M, Pengo P, Marson D, Posel Z, Franchi S, Bignardi L, Franchi P, Lucarini M, Posocco P, Pasquato L. Thiolate end-group regulates ligand arrangement, hydration and affinity for small compounds in monolayer-protected gold nanoparticles. J Colloid Interface Sci 2021; 607:1373-1381. [PMID: 34583042 DOI: 10.1016/j.jcis.2021.09.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
The ability to control the properties of monolayer protected gold nanoparticles (MPNPs) discloses unrevealed features stemming from collective properties of the ligands forming the monolayer and presents opportunities to design new materials. To date, the influence of ligand end-group size and capacity to form hydrogen bonds on structure and hydration of small MPNPs (<5 nm) has been poorly studied. Here, we show that both features determine ligands order, solvent accessibility, capacity to host hydrophobic compounds and interfacial properties of MPNPs. The polarity perceived by a radical probe and its binding constant with the monolayer investigated by electron spin resonance is rationalized by molecular dynamics simulations, which suggest that larger space-filling groups - trimethylammonium, zwitterionic and short polyethylene glycol - favor a radial organization of the thiolates, whereas smaller groups - as sulfonate - promote the formation of bundles. Zwitterionic ligands create a surface network of hydrogen bonds, which affects nanoparticle hydrophobicity and maximize the partition equilibrium constant of the probe. This study discloses the role of the chemistry of the end-group on monolayer features with effects that span from molecular- to nano-scale and opens the door to a shift in the conception of new MPNPs exploiting the end-group as a novel design motif.
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Affiliation(s)
- Elena Pellizzoni
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Maria Şologan
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Mario Daka
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Domenico Marson
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy)
| | - Zbyšek Posel
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy); Department of Informatics, Jan Evangelista Purkyně University, 400 96 Ústínad Labem, (Czech Republic)
| | - Stefano Franchi
- Elettra Sincrotrone Trieste S.C.p.A., 34149 Trieste, (Italy)
| | - Luca Bignardi
- Department of Physics, University of Trieste, 34127 Trieste, (Italy)
| | - Paola Franchi
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, (Italy)
| | - Marco Lucarini
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, (Italy).
| | - Paola Posocco
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy).
| | - Lucia Pasquato
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy).
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13
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Lyu Y, Scrimin P. Mimicking Enzymes: The Quest for Powerful Catalysts from Simple Molecules to Nanozymes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01219] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yanchao Lyu
- University of Padova, Department of Chemical Sciences, via Marzolo, 1, 35131 Padova, Italy
| | - Paolo Scrimin
- University of Padova, Department of Chemical Sciences, via Marzolo, 1, 35131 Padova, Italy
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14
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Lyu Y, Morillas-Becerril L, Mancin F, Scrimin P. Hydrolytic cleavage of nerve agent simulants by gold nanozymes. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125644. [PMID: 33773245 DOI: 10.1016/j.jhazmat.2021.125644] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Although banned by the Chemical Weapons Convention, organophosphorus nerve agents are still available and have been used in regional wars, terroristic attacks or for other crtaiminal purposes. Their degradation is of primary importance for the severe toxicity of these compounds. Here we report that gold nanoparticles passivated with thiolated molecules bearing 1,3,7-triazacyclononane and 1,3,7,10-tetraazacyclododecane ligands efficiently hydrolyze nerve agents simulants p-nitrophenyl diphenyl phosphate and methylparaoxon as transition metal complexes at 25 °C and pH 8 with half-lives of the order of a few minutes. Mechanistically, these catalysts show an enzyme-like behavior, hence they constitute an example of nanozymes. The catalytic site appears to involve a single metal ion and its recognition of the substrates is driven mostly by hydrophobic interactions. The ease of preparation and the mild conditions at which they operate, make these nanozymes appealing catalysts for the detoxification after contamination with organophosphorus nerve agents, particularly those poorly soluble in water.
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Affiliation(s)
- Yanchao Lyu
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | | | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
| | - Paolo Scrimin
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
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15
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Pecina A, Rosa-Gastaldo D, Riccardi L, Franco-Ulloa S, Milan E, Scrimin P, Mancin F, De Vivo M. On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes. ACS Catal 2021; 11:8736-8748. [PMID: 34476110 PMCID: PMC8397296 DOI: 10.1021/acscatal.1c01215] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/03/2021] [Indexed: 12/20/2022]
Abstract
![]()
Recent studies have
shown that gold nanoparticles (AuNPs) functionalized
with Zn(II) complexes can cleave phosphate esters and nucleic acids.
Remarkably, such synthetic nanonucleases appear to catalyze metal
(Zn)-aided hydrolytic reactions of nucleic acids similar to metallonuclease
enzymes. To clarify the reaction mechanism of these nanocatalysts,
here we have comparatively analyzed two nanonucleases with a >10-fold
difference in the catalytic efficiency for the hydrolysis of the 2-hydroxypropyl-4-nitrophenylphosphate
(HPNP, a typical RNA model substrate). We have used microsecond-long
atomistic simulations, integrated with NMR experiments, to investigate
the structure and dynamics of the outer coating monolayer of these
nanoparticles, either alone or in complex with HPNP, in solution.
We show that the most efficient one is characterized by coating ligands
that promote a well-organized monolayer structure, with the formation
of solvated bimetallic catalytic sites. Importantly, we have found
that these nanoparticles can mimic two-metal-ion enzymes for nucleic
acid processing, with Zn ions that promote HPNP binding at the reaction
center. Thus, the two-metal-ion-aided hydrolytic strategy of such
nanonucleases helps in explaining their catalytic efficiency for substrate
hydrolysis, in accordance with the experimental evidence. These mechanistic
insights reinforce the parallelism between such functionalized AuNPs
and proteins toward the rational design of more efficient catalysts.
