1
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Cheung DL. Surface Hydrophobicity Strongly Influences Adsorption and Conformation of Amyloid Beta Derived Peptides. Molecules 2024; 29:3634. [PMID: 39125038 PMCID: PMC11314246 DOI: 10.3390/molecules29153634] [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: 06/14/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The formation of amyloid fibrils is a common feature of many protein systems. It has implications in both health, as amyloid fibrils are implicated in over 30 degenerative diseases, and in the biological functions of proteins. Surfaces have long been known to affect the formation of fibrils but the specific effect depends on the details of both the surface and protein. Fully understanding the role of surfaces in fibrillization requires microscopic information on protein conformation on surfaces. In this paper replica exchange molecular dynamics simulation is used to investigate the model fibril forming protein, Aβ(10-40) (a 31-residue segment of the amyloid-beta protein) on surfaces of different hydrophobicity. Similar to other proteins Aβ(10-40) is found to adsorb strongly onto hydrophobic surfaces. It also adopts significantly different sets of conformations on hydrophobic and polar surfaces, as well as in bulk solution. On hydrophobic surfaces, it adopts partially helical structures, with the helices overlapping with beta-strand regions in the mature fibril. These may be helical intermediates on the fibril formation pathway, suggesting a mechanism for the enhanced fibril formation seen on hydrophobic surfaces.
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Affiliation(s)
- David L Cheung
- School of Biological and Chemical Sciences, University of Galway, University Road, H91 TK33 Galway, Ireland
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2
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Frigerio G, Donadoni E, Siani P, Vertemara J, Motta S, Bonati L, Gioia LD, Valentin CD. Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α Vβ 3 by atomistic molecular dynamics and machine learning. NANOSCALE 2024; 16:4063-4081. [PMID: 38334981 DOI: 10.1039/d3nr05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Active targeting strategies have been proposed to enhance the selective uptake of nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the effectiveness of this approach. However, no mechanistic studies have yet revealed the atomistic details of the interactions between ligand-activated NPs and integrins. As a case study, here we investigate, by means of advanced molecular dynamics simulations (MD) and machine learning methods (namely equilibrium MD, binding free energy calculations and training of self-organized maps), the interaction of a cyclic-RGD-conjugated PEGylated TiO2 NP (the nanodevice) with the extracellular segment of integrin αVβ3 (the target), the latter experimentally well-known to be over-expressed in several solid tumors. Firstly, we proved that the cyclic-RGD ligand binding to the integrin pocket is established and kept stable even in the presence of the cumbersome realistic model of the nanodevice. In this respect, the unsupervised machine learning analysis allowed a detailed comparison of the ligand/integrin binding in the presence and in the absence of the nanodevice, which unveiled differences in the chemical features. Then, we discovered that unbound cyclic RGDs conjugated to the NP largely contribute to the interactions between the nanodevice and the integrin. Finally, by increasing the density of cyclic RGDs on the PEGylated TiO2 NP, we observed a proportional enhancement of the nanodevice/target binding. All these findings can be exploited to achieve an improved targeting selectivity and cellular uptake, and thus a more successful clinical outcome.
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Affiliation(s)
- Giulia Frigerio
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Edoardo Donadoni
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Paulo Siani
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Stefano Motta
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Dipartimento di Scienze dell'Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Luca De Gioia
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy.
- BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, Italy
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3
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Tiwari V, Garg S, Karmakar T. Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters. ACS APPLIED BIO MATERIALS 2024; 7:685-691. [PMID: 36820798 DOI: 10.1021/acsabm.2c00997] [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] [Indexed: 02/24/2023]
Abstract
Monolayer-protected atomically precise metal nanoclusters (MPCs) have potential applications in catalysis, imaging, and drug delivery. Understanding their interactions with biomolecules such as peptides is of paramount interest for their use in cell imaging and drug delivery. Here we have carried out atomistic molecular dynamics simulations to investigate the interactions between MPCs and an anticancer peptide, melittin. Melittin gets attached to the MPCs surface by the formation of multiple hydrogen bonds between its amino acid residues with MPCs ligands. Additionally, the positively charged Lys, Arg, and peptide's N-terminal strongly anchor the peptide to the MPC metal surface, providing extra stabilization.
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Affiliation(s)
- Vikas Tiwari
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, 110016 New Delhi, India
| | - Sonali Garg
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, 110016 New Delhi, India
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, 110016 New Delhi, India
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4
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Sodomaco S, Gómez S, Giovannini T, Cappelli C. Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces. J Phys Chem A 2023; 127:10282-10294. [PMID: 37993110 DOI: 10.1021/acs.jpca.3c05560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.
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Affiliation(s)
- Sveva Sodomaco
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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5
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Cheung DL. Aggregation of an Amyloidogenic Peptide on Gold Surfaces. Biomolecules 2023; 13:1261. [PMID: 37627326 PMCID: PMC10452923 DOI: 10.3390/biom13081261] [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: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Solid surfaces have been shown to affect the aggregation and assembly of many biomolecular systems. One important example is the formation of protein fibrils, which can occur on a range of biological and synthetic surfaces. The rate of fibrillation depends on both the protein structure and the surface chemistry, with the different molecular and oligomer structures adopted by proteins on surfaces likely to be crucial. In this paper, the aggregation of the model amyloidogenic peptide, Aβ(16-22), corresponding to a hydrophobic segment of the amyloid beta protein on a gold surface is studied using molecular dynamics simulation. Previous simulations of this peptide on gold surfaces have shown that it adopts conformations on surfaces that are quite different from those in bulk solution. These simulations show that this then leads to significant differences in the oligomer structures formed in solution and on gold surfaces. In particular, oligomers formed on the surface are low in beta-strands so are unlike the structures formed in bulk solution. When oligomers formed in solution adsorb onto gold surfaces they can then restructure themselves. This can then help explain the inhibition of Aβ(16-22) fibrillation by gold surfaces and nanoparticles seen experimentally.
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Affiliation(s)
- David L Cheung
- School of Biological and Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
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6
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Dutta S, Gagliardi M, Bellucci L, Agostini M, Corni S, Cecchini M, Brancolini G. Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study. Front Mol Biosci 2022; 9:1006525. [DOI: 10.3389/fmolb.2022.1006525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.
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7
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Viola G, Barracchia CG, Tira R, Parolini F, Leo G, Bellanda M, Munari F, Capaldi S, D’Onofrio M, Assfalg M. New Paradigm for Nano-Bio Interactions: Multimolecular Assembly of a Prototypical Disordered Protein with Ultrasmall Nanoparticles. NANO LETTERS 2022; 22:8875-8882. [PMID: 36346924 PMCID: PMC9706667 DOI: 10.1021/acs.nanolett.2c02902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/24/2022] [Indexed: 05/20/2023]
Abstract
Understanding the interactions between nanoparticles (NPs) and proteins is crucial for the successful application of NPs in biological contexts. Protein adsorption is dependent on particle size, and protein binding to ultrasmall (1-3 nm) NPs is considered to be generally weak. However, most studies have involved structured biomacromolecules, while the interactions of ultrasmall NPs with intrinsically disordered proteins (IDPs) have remained elusive. IDPs are abundant in eukaryotes and found to associate with NPs intracellularly. As a model system, we focused on ultrasmall gold nanoparticles (usGNPs) and tau, a cytosolic IDP associated with Alzheimer's disease. Using site-resolved NMR, steady-state fluorescence, calorimetry, and circular dichroism, we reveal that tau and usGNPs form stable multimolecular assemblies, representing a new type of nano-bio interaction. Specifically, the observed interaction hot spots explain the influence of usGNPs on tau conformational transitions, with implications for the intracellular targeting of aberrant IDP aggregation.
