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Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (29 November 2019) | Viewed by 20569

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Special Issue Editor

Prof. Dr. Maria Cristina Menziani

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Guest Editor

Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
Interests: computational chemistry; computational spectroscopy; rational drug design; molecular dynamics; DFT; quantitative-structure activity relationships; protein-nanoparticle interactions
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Special Issue Information

Dear Colleagues,

Nanoparticles are enjoying rapid growth as promising tools for biomedical applications in the field of imaging, targeting, therapy and in vitro diagnostics.

In order to fully exploit their potential and reduce the gap between bench discoveries and clinical applications, precise control of the biological activity and the fate of nanoparticles is necessary. It is well-accepted that the actual biological identity of nanoparticles is provided by the adsorbed molecules on their surfaces, i.e. the biomolecular corona around nanoparticles, therefore, there is an urgent need to deepen our understending of the mechanisms that govern the interatomic interactions between nanoparticles and biological molecules.

Computational simulation provides fundamental knowledge enabling us to unravel the underlying principles and elucidate the molecular mechanisms of specific interactions and of the dynamics that nanoparticles induce on biological molecules upon binding.

This Special Issue will cover some of the recent significant advances in the field of modelling and computational simulations of the interactions between nanoparticles and biomolecules. Reviews, full papers and short communications covering the methodological and theoretical aspects and interdisciplinary approaches underlying the potential interpretation of experimental data and applications are all welcome.

Prof. Maria Cristina Menziani
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Nanoparticle biomolecule interactions
Nanoparticle DNA interactions
Nanoparticle membrane interactions
Structure-function relationships
Advanced molecular modelling techniques
Molecular dynamics simulations
Chemoinformatics

Published Papers (5 papers)

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Research

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15 pages, 4707 KiB

Open AccessArticle

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

by Giorgia Brancolini, Hender Lopez, Stefano Corni and Valentina Tozzini

Int. J. Mol. Sci. 2019, 20(16), 3866; https://doi.org/10.3390/ijms20163866 - 08 Aug 2019

Cited by 10 | Viewed by 2583

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. Full article

(This article belongs to the Special Issue Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations)

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13 pages, 1883 KiB

Open AccessArticle

Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles

by Francesco Tavanti, Alfonso Pedone and Maria Cristina Menziani

Int. J. Mol. Sci. 2019, 20(14), 3539; https://doi.org/10.3390/ijms20143539 - 19 Jul 2019

Cited by 34 | Viewed by 4828

Abstract

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration. Full article

(This article belongs to the Special Issue Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations)

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20 pages, 8142 KiB

Open AccessArticle

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

by Lara Giussani, Gloria Tabacchi, Salvatore Coluccia and Ettore Fois

Int. J. Mol. Sci. 2019, 20(12), 2965; https://doi.org/10.3390/ijms20122965 - 18 Jun 2019

Cited by 7 | Viewed by 3291

Abstract

Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas. Full article

(This article belongs to the Special Issue Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations)

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13 pages, 7772 KiB

Open AccessArticle

Quantitative Imaging of Gd Nanoparticles in Mice Using Benchtop Cone-Beam X-ray Fluorescence Computed Tomography System

by Siyuan Zhang, Liang Li, Jiayou Chen, Zhiqiang Chen, Wenli Zhang and Hongbing Lu

Int. J. Mol. Sci. 2019, 20(9), 2315; https://doi.org/10.3390/ijms20092315 - 10 May 2019

Cited by 39 | Viewed by 3882

Abstract

Nanoparticles (NPs) are currently under intensive research for their application in tumor diagnosis and therapy. X-ray fluorescence computed tomography (XFCT) is considered a promising non-invasive imaging technique to obtain the bio-distribution of nanoparticles which include high-Z elements (e.g., gadolinium (Gd) or gold (Au)). In the present work, a set of experiments with quantitative imaging of GdNPs in mice were performed using our benchtop XFCT device. GdNPs solution which consists of 20 mg/mL NaGdF4 was injected into a nude mouse and two tumor-bearing mice. Each mouse was then irradiated by a cone-beam X-ray source produced by a conventional X-ray tube and a linear-array photon counting detector with a single pinhole collimator was placed on one side of the beamline to record the intensity and spatial information of the X-ray fluorescent photons. The maximum likelihood iterative algorithm with scatter correction and attenuation correction method was applied for quantitative reconstruction of the XFCT images. The results show that the distribution of GdNPs in each target slice (containing liver, kidney or tumor) was well reconstructed and the concentration of GdNPs deposited in each organ was quantitatively estimated, which indicates that this benchtop XFCT system provides convenient tools for obtaining accurate concentration distribution of NPs injected into animals and has potential for imaging of nanoparticles in vivo. Full article

(This article belongs to the Special Issue Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations)

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Review

Jump to: Research

22 pages, 4838 KiB

Open AccessReview

Application of Solid-State Nanopore in Protein Detection

by Yuhan Luo, Linlin Wu, Jing Tu and Zuhong Lu

Int. J. Mol. Sci. 2020, 21(8), 2808; https://doi.org/10.3390/ijms21082808 - 17 Apr 2020

Cited by 21 | Viewed by 5350

Abstract

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks. Full article

(This article belongs to the Special Issue Understanding the Nanoparticle-Biomolecule Interactions: Insight Form Computational Modelling and Atomistic Simulations)

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