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Affiliation(s)
- Adam Pecina
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Daniele Rosa-Gastaldo
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sebastian Franco-Ulloa
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Emil Milan
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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16
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Franco-Ulloa S, Guarnieri D, Riccardi L, Pompa PP, De Vivo M. Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study. J Chem Theory Comput 2021; 17:4512-4523. [PMID: 34077229 PMCID: PMC8280734 DOI: 10.1021/acs.jctc.1c00127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Indexed: 11/28/2022]
Abstract
Functionalized metal nanoparticles (NPs) hold great promise as innovative tools in nanomedicine. However, one of the main challenges is how to optimize their association with the cell membrane, which is critical for their effective delivery. Recent findings show high cellular uptake rates for NPs coated with the polycationic cell-penetrating peptide gH625-644 (gH), although the underlying internalization mechanism is poorly understood. Here, we use extended coarse-grained simulations and free energy calculations to study systems that simultaneously include metal NPs, peptides, lipids, and sterols. In particular, we investigate the first encounter between multicomponent model membranes and 2.5 nm metal NPs coated with gH (gHNPs), based on the evidence from scanning transmission electron microscopy. By comparing multiple membrane and (membranotropic) NP models, we found that gHNP internalization occurs by forming an intermediate state characterized by specific stabilizing interactions formed by peptide-coated nanoparticles with multicomponent model membranes. This association mechanism is mainly characterized by interactions of gH with the extracellular solvent and the polar membrane surface. At the same time, the NP core interacts with the transmembrane (cholesterol-rich) fatty phase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Daniela Guarnieri
- Dipartimento
di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, Fisciano, l-84084 Salerno, Italy
| | - Laura Riccardi
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Pier Paolo Pompa
- Nanobiointeractions
& Nanodiagnostics, Istituto Italiano
di Tecnologia, Via Morego
30, 16163 Genova, Italy
| | - Marco De Vivo
- Molecular
Modeling and Drug Discovery Lab, Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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17
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Zhang Y, Dahal U, Feng ZV, Rosenzweig Z, Cui Q, Hamers RJ. Influence of Surface Ligand Molecular Structure on Phospholipid Membrane Disruption by Cationic Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7600-7610. [PMID: 34115507 DOI: 10.1021/acs.langmuir.1c01146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cationic nanoparticles are known to interact with biological membranes and often cause serious membrane damage. Therefore, it is important to understand the molecular mechanism for such interactions and the factors that impact the degree of membrane damage. Previously, we have demonstrated that spatial distribution of molecular charge at cationic nanoparticle surfaces plays an important role in determining the cellular uptake and membrane damage of these nanoparticles. In this work, using diamond nanoparticles (DNPs) functionalized with five different amine-based surface ligands and small phospholipid unilamellar vesicles (SUVs), we further investigate how chemical features and conformational flexibility of surface ligands impact nanoparticle/membrane interactions. 31P-NMR T2 relaxation measurements quantify the mobility changes in lipid dynamics upon exposing the SUVs to functional DNPs, and coarse-grained molecular dynamics simulations further elucidate molecular details for the different modes of DNP-SUV interactions depending on the surface ligands. Collectively, our results show that the length of the hydrophobic segment and conformational flexibility of surface ligands are two key factors that dictate the degree of membrane damage by the DNP, while the amount of surface charge alone is not predictive of the strength of interaction.
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Affiliation(s)
- Yongqian Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Udaya Dahal
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Z Vivian Feng
- Chemistry Department, Augsburg University, Minneapolis, Minnesota 55454, United States
| | - Zeev Rosenzweig
- Department of Chemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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18
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Morillas-Becerril L, Franco-Ulloa S, Fortunati I, Marotta R, Sun X, Zanoni G, De Vivo M, Mancin F. Specific and nondisruptive interaction of guanidium-functionalized gold nanoparticles with neutral phospholipid bilayers. Commun Chem 2021; 4:93. [PMID: 36697571 PMCID: PMC9814519 DOI: 10.1038/s42004-021-00526-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/05/2021] [Indexed: 01/28/2023] Open
Abstract
Understanding and controlling the interaction between nanoparticles and biological entities is fundamental to the development of nanomedicine applications. In particular, the possibility to realize nanoparticles capable of directly targeting neutral lipid membranes would be advantageous to numerous applications aiming at delivering nanoparticles and their cargos into cells and biological vesicles. Here, we use experimental and computational methodologies to analyze the interaction between liposomes and gold nanoparticles (AuNPs) featuring cationic headgroups in their protecting monolayer. We find that in contrast to nanoparticles decorated with other positively charged headgroups, guanidinium-coated AuNPs can bind to neutral phosphatidylcholine liposomes, inducing nondisruptive membrane permeabilization. Atomistic molecular simulations reveal that this ability is due to the multivalent H-bonding interaction between the phosphate residues of the liposome's phospholipids and the guanidinium groups. Our results demonstrate that the peculiar properties of arginine magic, an effect responsible for the membranotropic properties of some naturally occurring peptides, are also displayed by guanidinium-bearing functionalized AuNPs.
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Affiliation(s)
- Lucía Morillas-Becerril
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Sebastian Franco-Ulloa
- grid.25786.3e0000 0004 1764 2907Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy ,Present Address: Expert Analytics. Møllergata 8, Oslo, Norway
| | - Ilaria Fortunati
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Roberto Marotta
- grid.25786.3e0000 0004 1764 2907Electron Microscopy Facility (EMF), Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy
| | - Xiaohuan Sun
- grid.268415.cSchool of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu People’s Republic of China
| | - Giordano Zanoni
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
| | - Marco De Vivo
- grid.25786.3e0000 0004 1764 2907Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa, Italy
| | - Fabrizio Mancin
- grid.5608.b0000 0004 1757 3470Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, Italy
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19
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Riccardi L, Decherchi S, Rocchia W, Zanoni G, Cavalli A, Mancin F, De Vivo M. Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint. J Phys Chem Lett 2021; 12:5616-5622. [PMID: 34110174 PMCID: PMC8280747 DOI: 10.1021/acs.jpclett.1c01365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Ligand shell-protected gold nanoparticles can form nanoreceptors that recognize and bind to specific molecules in solution, with numerous potential innovative applications in science and industry. At this stage, the challenge is to rationally design such nanoreceptors to optimize their performance and boost their further development. Toward this aim, we have developed a new computational tool, Nanotron. This allows the analysis of molecular dynamics simulations of ligand shell-protected nanoparticles to define their exact surface morphology and pocket fingerprints of binding cavities in the coating monolayer. Importantly, from dissecting the well-characterized pairing formed by the guest salicylate molecule and specific host nanoreceptors, our work reveals that guest binding at such nanoreceptors occurs via preformed deep pockets in the host. Upon the interaction with the guest, such pockets undergo an induced-fit-like structural optimization for best host-guest fitting. Our findings and methodological advancement will accelerate the rational design of new-generation nanoreceptors.