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Affiliation(s)
- Giovanna Viola
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Roberto Tira
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Giulia Leo
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Massimo Bellanda
- Department
of Chemistry, University of Padova, 35131 Padova, Italy
| | - Francesca Munari
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Stefano Capaldi
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Michael Assfalg
- Department
of Biotechnology, University of Verona, 37134 Verona, Italy
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8
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John T, Adler J, Elsner C, Petzold J, Krueger M, Martin LL, Huster D, Risselada HJ, Abel B. Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation. J Colloid Interface Sci 2022; 622:804-818. [PMID: 35569410 DOI: 10.1016/j.jcis.2022.04.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/05/2022] [Accepted: 04/23/2022] [Indexed: 10/18/2022]
Abstract
The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer's and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parameters determine interfacial effects, we focus here on the role of nanoparticle (NP) size and curvature. We used thioflavin T (ThT) fluorescence assays to demonstrate the size-dependent effects of NPs on amyloid fibril formation for the peptides Aβ40, NNFGAIL, GNNQQNY and VQIYVK. While 5 nm gold NPs (AuNP-5) retarded or inhibited the aggregation of all peptides except NNFGAIL, larger 20 nm gold NPs (AuNP-20) tended to accelerate or not influence peptide aggregation. Differences in the NP effects for the peptides resulted from the different peptide properties (size, tendency to aggregate) and associated surface binding affinities. Additional dynamic light scattering (DLS), electron microscopy, and atomic force microscopy (AFM) experiments with the Aβ40 peptide confirmed size-dependent NP effects on peptide aggregation, and also suggested a structural influence on the formed fibrils. NPs can serve as a surface for the adsorption of peptide monomers and enable nucleation to oligomers and fibril formation. However, molecular dynamics (MD) simulations showed that peptide oligomers were less stable at smaller NPs. High surface curvatures destabilized prefibrillar structures, which provides a possible explanation for inhibitory effects on fibril growth, provided that peptide-NP surface binding was relevant for fibril formation. These mechanistic insights can support the design of future nanostructured materials.
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Affiliation(s)
- Torsten John
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany; School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Juliane Adler
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Christian Elsner
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
| | - Johannes Petzold
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstraße 13, 04103 Leipzig, Germany
| | - Lisandra L Martin
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Herre Jelger Risselada
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Institute for Theoretical Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany.
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9
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Wei X, Popov A, Hernandez R. Electric Potential of Citrate-Capped Gold Nanoparticles Is Affected by Poly(allylamine hydrochloride) and Salt Concentration. ACS APPLIED MATERIALS & INTERFACES 2022; 14:12538-12550. [PMID: 35230798 DOI: 10.1021/acsami.1c24526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structure near polyelectrolyte-coated gold nanoparticles (AuNPs) is of significant interest because of the increased use of AuNPs in technological applications and the possibility that the acquisition of polyelectrolytes can lead to novel chemistry in downstream environments. We use all-atom molecular dynamics (MD) simulations to reveal the electric potential around citrate-capped gold nanoparticles (cit-AuNPs) and poly(allylamine hydrochloride) (PAH)-wrapped cit-AuNP (PAH-AuNP). We focus on the effects of the overall ionic strength and the shape of the electric potential. The ionic number distributions for both cit-AuNP and PAH-AuNP are calculated using MD simulations at varying salt concentrations (0, 0.001, 0.005, 0.01, 0.05, 0.1, and 0.2 M NaCl). The net charge distribution (Z(r)) around the nanoparticle is determined from the ionic number distribution observed in the simulations and allows for the calculation of the electric potential (ϕ(r)). We find that the magnitude of ϕ(r) decreases with increasing salt concentration and upon wrapping by PAH. Using a hydrodynamic radius (RH) estimated from the literature and fits to the Debye-Hü̈ckel expression, we found and report the ζ potential for both cit-AuNP and PAH-AuNP at varying salt concentrations. For example, at 0.001 M NaCl, MD simulations suggest that ζ = -25.5 mV for cit-AuNP. Upon wrapping of cit-AuNP by one PAH chain, the resulting PAH-AuNP exhibits a reduced ζ potential (ζ = -8.6 mV). We also compare our MD simulation results for ϕ(r) to the classic Poisson-Boltzmann equation (PBE) approximation and the well-known Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. We find agreement with the limiting regimes─with respect to surface charge, salt concentration and particle size─in which the assumptions of the PBE and DLVO theory are known to be satisfied.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander Popov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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10
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Cantarutti C, Hunashal Y, La Rosa C, Condorelli M, Giorgetti S, Bellotti V, Fogolari F, Esposito G. The corona of protein-gold nanoparticle systems: the role of ionic strength. Phys Chem Chem Phys 2021; 24:1630-1637. [PMID: 34951613 DOI: 10.1039/d1cp04574a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The nature of the nanoparticle-protein corona is emerging as a key aspect in determining the impact of nanomaterials on proteins and in general on the biological response. We previously demonstrated that citrate-stabilized gold nanoparticles (Cit-AuNPs) interact with β2-microglobulin (β2m) preserving the protein native structure. Moreover, Cit-AuNPs are able to hinder in vitro fibrillogenesis of a β2m pathologic variant, namely D76N, by reducing the oligomeric association of the protein in solution. Here, we clarify the characteristics of the interaction between β2m and Cit-AuNPs by means of different techniques, i.e. surface enhanced Raman spectroscopy, NMR and quartz crystal microbalance with dissipation monitoring. All the results obtained clearly show that by simply changing the ionic strength of the medium it is possible to switch from a labile and transient nature of the protein-NP adduct featuring the so-called soft corona, to a more "hard" interaction with a layer of proteins having a longer residence time on the NP surface. This confirms that the interaction between β2m and Cit-AuNPs is dominated by electrostatic forces which can be tuned by modifying the ionic strength.
