Multiscale Modelling of Bionano Interface

López, Hender; Brandt, Erik G.; Mirzoev, Alexander; Zhurkin, Dmitry; Lyubartsev, Alexander P.; Lobaskin, Vladimir

doi:10.1007/978-3-319-47754-1_7

Cited by 17 publications

(27 citation statements)

References 62 publications

(76 reference statements)

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“…This strategy is quite elegant and allows for a complete assessment of the chemical nature of the interaction as well as for the protein affinity and behavior on the NP surface. However, this approach is also quite difficult, and the correlation between simulated conditions of interactions and reality is not always straight forward (Lopez et al, 2017).…”

Section: Analysis Of the Protein Coronamentioning

confidence: 99%

Recent Advances in Understanding the Protein Corona of Nanoparticles and in the Formulation of “Stealthy” Nanomaterials

Rampado

Crotti

Caliceti

et al. 2020

Front. Bioeng. Biotechnol.

234

166

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In the last decades, the staggering progress in nanotechnology brought around a wide and heterogeneous range of nanoparticle-based platforms for the diagnosis and treatment of many diseases. Most of these systems are designed to be administered intravenously. This administration route allows the nanoparticles (NPs) to widely distribute in the body and reach deep organs without invasive techniques. When these nanovectors encounter the biological environment of systemic circulation, a dynamic interplay occurs between the circulating proteins and the NPs, themselves. The set of proteins that bind to the NP surface is referred to as the protein corona (PC). PC has a critical role in making the particles easily recognized by the innate immune system, causing their quick clearance by phagocytic cells located in organs such as the lungs, liver, and spleen. For the same reason, PC defines the immunogenicity of NPs by priming the immune response to them and, ultimately, their immunological toxicity. Furthermore, the protein corona can cause the physical destabilization and agglomeration of particles. These problems induced to consider the PC only as a biological barrier to overcome in order to achieve efficient NP-based targeting. This review will discuss the latest advances in the characterization of PC, development of stealthy NP formulations, as well as the manipulation and employment of PC as an alternative resource for prolonging NP half-life, as well as its use in diagnostic applications.

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Section: Analysis Of the Protein Coronamentioning

confidence: 99%

Recent Advances in Understanding the Protein Corona of Nanoparticles and in the Formulation of “Stealthy” Nanomaterials

Rampado

Crotti

Caliceti

et al. 2020

Front. Bioeng. Biotechnol.

234

166

View full text Add to dashboard Cite

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“…It was expected that this representation could account only roughly for the binding mode geometry of the protein to NP; however, it was much less computationally expensive and required the optimization of fewer parameters. Furthermore, as the simulated NP is highly hydrophobic, the interaction parameters for the NP-P can be chosen by analogy with [24,29]. In this model, the NP and the amino acids were characterized by a hydrophobicity index, which can be defined in different ways, and only one single free parameter was needed to parameterize the FF.…”

Section: Methodsmentioning

confidence: 99%

“…In this model, the NP and the amino acids were characterized by a hydrophobicity index, which can be defined in different ways, and only one single free parameter was needed to parameterize the FF. Following the same scheme as in [24,29], electrostatics was represented with a Debye-Hückel potential, to account for the ionic strength of the solution. The functional forms and other details are reported in the Supplementary Materials (Section S2).…”

Section: Methodsmentioning

confidence: 99%

Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin

Brancolini

López

Corni

et al. 2019

IJMS

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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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“…In order to address the opportunities offered by modelling the toxicity and properties of nanoparticles, the European Commission funded five modelling projects: MODERN (Brehm et al, 2017), Mod-Enp-Tox (Vriens et al, 2017), PreNanoTox, MembraneNanoPart (Lopez et al, 2017) and NanoPUZZLES (Richarz et al, 2017) from 2013-2015 and a further project to assist in the management of data: eNanoMapper (Jeliazkova et al, 2015), from 2014 Ð 2017, within the EU NanoSafety Cluster (https://www.nanosafetycluster.eu/). Herein, these projects are collectively referred to as the NanoSafety Modelling Cluster, originally comprising the five projects and later joined by eNanoMapper.…”

Section: Introductionmentioning

confidence: 99%

Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology

Puzyn

Jeliazkova

Sarimveis

et al. 2018

Food and Chemical Toxicology

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Nanotechnology and the production of nanomaterials have been expanding rapidly in recent years. Since many types of engineered nanoparticles are suspected to be toxic to living organisms and to have a negative impact on the environment, the process of designing new nanoparticles and their applications must be accompanied by a thorough risk analysis. (Quantitative) Structure-Activity Relationship ([Q]SAR) modelling creates promising options among the available methods for the risk assessment. These in silico models can be used to predict a variety of properties, including the toxicity of newly designed nanoparticles. However, (Q)SAR models must be appropriately validated to ensure the clarity, consistency and reliability of predictions. This paper is a joint initiative from recently completed European research projects focused on developing (Q)SAR methodology for nanomaterials. The aim was to interpret and expand the guidance for the well-known "OECD Principles for the Validation, for Regulatory Purposes, of (Q)SAR Models", with reference to nano-(Q)SAR, and present our opinions on the criteria to be fulfilled for models developed for nanoparticles.

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Multiscale Modelling of Bionano Interface

Cited by 17 publications

References 62 publications

Recent Advances in Understanding the Protein Corona of Nanoparticles and in the Formulation of “Stealthy” Nanomaterials

Recent Advances in Understanding the Protein Corona of Nanoparticles and in the Formulation of “Stealthy” Nanomaterials

Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin

Perspectives from the NanoSafety Modelling Cluster on the validation criteria for (Q)SAR models used in nanotechnology

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