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Affiliation(s)
- Laura Riccardi
- Laboratory
of Molecular Modeling & Drug Discovery, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sergio Decherchi
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- BiKi
Technologies s.r.l., Via XX Settembre 33/10, 1621 Genova, Italy
| | - Walter Rocchia
- BiKi
Technologies s.r.l., Via XX Settembre 33/10, 1621 Genova, Italy
- CONCEPT
Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Giordano Zanoni
- Dipartimento
di Scienze Chimiche, Università di
Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Andrea Cavalli
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- BiKi
Technologies s.r.l., Via XX Settembre 33/10, 1621 Genova, Italy
| | - Fabrizio Mancin
- Dipartimento
di Scienze Chimiche, Università di
Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco De Vivo
- Laboratory
of Molecular Modeling & Drug Discovery, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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20
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Czescik J, Mancin F, Strömberg R, Scrimin P. The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme. Chemistry 2021; 27:8143-8148. [PMID: 33780067 PMCID: PMC8251847 DOI: 10.1002/chem.202100299] [Citation(s) in RCA: 7] [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: 01/25/2021] [Indexed: 01/08/2023]
Abstract
The cleavage of uridine 3'-phosphodiesters bearing alcohols with pKa ranging from 7.14 to 14.5 catalyzed by AuNPs functionalized with 1,4,7-triazacyclononane-Zn(II) complexes has been studied to unravel the source of catalysis by these nanosystems (nanozymes). The results have been compared with those obtained with two Zn(II) dinuclear catalysts for which the mechanism is fairly understood. Binding to the Zn(II) ions by the substrate and the uracil of uridine was observed. The latter leads to inhibition of the process and formation of less productive binding complexes than in the absence of the nucleobase. The nanozyme operates with these substrates mostly via a nucleophilic mechanism with little stabilization of the pentacoordinated phosphorane and moderate assistance in leaving group departure. This is attributed to a decrease of binding strength of the substrate to the catalytic site in reaching the transition state due to an unfavorable binding mode with the uracil. The nanozyme favors substrates with better leaving groups than the less acidic ones.
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
| | | | - Paolo Scrimin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
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21
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Mati IK, Edwards W, Marson D, Howe EJ, Stinson S, Posocco P, Kay ER. Probing Multiscale Factors Affecting the Reactivity of Nanoparticle-Bound Molecules. ACS NANO 2021; 15:8295-8305. [PMID: 33938222 DOI: 10.1021/acsnano.0c09190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The structures and physicochemical properties of surface-stabilizing molecules play a critical role in defining the properties, interactions, and functionality of hybrid nanomaterials such as monolayer-stabilized nanoparticles. Concurrently, the distinct surface-bound interfacial environment imposes very specific conditions on molecular reactivity and behavior in this setting. Our ability to probe hybrid nanoscale systems experimentally remains limited, yet understanding the consequences of surface confinement on molecular reactivity is crucial for enabling predictive nanoparticle synthon approaches for postsynthesis engineering of nanoparticle surface chemistry and construction of devices and materials from nanoparticle components. Here, we have undertaken an integrated experimental and computational study of the reaction kinetics for nanoparticle-bound hydrazones, which provide a prototypical platform for understanding chemical reactivity in a nanoconfined setting. Systematic variation of just one molecular-scale structural parameter-the distance between reactive site and nanoparticle surface-showed that the surface-bound reactivity is influenced by multiscale effects. Nanoparticle-bound reactions were tracked in situ using 19F NMR spectroscopy, allowing direct comparison to the reactions of analogous substrates in bulk solution. The surface-confined reactions proceed more slowly than their solution-phase counterparts, and kinetic inhibition becomes more significant for reactive sites positioned closer to the nanoparticle surface. Molecular dynamics simulations allowed us to identify distinct supramolecular architectures and unexpected dynamic features of the surface-bound molecules that underpin the experimentally observed trends in reactivity. This study allows us to draw general conclusions regarding interlinked structural and dynamical features across several length scales that influence interfacial reactivity in monolayer-confined environments.
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Affiliation(s)
- Ioulia K Mati
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K
| | - William Edwards
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K
| | - Domenico Marson
- Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Edward J Howe
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K
| | - Scott Stinson
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K
| | - Paola Posocco
- Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Euan R Kay
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K
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22
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Dutta S, Corni S, Brancolini G. Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex. Int J Mol Sci 2021; 22:3624. [PMID: 33807225 PMCID: PMC8037132 DOI: 10.3390/ijms22073624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide-nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure-function relationship, for technological and nanomedical applications.
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Affiliation(s)
- Sutapa Dutta
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy;
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
| | - Giorgia Brancolini
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
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23
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De Biasi F, Rosa-Gastaldo D, Mancin F, Rastrelli F. Hybrid nanoreceptors for high sensitivity detection of small molecules by NMR chemosensing. Chem Commun (Camb) 2021; 57:3002-3005. [PMID: 33623940 DOI: 10.1039/d0cc07559k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
"Nanoparticle-assisted NMR chemosensing" combines magnetization transfer NMR techniques with the recognition abilities of gold nanoparticles (AuNPs) to isolate the NMR spectrum of relevant organic species in mixtures. The efficiency of the magnetization transfer is crucial to set the detection limit of the technique. To this aim, a second generation of nanoreceptors obtained by the self-organization of 2 nm AuNPs onto the surface of bigger silica nanoparticles shows better magnetization transfer performances, allowing the detection of analytes in water down to 10 μM concentration using standard instrumentation.
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Affiliation(s)
- Federico De Biasi
- Department of Chemical Sciences, Università degli Studi di Padova Via Marzolo 1, 35131 Padova, Italy.
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24
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Chew AK, Dallin BC, Van Lehn RC. The Interplay of Ligand Properties and Core Size Dictates the Hydrophobicity of Monolayer-Protected Gold Nanoparticles. ACS NANO 2021; 15:4534-4545. [PMID: 33621066 DOI: 10.1021/acsnano.0c08623] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The hydrophobicity of monolayer-protected gold nanoparticles is a crucial design parameter that influences self-assembly, preferential binding to proteins and membranes, and other nano-bio interactions. Predicting the effects of monolayer components on nanoparticle hydrophobicity is challenging due to the nonadditive, cooperative perturbations to interfacial water structure that dictate hydrophobicity at the nanoscale. In this work, we quantify nanoparticle hydrophobicity by using atomistic molecular dynamics simulations to calculate local hydration free energies at the nanoparticle-water interface. The simulations reveal that the hydrophobicity of large gold nanoparticles is determined primarily by ligand end group chemistry, as expected. However, for small gold nanoparticles, long alkanethiol ligands interact to form anisotropic bundles that lead to substantial spatial variations in hydrophobicity even for homogeneous monolayer compositions. We further show that nanoparticle hydrophobicity is modulated by changing the ligand structure, ligand chemistry, and gold core size, emphasizing that single-ligand properties alone are insufficient to characterize hydrophobicity. Finally, we illustrate that hydration free energy measurements correlate with the preferential binding of propane as a representative hydrophobic probe molecule. Together, these results show that both physical and chemical properties influence the hydrophobicity of small nanoparticles and must be considered together when predicting gold nanoparticle interactions with biomolecules.