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Affiliation(s)
| | - Yamanappa Hunashal
- DAME, Università di Udine, 33100 Udine, Italy.,Science Division, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Carmelo La Rosa
- Dip. Scienze Chimiche, Università di Catania, 95125 Catania, Italy
| | | | - Sofia Giorgetti
- Dipartimento di Medicina Molecolare, Università di Pavia, 27100 Pavia, Italy
| | - Vittorio Bellotti
- Dipartimento di Medicina Molecolare, Università di Pavia, 27100 Pavia, Italy.,Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine, University College London, London NW3 2PF, UK
| | - Federico Fogolari
- DMIF, Università di Udine, 33100 Udine, Italy.,INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | - Gennaro Esposito
- Science Division, New York University Abu Dhabi, Abu Dhabi, UAE. .,INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
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11
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Singh A, Maharana SK, Shukla R, Kesharwani P. Nanotherapeutics approaches for targeting alpha synuclien protein in the management of Parkinson disease. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Wei X, Zhao Y, Zhuang Y, Hernandez R. Building blocks for autonomous computing materials: Dimers, trimers, and tetramers. J Chem Phys 2021; 155:154704. [PMID: 34686055 DOI: 10.1063/5.0064988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autonomous computing materials for data storage and computing offer an opportunity for next generation of computing devices. Patchy nanoparticle networks, for example, have been suggested as potential candidates for emulating neuronal networks and performing brain-like computing. Here, we use molecular dynamics (MD) simulations to show that stable dimers, trimers, and tetramers can be built from citrate capped gold nanoparticles (cit-AuNPs) linked by poly(allylamine hydrochloride) (PAH) chains. We use different lengths of PAHs to build polymer-networked nanoparticle assemblies that can emulate a complex neuronal network linked by axons of varying lengths. We find that the tetramer structure can accommodate up to 11 different states when the AuNP pairs are connected by either of two polymer linkers, PAH200 and PAH300. We find that the heavy AuNPs contribute to the assembly's structure stability. To further illustrate the stability, the AuNP-AuNP distances in dimer, trimer, and tetramer structures are reduced by steering the cit-AuNPs closer to each other. At different distances, these steered structures are all locally stable in a 10 ns MD simulation time scale because of their connection to the AuNPs. We also find that the global potential energy minimum is at short AuNP-AuNP distances where AuNPs collapse because the -NH3 + and -COO- attraction reduces the potential energy. The stability and application of these fundamental structures remain to be further improved through the use of alternative polymer linkers and nanoparticles.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yinong Zhao
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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13
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Salassi S, Caselli L, Cardellini J, Lavagna E, Montis C, Berti D, Rossi G. A Martini Coarse Grained Model of Citrate-Capped Gold Nanoparticles Interacting with Lipid Bilayers. J Chem Theory Comput 2021; 17:6597-6609. [PMID: 34491056 PMCID: PMC8515808 DOI: 10.1021/acs.jctc.1c00627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/29/2022]
Abstract
Citrate capping is one of the most common strategies to achieve the colloidal stability of Au nanoparticles (NPs) with diameters ranging from a few to hundreds of nanometers. Citrate-capped Au nanoparticles (CNPs) represent a step of the synthesis of Au NPs with specific functionalities, as CNPs can be further functionalized via ligand-exchange reactions, leading to the replacement of citrate with other organic ligands. In vitro, CNPs are also used to address the fundamental aspects of NP-membrane interactions, as they can directly interact with cells or model cell membranes. Their affinity for the bilayer is again mediated by the exchange of citrate with lipid molecules. Here, we propose a new computational model of CNPs compatible with the coarse grained Martini force field. The model, which we develop and validate through an extensive comparison with new all-atom molecular dynamics (MD) simulations and UV-vis and Fourier transform infrared spectroscopy data, is aimed at the MD simulation of the interaction between citrate-capped NPs and model phosphatidylcholine lipid membranes. As a test application we show that, during the interaction between a single CNP and a flat planar 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer, the citrate coating is spontaneously replaced by lipids on the surface of Au NPs, while the NP size and shape determine the final structural configuration of the NP-bilayer complex.
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Affiliation(s)
- Sebastian Salassi
- Department
of Physics, University of Genoa, Via Dodecaneso 33, Genoa 16146, Italy
| | - Lucrezia Caselli
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
- CSGI,
Consorzio Sistemi a Grande Interfase and Department of Chemistry “Ugo
Schiff” University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Jacopo Cardellini
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
- CSGI,
Consorzio Sistemi a Grande Interfase and Department of Chemistry “Ugo
Schiff” University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Enrico Lavagna
- Department
of Physics, University of Genoa, Via Dodecaneso 33, Genoa 16146, Italy
| | - Costanza Montis
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
- CSGI,
Consorzio Sistemi a Grande Interfase and Department of Chemistry “Ugo
Schiff” University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Debora Berti
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
- CSGI,
Consorzio Sistemi a Grande Interfase and Department of Chemistry “Ugo
Schiff” University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Giulia Rossi
- Department
of Physics, University of Genoa, Via Dodecaneso 33, Genoa 16146, Italy
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14
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Tavanti F, Menziani MC. Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles. Int J Mol Sci 2021; 22:ijms22168722. [PMID: 34445432 PMCID: PMC8395736 DOI: 10.3390/ijms22168722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 01/23/2023] Open
Abstract
Protein interactions with engineered gold nanoparticles (AuNPs) and the consequent formation of the protein corona are very relevant and poorly understood biological phenomena. The nanoparticle coverage affects protein binding modalities, and the adsorbed protein sites influence interactions with other macromolecules and cells. Here, we studied four common blood proteins, i.e., hemoglobin, serum albumin, α1-antiproteinase, and complement C3, interacting with AuNPs covered by hydrophobic 11-mercapto-1-undecanesulfonate (MUS). We use Molecular Dynamics and the Martini coarse−grained model to gain quantitative insight into the kinetics of the interaction, the physico-chemical characteristics of the binding site, and the nanoparticle adsorption capacity. Results show that proteins bind to MUS−capped AuNPs through strong hydrophobic interactions and that they adapt to the AuNP surfaces to maximize the contact surface, but no dramatic change in the secondary structure of the proteins is observed. We suggest a new method to calculate the maximum adsorption capacity of capped AuNPs based on the effective surface covered by each protein, which better represents the realistic behavior of these systems.
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Affiliation(s)
- Francesco Tavanti
- CNR-NANO Research Center S3, Via Campi 213/a, 41125 Modena, Italy
- Correspondence:
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
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15
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Reinhardt M, Bruce NJ, Kokh DB, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics. J Chem Theory Comput 2021; 17:3510-3524. [PMID: 33784462 DOI: 10.1021/acs.jctc.0c01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian dynamics simulations can be carried out with the approximation of rigid body solutes moving through a continuum solvent. This allows the precomputation of interaction potential grids for the solutes, thereby allowing the computationally efficient calculation of forces. However, hydrodynamic and long-range electrostatic interactions cannot be fully treated with grid-based approaches alone. Here, we develop a treatment of both hydrodynamic and electrostatic interactions to include the presence of surfaces by modeling grid-based and long-range interactions. We describe its application to simulate the self-association and many-molecule adsorption of the well-characterized protein hen egg-white lysozyme to mica-like and silica-like surfaces. We find that the computational model can recover a number of experimental observables of the adsorption process and provide insights into their determinants. The computational model is implemented in the Simulation of Diffusional Association (SDA) software package.