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Affiliation(s)
- Alex K Chew
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Bradley C Dallin
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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25
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Xu Z, Fang N, Zhao Y. Calix[4]trap: A Bioinspired Host Equipped with Dual Selection Mechanisms. J Am Chem Soc 2021; 143:3162-3168. [PMID: 33606533 DOI: 10.1021/jacs.0c12223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Regulation of recognition events evolving in time and space is vital for living organisms. During evolution, organisms have developed distinct and orthogonal mechanisms to achieve selective recognition, avoiding mutual interference. Although the merging of multiple selection mechanisms into a single artificial host may lead to a more adaptable recognition system with unparalleled selectivity, successful implementation of this strategy is rare. Inspired by the intriguing structures and recognition properties of two well-known biological ion binders-valinomycin and K+ channels-we herein report a series of hosts equipped with dual guest selection mechanisms. These hosts simultaneously possess a preorganized binding cavity and a confined ion translocation tunnel, which are crucial to the record-setting K+/Na+ selectivity and versatile capabilities to discriminate against a wide range of ion pairs, such as K+/Rb+, K+/Ba2+, and Rb+/Cs+. Mechanistic studies verify that the host's portal is capable of discriminating cations by their size, enabling varied ion uptake rates. The confined tunnel bearing consecutive binding sites promotes complete desolvation of ions during their inclusion into the buried cavity, mimicking the ion translocation within ion channels. Our results demonstrate that the capability to manipulate guest recognition both in equilibrium and out-of-equilibrium states allows the host to effectively discriminate diverse guests via distinct mechanisms. The strategy to merge orthogonal selection mechanisms paves a new avenue to creating more robust hosts that may function in complex biological environments where many recognition events occur concurrently.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Nie Fang
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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26
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Czescik J, Zamolo S, Darbre T, Rigo. R, Sissi C, Pecina A, Riccardi L, De Vivo M, Mancin F, Scrimin P. A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angew Chem Int Ed Engl 2021; 60:1423-1432. [PMID: 32985766 PMCID: PMC7839518 DOI: 10.1002/anie.202012513] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Indexed: 12/18/2022]
Abstract
Similarly to enzymes, functionalized gold nanoparticles efficiently catalyze chemical reactions, hence the term nanozymes. Herein, we present our results showing how surface-passivated gold nanoparticles behave as synthetic nanonucleases, able to cleave pBR322 plasmid DNA with the highest efficiency reported so far for catalysts based on a single metal ion mechanism. Experimental and computational data indicate that we have been successful in creating a catalytic site precisely mimicking that suggested for natural metallonucleases relying on a single metal ion for their activity. It comprises one Zn(II) ion to which a phosphate diester of DNA is coordinated. Importantly, as in nucleic acids-processing enzymes, a positively charged arginine plays a key role by assisting with transition state stabilization and by reducing the pKa of the nucleophilic alcohol of a serine. Our results also show how designing a catalyst for a model substrate (bis-p-nitrophenylphosphate) may provide wrong indications as for its efficiency when it is tested against the real target (plasmid DNA).
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Susanna Zamolo
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3CH-3012BernSwitzerland
| | - Tamis Darbre
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3CH-3012BernSwitzerland
| | - Riccardo Rigo.
- Department of Pharmaceutical and Pharmacological SciencesUniversity of Padovavia Marzolo 535131PadovaItaly
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological SciencesUniversity of Padovavia Marzolo 535131PadovaItaly
| | - Adam Pecina
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT)Via Morego 3016163GenovaItaly
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
| | - Paolo Scrimin
- Department of Chemical SciencesUniversity of Padovavia Marzolo, 135131PadovaItaly
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27
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Czescik J, Zamolo S, Darbre T, Rigo. R, Sissi C, Pecina A, Riccardi L, De Vivo M, Mancin F, Scrimin P. A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joanna Czescik
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
- Current address: School of Life and Health Sciences Aston University B4 7ET Birmingham UK
| | - Susanna Zamolo
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 CH-3012 Bern Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry University of Bern Freiestrasse 3 CH-3012 Bern Switzerland
| | - Riccardo Rigo.
- Department of Pharmaceutical and Pharmacological Sciences University of Padova via Marzolo 5 35131 Padova Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences University of Padova via Marzolo 5 35131 Padova Italy
| | - Adam Pecina
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery Istituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences University of Padova via Marzolo, 1 35131 Padova Italy
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28
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Franco-Ulloa S, Tatulli G, Bore SL, Moglianetti M, Pompa PP, Cascella M, De Vivo M. Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions. Nat Commun 2020; 11:5422. [PMID: 33110063 PMCID: PMC7591489 DOI: 10.1038/s41467-020-19164-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/30/2020] [Indexed: 01/05/2023] Open
Abstract
The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we developed a theoretical model to estimate the stoichiometry of small, charged ligands (like citrate) chemisorbed onto spherical metallic nanoparticles and coupled it with atomistic molecular dynamics simulations to define the uncovered solvent-accessible surface area of the nanoparticle. Then, we integrated coarse-grained molecular dynamics simulations and two-body free energy calculations to define dispersion state phase diagrams for charged metal nanoparticles in a range of medium’s ionic strength, a known trigger for aggregation. Ultraviolet-visible spectroscopy experiments of citrate-capped nanocolloids validated our predictions and extended our results to nanoparticles up to 35 nm. Altogether, our results disclose a complex interplay between the particle size, its surface charge density, and the ionic strength of the medium, which ultimately clarifies how these variables impact colloidal stability. Citrate-stabilized metallic colloids are key materials towards chemosensing and catalysis applications. Here the authors introduce a new theoretical model to estimate how the stoichiometry of citrate molecules absorbed onto spherical metallic nanoparticles influences their aggregation phenomena.