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Affiliation(s)
- Martin Reinhardt
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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16
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Wei X, Zhao Y, Zhuang Y, Hernandez R. Engineered nanoparticle network models for autonomous computing. J Chem Phys 2021; 154:214702. [PMID: 34240993 DOI: 10.1063/5.0048898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Materials that exhibit synaptic properties are a key target for our effort to develop computing devices that mimic the brain intrinsically. If successful, they could lead to high performance, low energy consumption, and huge data storage. A 2D square array of engineered nanoparticles (ENPs) interconnected by an emergent polymer network is a possible candidate. Its behavior has been observed and characterized using coarse-grained molecular dynamics (CGMD) simulations and analytical lattice network models. Both models are consistent in predicting network links at varying temperatures, free volumes, and E-field (E⃗) strengths. Hysteretic behavior, synaptic short-term plasticity and long-term plasticity-necessary for brain-like data storage and computing-have been observed in CGMD simulations of the ENP networks in response to E-fields. Non-volatility properties of the ENP networks were also confirmed to be robust to perturbations in the dielectric constant, temperature, and affine geometry.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yinong Zhao
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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17
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Dutta S, Bellucci L, Agostini M, Gagliardi M, Corni S, Cecchini M, Brancolini G. Atomistic simulations of gold surface functionalization for nanoscale biosensors applications. NANOTECHNOLOGY 2021; 32:095702. [PMID: 33137790 DOI: 10.1088/1361-6528/abc6dc] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.
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Affiliation(s)
- Sutapa Dutta
- Dipartimento di Scienze Chimiche, Università di Padova, I-35131 Padova, Italy
- Istituto Nanoscienze-CNR-NANO, Center S3, via G. Campi 213/A, I-41125 Modena, Italy
| | - Luca Bellucci
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Matteo Agostini
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Mariacristina Gagliardi
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università di Padova, I-35131 Padova, Italy
- Istituto Nanoscienze-CNR-NANO, Center S3, via G. Campi 213/A, I-41125 Modena, Italy
| | - Marco Cecchini
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Giorgia Brancolini
- Istituto Nanoscienze-CNR-NANO, Center S3, via G. Campi 213/A, I-41125 Modena, Italy
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18
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An investigation of the effect of PVP-coated silver nanoparticles on the interaction between clonazepam and bovine serum albumin based on molecular dynamics simulations and molecular docking. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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19
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koraychy EE, Meddad M, Badawi M, Mazroui M. Sintering and deposition of homo- and heteronanoparticles of aluminum and nickel on aluminum (100) substrate. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Maschio MC, Fregoni J, Molteni C, Corni S. Proline isomerization effects in the amyloidogenic protein β2-microglobulin. Phys Chem Chem Phys 2021; 23:356-367. [DOI: 10.1039/d0cp04780e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein β2-microglobulin can aggregate in insoluble amyloid fibrils. By relying on extensive sampling simulations, we study the Pro32 isomerization as a possible triggering factor leading to structural modifications in β2-m.
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Affiliation(s)
| | - Jacopo Fregoni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
| | - Carla Molteni
- Department of Physics
- King's College London
- Strand
- London WC2R 2LS
- UK
| | - Stefano Corni
- CNR-Nano S3
- Modena
- Italy
- Department of Chemical Sciences
- University of Padova
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21
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Tavanti F, Pedone A, Menziani MC. Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations. Int J Mol Sci 2020; 22:ijms22010026. [PMID: 33375086 PMCID: PMC7792802 DOI: 10.3390/ijms22010026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles. Importantly, upon binding, amyloid monomers show a reduced propensity in forming β-sheets secondary structures that are characteristics of mature amyloid fibrils.
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Affiliation(s)
- Francesco Tavanti
- CNR-NANO Research Center, Via Campi 213/a, 41125 Modena, Italy
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
- Correspondence:
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
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22
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D’Onofrio M, Munari F, Assfalg M. Alpha-Synuclein-Nanoparticle Interactions: Understanding, Controlling and Exploiting Conformational Plasticity. Molecules 2020; 25:E5625. [PMID: 33260436 PMCID: PMC7731430 DOI: 10.3390/molecules25235625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson's disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered but can adopt multiple alternative conformations under given conditions, such as upon adsorption to nanoscale surfaces. The study of αS-nanoparticle interactions allows us to better understand the behavior of the protein and provides the basis for developing systems capable of mitigating the formation of toxic aggregates as well as for designing hybrid nanomaterials with novel functionalities for applications in various research areas. In this review, we summarize current progress on αS-nanoparticle interactions with an emphasis on the conformational plasticity of the biomolecule.
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Affiliation(s)
| | | | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (M.D.); (F.M.)
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23
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Insights into a Protein-Nanoparticle System by Paramagnetic Perturbation NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25215187. [PMID: 33171781 PMCID: PMC7664681 DOI: 10.3390/molecules25215187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/12/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
Background: The interaction between proteins and nanoparticles is a very relevant subject because of the potential applications in medicine and material science in general. Further interest derives from the amyloidogenic character of the considered protein, β2-microglobulin (β2m), which may be regarded as a paradigmatic system for possible therapeutic strategies. Previous evidence showed in fact that gold nanoparticles (AuNPs) are able to inhibit β2m fibril formation in vitro. Methods: NMR (Nuclear Magnetic Resonance) and ESR (Electron Spin Resonance) spectroscopy are employed to characterize the paramagnetic perturbation of the extrinsic nitroxide probe Tempol on β2m in the absence and presence of AuNPs to determine the surface accessibility properties and the occurrence of chemical or conformational exchange, based on measurements conducted under magnetization equilibrium and non-equilibrium conditions. Results: The nitroxide perturbation analysis successfully identifies the protein regions where protein-protein or protein-AuNPs interactions hinder accessibility or/and establish exchange contacts. These information give interesting clues to recognize the fibrillation interface of β2m and hypothesize a mechanism for AuNPs fibrillogenesis inhibition. Conclusions: The presented approach can be advantageously applied to the characterization of the interface in protein-protein and protein-nanoparticles interactions.
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24
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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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25
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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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26
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Tavanti F, Pedone A, Menziani MC, Alexander-Katz A. Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils. ACS Chem Neurosci 2020; 11:3153-3160. [PMID: 32926781 DOI: 10.1021/acschemneuro.0c00497] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.
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Affiliation(s)
- Francesco Tavanti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
- CNR-NANO Istituto Nanoscienze, Centro S3, Via Campi 213/A, I-41125 Modena, Italy
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Massachusetts Avenue, 77, Cambridge, Massachusetts 02142, United States
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27
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Sahraei A, Mohammadi F, Boukherroub R, Szunerits S. Formation of a Highly Stable and Nontoxic Protein Corona upon Interaction of Human α-1-Acid Glycoprotein (AGP) with Citrate-Stabilized Silver Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10321-10330. [PMID: 32842747 DOI: 10.1021/acs.langmuir.0c01018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Given the importance of protein corona in determining cellular responses to nanoparticles, numerous studies have been devoted to finding stable, biocompatible, and nontoxic protein corona. In this work, the interaction between human α-1-acid glycoprotein (AGP) and citrate-stabilized silver (Ag-CIT) nanoparticles of about 10 nm was methodically studied using molecular docking simulation approach and various experimental techniques. It could be shown that a stable Ag-CIT/AGP bioconjugate was formed with a high binding constant of 109 M-1, several orders of magnitude larger than that of other highly abundant serum proteins. Formation of AGP corona was accompanied by conserving the native conformation of the protein and further associated with a considerable decrease in the cytotoxicity of the silver nanoparticles.
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Affiliation(s)
- Amin Sahraei
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Fakhrossadat Mohammadi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Rabah Boukherroub
- University Lille, CNRS, Centrale Lille, University Polytechnique Hauts-de-France, UMR 8520-IEMN, F-59000 Lille, France
| | - Sabine Szunerits
- University Lille, CNRS, Centrale Lille, University Polytechnique Hauts-de-France, UMR 8520-IEMN, F-59000 Lille, France
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28
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Narasimh An AK, Chakaravarthi G, Rao MSR, Arunachalam K. Study of absorption of radio frequency field by gold nanoparticles and nanoclusters in biological medium. Electromagn Biol Med 2020; 39:183-195. [PMID: 32408843 DOI: 10.1080/15368378.2020.1762637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Gold nanoparticles (AuNPs) and gold nanoclusters (AuNCs) are gaining interest in medical diagnosis and therapy as they are bio-compatible and are easy to functionalize. Their interaction with radiofrequency (RF) field for hyperthermia treatment is ambiguous and needs further investigation. A systematic study of the absorption of capacitive RF field by AuNPs and AuNCs dispersed in phosphate-buffered saline (PBS) is reported here in tissue mimicking phantom. The stability of AuNPs and AuNCs dispersed in PBS was confirmed for a range of pH and temperature expected during RF hyperthermia treatment. Colloidal gold solutions with AuNPs (10 nm) and AuNCs (2 nm), and control, i.e. PBS without nanogold, were loaded individually in 3 ml wells in a tissue phantom. Phantom heating was carried out using 27 MHz short-wave diathermy equipment at 200 and 400 W for control and colloidal gold solutions. Experiments were conducted for colloidal gold at varying gold concentrations (10-100 µg/ml). Temperature rise measured in the phantom wells did not show dependence on the concentration and size of the AuNPs. Furthermore, temperature rise recorded in the control was comparable with the measurements recorded in both nanogold suspensions (2, 10 nm). Dielectric property measurements of control and colloidal gold showed <3% difference in electrical conductivity between the control and colloidal gold for both nanoparticle sizes. From the measurements, it is concluded that AuNPs and AuNCs do not enhance the absorption of RF-capacitive field and power absorption observed in the biological medium is due to the ions present in the medium.
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Affiliation(s)
- Ashwin Kumar Narasimh An
- Department of Biomedical Engineering, SRM Institute of Science and Technology , Kattankulathur, India
| | - Geetha Chakaravarthi
- Department of Instrumentation and Control Engineering, NIT Trichy , Tiruchirappalli, India
| | - M S Ramachandra Rao
- Nano Functional Materials Technology Centre, Department of Physics, Indian Institute of Technology Madras , Chennai, India
| | - Kavitha Arunachalam
- Department of Engineering Design, Indian Institute of Technology Madras , Chennai, India
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29
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Tira R, De Cecco E, Rigamonti V, Santambrogio C, Barracchia CG, Munari F, Romeo A, Legname G, Prosperi D, Grandori R, Assfalg M. Dynamic molecular exchange and conformational transitions of alpha-synuclein at the nano-bio interface. Int J Biol Macromol 2020; 154:206-216. [DOI: 10.1016/j.ijbiomac.2020.03.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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30
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Daly CA, Allen C, Rozanov N, Chong G, Melby ES, Kuech TR, Lohse SE, Murphy CJ, Pedersen JA, Hernandez R. Surface Coating Structure and Its Interaction with Cytochrome c in EG 6-Coated Nanoparticles Varies with Surface Curvature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5030-5039. [PMID: 32302137 DOI: 10.1021/acs.langmuir.0c00681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The composition, orientation, and conformation of proteins in biomolecular coronas acquired by nanoparticles in biological media contribute to how they are identified by a cell. While numerous studies have investigated protein composition in biomolecular coronas, relatively little detail is known about how the nanoparticle surface influences the orientation and conformation of the proteins associated with them. We previously showed that the peripheral membrane protein cytochrome c adopts preferred poses relative to negatively charged 3-mercaptopropionic acid (MPA)-gold nanoparticles (AuNPs). Here, we employ molecular dynamics simulations and complementary experiments to establish that cytochrome c also assumes preferred poses upon association with nanoparticles functionalized with an uncharged ligand, specifically ω-(1-mercaptounde-11-cyl)hexa(ethylene glycol) (EG6). We find that the display of the EG6 ligands is sensitive to the curvature of the surface-and, consequently, the effective diameter of the nearly spherical nanoparticle core-which in turn affects the preferred poses of cytochrome c.
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Affiliation(s)
- Clyde A Daly
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Caley Allen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikita Rozanov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gene Chong
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric S Melby
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas R Kuech
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel E Lohse
- Department of Chemistry, University of Illinois-Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois-Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Departments of Soil Science, Chemistry, and Civil & Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Departments of Chemical & Biomolecular Engineering and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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31
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Sen S, Vuković L, Král P. Computational screening of nanoparticles coupling to Aβ40 peptides and fibrils. Sci Rep 2019; 9:17804. [PMID: 31780663 PMCID: PMC6883061 DOI: 10.1038/s41598-019-52594-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
Blocking the formation, growth, and breaking of amyloid fibrils by synthetic nanosystems could provide a treatment of neurodegenerative diseases. With this in mind, here atomistic molecular dynamics simulations are used to screen for nanoparticles (NPs), covered with different mixtures of ligands, including positively and negatively charged ligands, Aβ40-cut-peptide, and synthetic inhibitor ligands, in their selective coupling to Aβ40 peptides and their fibrils. The simulations reveal that only Aβ40-cut-peptide-covered NPs have strong and selective coupling to Aβ40 monomers. On the other hand, positive, positive-neutral, Janus, and peptide NPs couple to the beta sheet surfaces of Aβ40 fibrils and only the negative-neutral NPs couple to the fibril tips.
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Affiliation(s)
- Soumyo Sen
- University of Illinois at Urbana-Champaign, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, Urbana-Champaign, 61801, United States
| | - Lela Vuković
- University of Texas at El Paso, Department of Chemistry and Biochemistry, El Paso, 79968, United States.
| | - Petr Král
- University of Illinois at Chicago, Departments of Chemistry, Physics, Biopharmaceutical Sciences and Chemical Engineering, Chicago, 60607, United States.