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Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Giuseppina Tatulli
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033 Blindern, 0315, Oslo, Norway
| | - Mauro Moglianetti
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Pier Paolo Pompa
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, P.O. Box 1033 Blindern, 0315, Oslo, Norway.
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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29
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Franco-Ulloa S, Tatulli G, Bore SL, Moglianetti M, Pompa PP, Cascella M, De Vivo M. Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions. Nat Commun 2020. [DOI: 10.2149/tmh1973.23.227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AbstractThe fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we developed a theoretical model to estimate the stoichiometry of small, charged ligands (like citrate) chemisorbed onto spherical metallic nanoparticles and coupled it with atomistic molecular dynamics simulations to define the uncovered solvent-accessible surface area of the nanoparticle. Then, we integrated coarse-grained molecular dynamics simulations and two-body free energy calculations to define dispersion state phase diagrams for charged metal nanoparticles in a range of medium’s ionic strength, a known trigger for aggregation. Ultraviolet-visible spectroscopy experiments of citrate-capped nanocolloids validated our predictions and extended our results to nanoparticles up to 35 nm. Altogether, our results disclose a complex interplay between the particle size, its surface charge density, and the ionic strength of the medium, which ultimately clarifies how these variables impact colloidal stability.
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30
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Ferreira RS, Lira AL, Sousa AA. Quantitative mechanistic model for ultrasmall nanoparticle-protein interactions. NANOSCALE 2020; 12:19230-19240. [PMID: 32929438 DOI: 10.1039/d0nr04846a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To date, extensive effort has been devoted toward the characterization of protein interactions with synthetic nanostructures. However, much remains to be understood, particularly concerning microscopic mechanisms of interactions. Here, we have conducted a detailed investigation of the kinetics of nanoparticle-protein complexation to gain deeper insights into the elementary steps and molecular events along the pathway for complex formation. Toward that end, the binding kinetics between p-mercaptobenzoic acid-coated ultrasmall gold nanoparticles (AuMBA) and fluorescently-labeled ubiquitin was investigated at millisecond time resolution using stopped-flow spectroscopy. It was found that both the association and dissociation kinetics consisted of multiple exponential phases, hence suggesting a complex, multi-step reaction mechanism. The results fit into a picture where complexation proceeds through the formation of a weakly-bound first-encounter complex with an apparent binding affinity (KD) of ∼9 μM. Encounter complex formation is followed by unimolecular tightening steps of partial desolvation/ion removal and conformational rearrangement, which, collectively, achieve an almost 100-fold increase in affinity of the final bound state (apparent KD ∼0.1 μM). The final state is found to be weakly stabilized, displaying an average lifetime in the range of seconds. Screening of the electrostatic forces at high ionic strength weakens the AuMBA-ubiquitin interactions by destabilizing the encounter complex, whereas the average lifetime of the final bound state remains largely unchanged. Overall, our rapid kinetics investigation has revealed novel quantitative insights into the molecular-level mechanisms of ultrasmall nanoparticle-protein interactions.
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Affiliation(s)
- Rodrigo S Ferreira
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
| | - André L Lira
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
| | - Alioscka A Sousa
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP 04044-020, Brazil.
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31
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Maysinger D, Zhang Q, Kakkar A. Dendrimers as Modulators of Brain Cells. Molecules 2020; 25:E4489. [PMID: 33007959 PMCID: PMC7582352 DOI: 10.3390/molecules25194489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022] Open
Abstract
Nanostructured hyperbranched macromolecules have been extensively studied at the chemical, physical and morphological levels. The cellular structural and functional complexity of neural cells and their cross-talk have made it rather difficult to evaluate dendrimer effects in a mixed population of glial cells and neurons. Thus, we are at a relatively early stage of bench-to-bedside translation, and this is due mainly to the lack of data valuable for clinical investigations. It is only recently that techniques have become available that allow for analyses of biological processes inside the living cells, at the nanoscale, in real time. This review summarizes the essential properties of neural cells and dendrimers, and provides a cross-section of biological, pre-clinical and early clinical studies, where dendrimers were used as nanocarriers. It also highlights some examples of biological studies employing dendritic polyglycerol sulfates and their effects on glia and neurons. It is the aim of this review to encourage young scientists to advance mechanistic and technological approaches in dendrimer research so that these extremely versatile and attractive nanostructures gain even greater recognition in translational medicine.
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Affiliation(s)
- Dusica Maysinger
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada;
| | - Qiaochu Zhang
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada;
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, QC H3A 0B8, Canada
| | - Ashok Kakkar
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, QC H3A 0B8, Canada
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32
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Affiliation(s)
- Luca Gabrielli
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Federico Rastrelli
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
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33
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Mikolajczak DJ, Berger AA, Koksch B. Catalytically Active Peptide-Gold Nanoparticle Conjugates: Prospecting for Artificial Enzymes. Angew Chem Int Ed Engl 2020; 59:8776-8785. [PMID: 31905254 PMCID: PMC7318681 DOI: 10.1002/anie.201908625] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of peptides onto the surface of gold nanoparticles has emerged as a promising strategy towards the creation of artificial enzymes. The resulting high local peptide density surrounding the nanoparticle leads to cooperative and synergistic effects, which result in rate accelerations and distinct catalytic properties compared to the unconjugated peptide. This Minireview summarizes contributions to and progress made in the field of catalytically active peptide-gold nanoparticle conjugates. The origin of distinct properties, as well as potential applications, are also discussed.
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Affiliation(s)
- Dorian J. Mikolajczak
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
| | - Allison A. Berger
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
| | - Beate Koksch
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
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34
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Marson D, Posel Z, Posocco P. Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer-Protected Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5671-5679. [PMID: 32348150 PMCID: PMC8007095 DOI: 10.1021/acs.langmuir.9b03686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/21/2020] [Indexed: 06/11/2023]
Abstract
The sensing of small molecules poses the challenge of developing devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e., covering ligands), along with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target has relied on trial-and-error approaches, with ligand chemistry being the main criterion used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM-covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems.