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32
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Perera YR, Hill RA, Fitzkee NC. Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques. Isr J Chem 2019; 59:962-979. [PMID: 34045771 PMCID: PMC8152826 DOI: 10.1002/ijch.201900080] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022]
Abstract
In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub-categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small-molecule interactions are easily probed using NMR spectroscopy, studying protein-NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP-protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique for in situ analysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces.
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Affiliation(s)
- Y Randika Perera
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Rebecca A Hill
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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33
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Brancolini G, Lopez H, Corni S, Tozzini V. Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin. Int J Mol Sci 2019; 20:ijms20163866. [PMID: 31398866 PMCID: PMC6719018 DOI: 10.3390/ijms20163866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/01/2019] [Accepted: 08/03/2019] [Indexed: 12/21/2022] Open
Abstract
A large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, “minimalist” models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed. In this representation, the surface details (coating, roughness, etc.) are lost. These, however, and the specificity of the functionalization, have been shown to have fundamental roles for the interaction with proteins. We presented a mixed-resolution coarse-grained (CG) model for gold NPs in which the surface chemistry is reintroduced as superficial smaller beads. We compared molecular dynamics simulations of the amyloid β2-microglobulin represented at the minimalist level interacting with NPs represented with this model or at the MS level. Our finding highlights the importance of describing the surface of the NP at a finer level as the chemical-physical properties of the surface of the NP are crucial to correctly understand the protein-nanoparticle association.
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Affiliation(s)
- Giorgia Brancolini
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy.
| | - Hender Lopez
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, Kevin Street, Dublin D08 NF82, Ireland
| | - Stefano Corni
- Istituto Nanoscienze, CNR-NANO S3, via G. Campi 213/A, 41125 Modena, Italy
- Dipartimento di Scienze Chimiche, Università di Padova, 35131 Padova, Italy
| | - Valentina Tozzini
- Istituto Nanoscienze-National Research Council (CNR) and National Enterprise for nanoScience and nanoTechnology (NEST) Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy.
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34
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Brancolini G, Tozzini V. Building Minimalist Models for Functionalized Metal Nanoparticles. Front Mol Biosci 2019; 6:50. [PMID: 31312634 PMCID: PMC6614485 DOI: 10.3389/fmolb.2019.00050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/17/2019] [Indexed: 01/11/2023] Open
Affiliation(s)
| | - Valentina Tozzini
- Istituto Nanoscienze-CNR and NEST-Scuola Normale Superiore, Pisa, Italy
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35
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Tollefson EJ, Allen CR, Chong G, Zhang X, Rozanov ND, Bautista A, Cerda JJ, Pedersen JA, Murphy CJ, Carlson EE, Hernandez R. Preferential Binding of Cytochrome c to Anionic Ligand-Coated Gold Nanoparticles: A Complementary Computational and Experimental Approach. ACS NANO 2019; 13:6856-6866. [PMID: 31082259 DOI: 10.1021/acsnano.9b01622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.
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Affiliation(s)
- Emily J Tollefson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Caley R Allen
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Gene Chong
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Xi Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Nikita D Rozanov
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Anthony Bautista
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jennifer J Cerda
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Catherine J Murphy
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Erin E Carlson
- Department of Chemistry , University of Minnesota-Twin Cities , Minneapolis , Minnesota 55455 , United States
| | - Rigoberto Hernandez
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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36
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Brancolini G, Bellucci L, Maschio MC, Di Felice R, Corni S. The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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John T, Gladytz A, Kubeil C, Martin LL, Risselada HJ, Abel B. Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles. NANOSCALE 2018; 10:20894-20913. [PMID: 30225490 DOI: 10.1039/c8nr04506b] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Society is increasingly exposed to nanoparticles as they are ubiquitous in nature and introduced as man-made air pollutants and as functional ingredients in cosmetic products as well as in nanomedicine. Nanoparticles differ in size, shape and material properties. In addition to their intended function, the side effects on biochemical processes in organisms remain unclear. Nanoparticles can significantly influence the nucleation and aggregation process of peptides. The development of several neurodegenerative diseases, such as Alzheimer's disease, is related to the aggregation of peptides into amyloid fibrils. However, there is no comprehensive or universal mechanism to predict or explain apparent acceleration or inhibition of these aggregation processes. In this work, selected studies and possible mechanisms for amyloid peptide nucleation and aggregation, in the presence of nanoparticles, are highlighted. These studies are discussed in the context of recent data from our group on the role of gold nanoparticles in amyloid peptide aggregation using experimental methods and large-scale molecular dynamics simulations. A complex interplay of the surface properties of the nanoparticles, the properties of the peptides, as well as the resulting forces between both the nanoparticles and the peptides, appear to determine whether amyloid peptide aggregation is influenced, catalysed or inhibited by the presence of nanoparticles.
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Affiliation(s)
- Torsten John
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.
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38
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Connell DJ, Gebril A, Khan MAH, Patwardhan SV, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Rationalising drug delivery using nanoparticles: a combined simulation and immunology study of GnRH adsorbed to silica nanoparticles. Sci Rep 2018; 8:17115. [PMID: 30459397 PMCID: PMC6244087 DOI: 10.1038/s41598-018-35143-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/26/2018] [Indexed: 11/30/2022] Open
Abstract
Silica nanoparticles (SiNPs) have been shown to have significant potential for drug delivery and as adjuvants for vaccines. We have simulated the adsorption of GnRH-I (gonadotrophin releasing hormone I) and a cysteine-tagged modification (cys-GnRH-I) to model silica surfaces, as well as its conjugation to the widely-used carrier protein bovine serum albumin (BSA). Our subsequent immunological studies revealed no significant antibody production was caused by the peptide-SiNP systems, indicating that the treatment was not effective. However, the testosterone response with the native peptide-SiNPs indicated a drug effect not found with cys-GnRH-I-SiNPs; this behaviour is explained by the specific orientation of the peptides at the silica surface found in the simulations. With the BSA systems, we found significant testosterone reduction, particularly for the BSA-native conjugates, and an antibody response that was notably higher with the SiNPs acting as an adjuvant; this behaviour again correlates well with the epitope presentation predicted by the simulations. The range of immunological and hormone response can therefore be interpreted and understood by the simulation results and the presentation of the peptides to solution, paving the way for the future rational design of drug delivery and vaccine systems guided by biomolecular simulation.
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Affiliation(s)
- David J Connell
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Ayman Gebril
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Mohammad A H Khan
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Siddharth V Patwardhan
- Department of Chemical and Biological Engineering, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Karina Kubiak-Ossowska
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Valerie A Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK.