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Affiliation(s)
- Domenico Marson
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
| | - Zbyšek Posel
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
- Department
of Informatics, Jan Evangelista Purkyně
University, 40096 Ústí nad Labem, Czech Republic
| | - Paola Posocco
- Department
of Engineering and Architecture, University
of Trieste, 34127 Trieste, Italy
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35
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De Biasi F, Mancin F, Rastrelli F. Nanoparticle-assisted NMR spectroscopy: A chemosensing perspective. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:70-88. [PMID: 32471535 DOI: 10.1016/j.pnmrs.2019.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 06/11/2023]
Abstract
Sensing methodologies for the detection of target compounds in mixtures are important in many different contexts, ranging from medical diagnosis to environmental analysis and quality assessment. Ideally, such detection methods should allow for both identification and quantification of the targets, minimizing the possibility of false positives. With very few exceptions, most of the available sensing techniques rely on the selective interaction of the analyte with some detector, which in turn produces a signal as a result of the interaction. This approach hence provides indirect information on the targets, whose identity is generally ensured by comparison with known standards, if available, or by the selectivity of the sensor system itself. Pursuing a different approach, NMR chemosensing aims at generating signals directly from the analytes, in the form of a (complete) NMR spectrum. In this way, not only are the targets unequivocally identified, but it also becomes possible to identify and assign the structures of unknown species. In this review we show how relaxation- and diffusion-based NMR techniques, assisted by appropriate nanoparticles, can be used to edit the 1H NMR spectrum of a mixture and extract the signals of specific target compounds. Monolayer-protected nanoparticles, in particular those made from gold, are well suited to this task because they provide a versatile, protein-size support to build or incorporate supramolecular receptors. Remarkably, the self-organized and multifunctional nature of the nanoparticle coating allows exploitation of different kinds of non-covalent interactions, to provide tailored binding sites for virtually any class of molecules. From the NMR standpoint, the reduced translational and rotational diffusion rates of bulky nanoparticles offer a way to manipulate the states of the monolayer spins and build a reservoir of magnetization that can be selectively transferred to the interacting analytes. In addition, the low correlation time and the enhanced rigidity of the coating molecules (due to their grafting and crowding on the particle surface) promote efficient spin diffusion, useful in saturation transfer experiments. The optimized combination of NMR experiments and nanoreceptors can ultimately allow the detection of relevant analytes in the micromolar concentration range, paving the way to applications in the diagnostic field and beyond.
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Affiliation(s)
- Federico De Biasi
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Federico Rastrelli
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy.
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36
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Mikolajczak DJ, Berger AA, Koksch B. Catalytically Active Peptide–Gold Nanoparticle Conjugates: Prospecting for Artificial Enzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201908625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dorian J. Mikolajczak
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
| | - Allison A. Berger
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
| | - Beate Koksch
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
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37
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Sun X, Rosa-Gastaldo D, De Biasi F, Rastrelli F, Mancin F. 1 H NMR Chemosensing of Potassium Ions Enabled by Guest-Induced Selectivity Switch of a Gold Nanoparticle/Crown Ether Nanoreceptor. Chempluschem 2020; 84:1498-1502. [PMID: 31943937 DOI: 10.1002/cplu.201900028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/19/2019] [Indexed: 12/30/2022]
Abstract
A sensing protocol to detect potassium ions in water by 1 H NMR spectroscopy is described. The method exploits the K+ -modulated affinity of 18-crown-6 functionalized gold nanoparticles towards organic ions, combined with NOE magnetization transfer. Binding of K+ to the crown ether moieties switches the nanoreceptor preference (and its ability to transfer magnetization) from organic cations (tyramine) to organic anions (phloretate). In this way, a ratiometric NMR signal is produced with a detection limit of 0.6 mM. Detection can be performed in 20 min with standard instruments and with little interference from other alkali and alkaline earth metal ions present in the sample.
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Affiliation(s)
- Xiaohuan Sun
- Dipartimento di Scienze chimiche, Università di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Daniele Rosa-Gastaldo
- Dipartimento di Scienze chimiche, Università di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Federico De Biasi
- Dipartimento di Scienze chimiche, Università di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Federico Rastrelli
- Dipartimento di Scienze chimiche, Università di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze chimiche, Università di Padova, Via Marzolo 1, 35131, Padova, Italy
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Das M, Dahal U, Mesele O, Liang D, Cui Q. Molecular Dynamics Simulation of Interaction between Functionalized Nanoparticles with Lipid Membranes: Analysis of Coarse-Grained Models. J Phys Chem B 2019; 123:10547-10561. [DOI: 10.1021/acs.jpcb.9b08259] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Mitradip Das
- School of Chemical Sciences, National Institute of Science Education and Research, Khordha, Odisha, India, 752050
- Homi Bhabha National Institute, Training School
Complex, Anushaktinagar, Mumbai, Maharashtra, India, 400094
| | - Udaya Dahal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Oluwaseun Mesele
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dongyue Liang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Abstract
We herein describe the design and synthesis of a catalytically active peptide–gold nanoparticle conjugate (Pep-Au-NP) that binds Zn(II) within its peptide monolayer and develops carbonic anhydrase activity. Specifically, a modified variant of the β-sheet forming IHIHIQI-peptide (IHQ), which forms an interstrand 3-His Zn(II)-binding site, was used as a ligand for spherical gold nanoparticles (Au-NPs). The resulting immobilized peptide maintains its ability to form β-sheets, as determined by circular dichroism (CD)-spectroscopy and, thus, maintains its ability to form Zn(II)-binding sites. The addition of Zn(II)-ions to the peptide–gold nanoparticle conjugates (Au@IHQ-NP) resulted in significant improvements in rates of ester hydrolysis of 4-nitrophenyl acetate (4-NPA) and the hydration of CO2 compared to the unconjugated peptide variants. Recycling of the catalyst revealed that Au@IHQ-NP remains intact with at least 94% of its initial activity after five rounds of CO2 hydration. The herein reported results reveal that Pep-Au-NPs are able to perform reactions catalyzed by natural metalloenzymes and open up new possibilities for the implementation of these conjugates.
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40
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Recent developments in functionalized polymer nanoparticles for efficient drug delivery system. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.nanoso.2019.100397] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Maysinger D, Ji J. Nanostructured Modulators of Neuroglia. Curr Pharm Des 2019; 25:3905-3916. [PMID: 31512994 DOI: 10.2174/1381612825666190912163339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/08/2019] [Indexed: 01/08/2023]
Abstract
Biological and synthetic nanostructures can influence both glia and neurons in the central nervous system. Neurons represent only a small proportion (about 10%) of cells in the brain, whereas glial cells are the most abundant cell type. Non-targeted nanomedicines are mainly internalized by glia, in particular microglia, and to a lesser extent by astrocytes. Internalized nanomedicines by glia indirectly modify the functional status of neurons. The mechanisms of biochemical, morphological and functional changes of neural cells exposed to nanomedicines are still not well-understood. This minireview provides a cross-section of morphological and biochemical changes in glial cells and neurons exposed to different classes of hard and soft nanostructures.