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39
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Applications of rice protein in nanomaterials synthesis, nanocolloids of rice protein, and bioapplicability. Int J Biol Macromol 2018; 120:394-404. [PMID: 30144545 DOI: 10.1016/j.ijbiomac.2018.08.101] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/07/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022]
Abstract
Rice protein conjugated nanomaterials were synthesized and characterized by using anionic and cationic forms of rice protein. Both forms showed unique characteristic features when used in in situ reaction conditions for synthesizing the protein stabilized gold (Au) and silver (Ag) nanoparticles (NPs). Au NPs synthesis was highly facilitated than Ag NPs synthesis while the reverse was true when rice protein was simply used in the basic medium. Photophysical behavior clearly showed the contributions of both electrostatic and non-electrostatic interactions driving the rice protein surface adsorption on nanometallic surfaces. Rice protein conjugated NPs were easily transferred and extracted into the organic phase while the extraction process was related to the amount of protein coating. Under the controlled pH reaction conditions, rice protein - dye colored NPs were synthesized which were further characterized by the DLS and SDS Page analysis. Both rice protein conjugated Au/Ag NPs and rice protein NPs showed remarkable biocompatibility with blood cells. These NPs demonstrated their excellent ability to selectively extract protein fractions from complex biological fluid like serum. The results proposed significant applications of rice protein conjugated NPs in biological systems as well as bio-nanotechnology.
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40
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Dongmo Foumthuim CJ, Corazza A, Esposito G, Fogolari F. Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces. MOLECULAR BIOSYSTEMS 2018; 13:2625-2637. [PMID: 29051937 DOI: 10.1039/c7mb00464h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.
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41
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Bortot A, Zanzoni S, D'Onofrio M, Assfalg M. Specific Interaction Sites Determine Differential Adsorption of Protein Structural Isomers on Nanoparticle Surfaces. Chemistry 2018; 24:5911-5919. [PMID: 29446497 DOI: 10.1002/chem.201705994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 11/08/2022]
Abstract
In biological systems, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric ubiquitin (Ub) dimers by NPs was investigated by solution NMR spectroscopy. Lys63- and Lys48-linked Ub2 were adsorbed by large anionic NPs with different affinities, whereas the binding strength was similar in the cases of smaller particles. After the incorporation of paramagnetic tags into NPs, the observed site-resolved paramagnetic footprints provided a high-resolution map of the different protein surfaces binding to NPs. The approach described could be extended to further protein isoforms and more specialized NP systems to allow better control of the interactions between NPs and protein targets.
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Affiliation(s)
- Andrea Bortot
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Serena Zanzoni
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
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42
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Brancolini G, Maschio MC, Cantarutti C, Corazza A, Fogolari F, Bellotti V, Corni S, Esposito G. Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants. NANOSCALE 2018; 10:4793-4806. [PMID: 29469914 DOI: 10.1039/c7nr06808e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere with the formation of protein dimers and multimers in solution. A very special class of interactors are nanoparticles thanks to the extremely efficient extension of their interaction surface. In particular citrate-coated gold nanoparticles (cit-AuNPs) were recently investigated with amyloidogenic protein β2-microglobulin (β2m). Here we present the computational studies on two challenging models known for their enhanced amyloidogenic propensity, namely ΔN6 and D76N β2m naturally occurring variants, and disclose the role of cit-AuNPs on their fibrillogenesis. The proposed interaction mechanism lies in the interference of the cit-AuNPs with the protein dimers at the early stages of aggregation, that induces dimer disassembling. As a consequence, natural fibril formation can be inhibited. Relying on the comparison between atomistic simulations at multiple levels (enhanced sampling molecular dynamics and Brownian dynamics) and protein structural characterisation by NMR, we demonstrate that the cit-AuNPs interactors are able to inhibit protein dimer assembling. As a consequence, the natural fibril formation is also inhibited, as found in experiment.
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Affiliation(s)
- Giorgia Brancolini
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.
| | | | - Cristina Cantarutti
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy
| | - Alessandra Corazza
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy
| | - Federico Fogolari
- Dipartimento di Scienza Mediche e Biologiche (DSMB), University of Udine, Piazzale Kolbe 3, 33100 Udine, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy
| | - Vittorio Bellotti
- Dipartimento di Medicina Molecolare, Universita' di Pavia, Via Taramelli 3, 27100 Pavia, Italy and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy and Division of Medicine, University College of London, London NW3 2PF, UK
| | - Stefano Corni
- Department of Chemical Science, University of Padova, via VIII Febbraio 2, 35122 Padova and Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Gennaro Esposito
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy. and Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro, 305 - 00136 Roma, Italy and Science and Math Division, New York University at Abu Dhabi, Abu Dhabi, United Arab Emirates.
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43
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Cantarutti C, Bertoncin P, Posocco P, Hunashal Y, Giorgetti S, Bellotti V, Fogolari F, Esposito G. The interaction of β2-microglobulin with gold nanoparticles: impact of coating, charge and size. J Mater Chem B 2018; 6:5964-5974. [PMID: 32254716 DOI: 10.1039/c8tb01129j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gold nanoparticles (AuNPs) have been proved to be ideal scaffolds to build nanodevices whose performance can be tuned by changing their coating.
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Affiliation(s)
| | - Paolo Bertoncin
- Dipartimento di Scienze della Vita
- Università di Trieste
- 34128 Trieste
- Italy
| | - Paola Posocco
- Dipartimento di Ingegneria ed Architettura
- Università di Trieste
- 34127 Trieste
- Italy
| | | | - Sofia Giorgetti
- Dipartimento di Medicina Molecolare
- Università di Pavia
- 27100 Pavia
- Italy
| | - Vittorio Bellotti
- Dipartimento di Medicina Molecolare
- Università di Pavia
- 27100 Pavia
- Italy
- Division of Medicine
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44
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Ding HM, Ma YQ. Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity. NANOSCALE HORIZONS 2018; 3:6-27. [PMID: 32254106 DOI: 10.1039/c7nh00138j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.
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Affiliation(s)
- Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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45
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D’Urso L, Condorelli M, Puglisi O, Tempra C, Lolicato F, Compagnini G, La Rosa C. Detection and characterization at nM concentration of oligomers formed by hIAPP, Aβ(1–40) and their equimolar mixture using SERS and MD simulations. Phys Chem Chem Phys 2018; 20:20588-20596. [DOI: 10.1039/c7cp08552d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report a structural investigation on IAPP, Aβ(1–40) and their equimolar mixture at nM concentration using SERS spectroscopy and molecular dynamic simulations.
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Affiliation(s)
- Luisa D’Urso
- Department of Chemical Sciences
- Viale A. Doria 6-95125 Catania
- Italy
| | | | - Orazio Puglisi
- Department of Chemical Sciences
- Viale A. Doria 6-95125 Catania
- Italy
| | - Carmelo Tempra
- Department of Chemical Sciences
- Viale A. Doria 6-95125 Catania
- Italy
| | - Fabio Lolicato
- Department of Physics
- University of Helsinki
- FI-00014 Helsinki
- Finland
- Laboratory of Physics
| | | | - Carmelo La Rosa
- Department of Chemical Sciences
- Viale A. Doria 6-95125 Catania
- Italy
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46
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Cantarutti C, Raj G, Fogolari F, Giorgetti S, Corazza A, Bellotti V, Naumov P, Esposito G. Interference of citrate-stabilized gold nanoparticles with β2-microglobulin oligomeric association. Chem Commun (Camb) 2018; 54:5422-5425. [DOI: 10.1039/c8cc01053f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Citrate-coated gold nanoparticles interfere with the association equilibria of β2-microglobulin and thus inhibit the early events of fibrillogenesis.
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Affiliation(s)
| | - Gijo Raj
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | | | - Sofia Giorgetti
- Dipartimento di Medicina Molecolare
- Università di Pavia
- 27100 Pavia
- Italy
| | | | - Vittorio Bellotti
- Dipartimento di Medicina Molecolare
- Università di Pavia
- 27100 Pavia
- Italy
- Division of Medicine
| | - Panče Naumov
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - Gennaro Esposito
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
- INBB
- 00136 Roma
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47
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Zhang X, Song C, Ma G, Wei W. Mechanical determination of particle–cell interactions and the associated biomedical applications. J Mater Chem B 2018; 6:7129-7143. [DOI: 10.1039/c8tb01590b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mechanical determination of particle–cell interactions and the associated biomedical applications.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Cui Song
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
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48
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Short-Chain Alkanethiol Coating for Small-Size Gold Nanoparticles Supporting Protein Stability. MAGNETOCHEMISTRY 2017. [DOI: 10.3390/magnetochemistry3040040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Farrell MJ, Reaume RJ, Pradhan AK. Visual Detection of Denatured Glutathione Peptides: A Facile Method to Visibly Detect Heat Stressed Biomolecules. Sci Rep 2017; 7:2604. [PMID: 28572597 PMCID: PMC5453926 DOI: 10.1038/s41598-017-02899-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
Every year pharmaceutical companies use significant resources to mitigate aggregation of pharmaceutical drug products. Specifically, peptides and proteins that have been denatured or degraded can lead to adverse patient reactions such as undesired immune responses. Current methods to detect aggregation of biological molecules are limited to costly and time consuming processes such as high pressure liquid chromatography, ultrahigh pressure liquid chromatography and SDS-PAGE gels. Aggregation of pharmaceutical drug products can occur during manufacturing, processing, packaging, shipment and storage. Therefore, a facile in solution detection method was evaluated to visually detect denatured glutathione peptides, utilizing gold nanoparticle aggregation via 3-Aminopropyltreithoxysilane. Glutathione was denatured using a 70 °C water bath to create an accelerated heat stressed environment. The peptide, gold nanoparticle and aminosilane solution was then characterized via, UV-Vis spectroscopy, FTIR spectroscopy, dynamic light scattering and scanning electron microscopy. Captured images and resulting absorbance spectra of the gold nanoparticle, glutathione, and aminosilane complex demonstrated visual color changes detectable with the human eye as a function of the denaturation time. This work serves as an extended proof of concept for fast in solution detection methods for glutathione peptides that have experienced heat stress.
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Affiliation(s)
- Monique J Farrell
- Center for Materials Research, Norfolk State University, 700 Park Ave., Norfolk, VA, 23504, USA
| | - Robert J Reaume
- Center for Materials Research, Norfolk State University, 700 Park Ave., Norfolk, VA, 23504, USA
| | - Aswini K Pradhan
- Center for Materials Research, Norfolk State University, 700 Park Ave., Norfolk, VA, 23504, USA.
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50
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Cantarutti C, Raimondi S, Brancolini G, Corazza A, Giorgetti S, Ballico M, Zanini S, Palmisano G, Bertoncin P, Marchese L, Patrizia Mangione P, Bellotti V, Corni S, Fogolari F, Esposito G. Citrate-stabilized gold nanoparticles hinder fibrillogenesis of a pathological variant of β 2-microglobulin. NANOSCALE 2017; 9:3941-3951. [PMID: 28265615 DOI: 10.1039/c6nr09362k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoparticles have repeatedly been shown to enhance fibril formation when assayed with amyloidogenic proteins. Recently, however, evidence casting some doubt about the generality of this conclusion started to emerge. Therefore, to investigate further the influence of nanoparticles on the fibrillation process, we used a naturally occurring variant of the paradigmatic amyloidogenic protein β2-microglobulin (β2m), namely D76N β2m where asparagine replaces aspartate at position 76. This variant is responsible for aggressive systemic amyloidosis. After characterizing the interaction of the variant with citrate-stabilized gold nanoparticles (Cit-AuNPs) by NMR and modeling, we analyzed the fibril formation by three different methods: thioflavin T fluorescence, native agarose gel electrophoresis and transmission electron microscopy. The NMR evidence indicated a fast-exchange interaction involving preferentially specific regions of the protein that proved, by subsequent modeling, to be consistent with a dimeric adduct interacting with Cit-AuNPs. The fibril detection assays showed that AuNPs are able to hamper D76N β2m fibrillogenesis through an effective interaction that competes with protofibril formation or recruitment. These findings open promising perspectives for the optimization of the nanoparticle surface to design tunable interactions with proteins.
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Affiliation(s)
| | - Sara Raimondi
- Dipartimento Medicina Molecolare, Università di Pavia, Via Taramelli 3, 27100 Pavia, Italy and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | | | - Alessandra Corazza
- DSMB, Università di Udine, P.le Kolbe 4, 33100 Udine, Italy. and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | - Sofia Giorgetti
- Dipartimento Medicina Molecolare, Università di Pavia, Via Taramelli 3, 27100 Pavia, Italy and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | - Maurizio Ballico
- Science and Math Division, New York University at Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefano Zanini
- Science and Math Division, New York University at Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Giovanni Palmisano
- Department of Chemical and Environmental Engineering, Masdar Institute of Science and Technology, PO Box 54224, Abu Dhabi, United Arab Emirates
| | - Paolo Bertoncin
- Dipartimento Scienze della Vita, Università di Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Loredana Marchese
- Dipartimento Medicina Molecolare, Università di Pavia, Via Taramelli 3, 27100 Pavia, Italy and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | - P Patrizia Mangione
- Dipartimento Medicina Molecolare, Università di Pavia, Via Taramelli 3, 27100 Pavia, Italy and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy and Division of Medicine, University College of London, London NW3 2PF, UK
| | - Vittorio Bellotti
- Dipartimento Medicina Molecolare, Università di Pavia, Via Taramelli 3, 27100 Pavia, Italy and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy and Division of Medicine, University College of London, London NW3 2PF, UK
| | - Stefano Corni
- CNR Istituto Nanoscienze, Via Campi 213/A, 41125 Modena, Italy.
| | - Federico Fogolari
- DSMB, Università di Udine, P.le Kolbe 4, 33100 Udine, Italy. and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy
| | - Gennaro Esposito
- DSMB, Università di Udine, P.le Kolbe 4, 33100 Udine, Italy. and INBB, Viale Medaglie d'Oro 305, 00136 Roma, Italy and Science and Math Division, New York University at Abu Dhabi, Abu Dhabi, United Arab Emirates
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