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Affiliation(s)
- Dusica Maysinger
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3AOG4, Canada
| | - Jeff Ji
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3AOG4, Canada
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42
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Factors Influencing the Activity of Nanozymes in the Cleavage of an RNA Model Substrate. Molecules 2019; 24:molecules24152814. [PMID: 31374998 PMCID: PMC6696475 DOI: 10.3390/molecules24152814] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 11/16/2022] Open
Abstract
A series of 2-nm gold nanoparticles passivated with different thiols all featuring at least one triazacyclonanone-Zn(II) complex and different flanking units (a second Zn(II) complex, a triethyleneoxymethyl derivative or a guanidinium of arginine of a peptide) were prepared and studied for their efficiency in the cleavage of the RNA-model substrate 2-hydroxypropyl-p-nitrophenyl phosphate. The source of catalysis for each of them was elucidated from the kinetic analysis (Michaelis–Menten profiles, pH dependence and kinetic isotope effect). The data indicated that two different mechanisms were operative: One involving two Zn(II) complexes and the other one involving a single Zn(II) complex and a flanking guanidinium cation. The mechanism based on a dinuclear catalytic site appeared more efficient than the one based on the cooperativity between a metal complex and a guanidinium.
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43
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Riccardi L, De Biasi F, De Vivo M, Bürgi T, Rastrelli F, Salassa G. Dynamic Origin of Chirality Transfer between Chiral Surface and Achiral Ligand in Au 38 Clusters. ACS NANO 2019; 13:7127-7134. [PMID: 31199121 DOI: 10.1021/acsnano.9b02552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The transfer of chirality between nanomolecules is at the core of several applications in chiral technology such as sensing and catalysis. However, the origin of this phenomenon and how exactly nanoscale objects transfer chirality to molecules in their vicinity remain largely obscure. Here, we show that the transfer of chirality for the intrinsically chiral gold cluster Au38(SR)24 is site dependent; that is, it differs depending on the ligand-binding sites. This is closely related to the dynamic nature of the ligands on the cluster surface. Using a combination of NMR techniques and molecular dynamics simulations, we could assign the four symmetry-unique ligands on the cluster. The study reveals largely different conformational dynamics of the bound ligands, explaining the diverse diastereotopicities observed for the CH2 protons of the ligands. Although chirality is a structural property, our study reveals the importance of dynamics for the transfer of chirality.
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Affiliation(s)
- Laura Riccardi
- Laboratory of Molecular Modeling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Federico De Biasi
- Dipartimento di Scienze Chimiche , Università di Padova , Via Marzolo 1 , 35131 Padova , Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , Italy
| | - Thomas Bürgi
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest-Ansermet , 1211 Geneva 4, Switzerland
| | - Federico Rastrelli
- Dipartimento di Scienze Chimiche , Università di Padova , Via Marzolo 1 , 35131 Padova , Italy
| | - Giovanni Salassa
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest-Ansermet , 1211 Geneva 4, Switzerland
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44
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Sun X, Riccardi L, De Biasi F, Rastrelli F, De Vivo M, Mancin F. Molecular‐Dynamics‐Simulation‐Directed Rational Design of Nanoreceptors with Targeted Affinity. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaohuan Sun
- Dipartimento di Scienze ChimicheUniveristà di Padova Via Marzolo 1 35131 Padova Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Federico De Biasi
- Dipartimento di Scienze ChimicheUniveristà di Padova Via Marzolo 1 35131 Padova Italy
| | - Federico Rastrelli
- Dipartimento di Scienze ChimicheUniveristà di Padova Via Marzolo 1 35131 Padova Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug DiscoveryIstituto Italiano di Tecnologia (IIT) Via Morego 30 16163 Genova Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze ChimicheUniveristà di Padova Via Marzolo 1 35131 Padova Italy
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45
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Sun X, Riccardi L, De Biasi F, Rastrelli F, De Vivo M, Mancin F. Molecular-Dynamics-Simulation-Directed Rational Design of Nanoreceptors with Targeted Affinity. Angew Chem Int Ed Engl 2019; 58:7702-7707. [PMID: 30964595 DOI: 10.1002/anie.201902316] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Indexed: 11/07/2022]
Abstract
Here, we demonstrate the possibility of rationally designing nanoparticle receptors with targeted affinity and selectivity for specific small molecules. We used atomistic molecular-dynamics (MD) simulations to gradually mutate and optimize the chemical structure of the molecules forming the coating monolayer of gold nanoparticles (1.7 nm gold-core size). The MD-directed design resulted in nanoreceptors with a 10-fold improvement in affinity for the target analyte (salicylate) and a 100-fold decrease of the detection limit by NMR-chemosensing from the millimolar to the micromolar range. We could define the exact binding mode, which features prolonged contacts and deep penetration of the guest into the monolayer, as well as a distinct shape of the effective binding pockets characterized by exposed interacting points.
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Affiliation(s)
- Xiaohuan Sun
- Dipartimento di Scienze Chimiche, Univeristà di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genova, Italy
| | - Federico De Biasi
- Dipartimento di Scienze Chimiche, Univeristà di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Federico Rastrelli
- Dipartimento di Scienze Chimiche, Univeristà di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genova, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Univeristà di Padova, Via Marzolo 1, 35131, Padova, Italy
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46
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Wu M, Vartanian AM, Chong G, Pandiakumar AK, Hamers RJ, Hernandez R, Murphy CJ. Solution NMR Analysis of Ligand Environment in Quaternary Ammonium-Terminated Self-Assembled Monolayers on Gold Nanoparticles: The Effect of Surface Curvature and Ligand Structure. J Am Chem Soc 2019; 141:4316-4327. [PMID: 30763078 DOI: 10.1021/jacs.8b11445] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report a solution NMR-based analysis of (16-mercaptohexadecyl)trimethylammonium bromide (MTAB) self-assembled monolayers on colloidal gold nanospheres (AuNSs) with diameters from 1.2 to 25 nm and gold nanorods (AuNRs) with aspect ratios from 1.4 to 3.9. The chemical shift analysis of the proton signals from the solvent-exposed headgroups of bound ligands suggests that the headgroups are saturated on the ligand shell as the sizes of the nanoparticles increase beyond ∼10 nm. Quantitative NMR shows that the ligand density of MTAB-AuNSs is size-dependent. Ligand density ranges from ∼3 molecules per nm2 for 25 nm particles to up to 5-6 molecules per nm2 in ∼10 nm and smaller particles for in situ measurements of bound ligands; after I2/I- treatment to etch away the gold cores, ligand density ranges from ∼2 molecules per nm2 for 25 nm particles to up to 4-5 molecules per nm2 in ∼10 nm and smaller particles. T2 relaxation analysis shows greater hydrocarbon chain ordering and less headgroup motion as the diameter of the particles increases from 1.2 nm to ∼13 nm. Molecular dynamics simulations of 4, 6, and 8 nm (11-mercaptoundecyl)trimethylammonium bromide-capped AuNSs confirm greater hydrophobic chain packing order and saturation of charged headgroups within the same spherical ligand shell at larger nanoparticle sizes and higher ligand densities. Combining the NMR studies and MD simulations, we suggest that the headgroup packing limits the ligand density, rather than the sulfur packing on the nanoparticle surface, for ∼10 nm and larger particles. For MTAB-AuNRs, no chemical shift data nor ligand density data suggest that two populations of ligands that might correspond to side-ligands and end-ligands exist; yet T2 relaxation dynamics data suggest that headgroup mobility depends on aspect ratio and absolute nanoparticle dimensions.
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Affiliation(s)
- Meng Wu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ariane M Vartanian
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Gene Chong
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Arun Kumar Pandiakumar
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Robert J Hamers
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Rigoberto Hernandez
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Catherine J Murphy
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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47
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Franco-Ulloa S, Riccardi L, Rimembrana F, Pini M, De Vivo M. NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles. J Chem Theory Comput 2019; 15:2022-2032. [PMID: 30758952 DOI: 10.1021/acs.jctc.8b01304] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Functionalized nanoparticles (NPs) are at the frontier of nanoscience. They hold the promise of innovative applications for human health and technology. In this context, molecular dynamics (MD) simulations of NPs are increasingly employed to understand the fundamental structural and dynamical features of NPs. While informative, such simulations demand a laborious two-step process for their setup. In-house scripts are required to (i) construct complex 3D models of the inner metal core and outer layer of organic ligands, and (ii) correctly assign force-field parameters to these composite systems. Here, we present NanoModeler ( www.nanomodeler.it ), the first Webserver designed to automatically generate and parametrize model systems of monolayer-protected gold NPs and gold nanoclusters. The only required input is a structure file of one or two ligand(s) to be grafted onto the gold core, with the option of specifying homogeneous or heterogeneous NP morphologies. NanoModeler then generates 3D models of the nanosystem and the associated topology files. These files are ready for use with the Gromacs MD engine, and they are compatible with the AMBER family of force fields. We illustrate NanoModeler's capabilities with MD simulations of selected representative NP model systems. NanoModeler is the first platform to automate and standardize the construction and parametrization of realistic models for atomistic simulations of gold NPs and gold nanoclusters.
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Affiliation(s)
- Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab , Istituto Italiano di Tecnologia , via Morego 30 , Genova 16163 , Italy
| | - Laura Riccardi
- Molecular Modeling and Drug Discovery Lab , Istituto Italiano di Tecnologia , via Morego 30 , Genova 16163 , Italy
| | - Federico Rimembrana
- Molecular Modeling and Drug Discovery Lab , Istituto Italiano di Tecnologia , via Morego 30 , Genova 16163 , Italy
| | - Mattia Pini
- Molecular Modeling and Drug Discovery Lab , Istituto Italiano di Tecnologia , via Morego 30 , Genova 16163 , Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab , Istituto Italiano di Tecnologia , via Morego 30 , Genova 16163 , Italy
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48
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De Biasi F, Rosa-Gastaldo D, Sun X, Mancin F, Rastrelli F. Nanoparticle-Assisted NMR Spectroscopy: Enhanced Detection of Analytes by Water-Mediated Saturation Transfer. J Am Chem Soc 2019; 141:4870-4877. [DOI: 10.1021/jacs.8b13225] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Federico De Biasi
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Daniele Rosa-Gastaldo
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Xiaohuan Sun
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
| | - Federico Rastrelli
- Department of Chemical Sciences, Università degli Studi di Padova, via Marzolo 1, 35131 Padova, Italy
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49
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Mikolajczak DJ, Scholz J, Koksch B. Tuning the Catalytic Activity and Substrate Specificity of Peptide-Nanoparticle Conjugates. ChemCatChem 2018. [DOI: 10.1002/cctc.201801521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Dorian J. Mikolajczak
- Department of Biology Chemistry and Pharmacy; Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
| | - Jonas Scholz
- Department of Biology Chemistry and Pharmacy; Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
| | - Beate Koksch
- Department of Biology Chemistry and Pharmacy; Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
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50
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Mass spectrometry and Monte Carlo method mapping of nanoparticle ligand shell morphology. Nat Commun 2018; 9:4478. [PMID: 30367040 PMCID: PMC6203843 DOI: 10.1038/s41467-018-06939-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/02/2018] [Indexed: 01/26/2023] Open
Abstract
Janus, patchy, stripe-like, or random arrangements of molecules within the ligand shell of nanoparticles affect many properties. Among all existing ligand shell morphology characterization methods, the one based on mass spectroscopy is arguably the simplest. Its greatest limitation is that the results are qualitative. Here, we use a tailor-made Monte Carlo type program that fits the whole MALDI spectrum and generates a 3D model of the ligand shell. Quantitative description of the ligand shell in terms of nearest neighbor distribution and characteristic length scale can be readily extracted by the model, and are compared with the results of other characterization methods. A parameter related to the intermolecular interaction is extracted when this method is combined with NMR. This approach could become the routine method to characterize the ligand shell morphology of many nanoparticles and we provide an open access program to facilitate its use. Determining the arrangement of ligands on a nanoparticle is challenging, given the limitations of existing characterization tools. Here, the authors describe an accessible method for resolving ligand shell morphology that uses simple MALDI-TOF mass spectrometry measurements in conjunction with an open-access Monte Carlo fitting program.
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