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Advances in Nanoparticles-Biomolecules Interactions
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Advances in Nanoparticles-Biomolecules Interactions

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 (27 August 2021) | Viewed by 15064

Special Issue Editors

Prof. Dr. Maria Cristina Menziani

E-Mail Website1 Website2
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
Special Issues, Collections and Topics in MDPI journals
Dr. Francesco Tavanti

E-Mail Website
Guest Editor
CNR Nano, Via Campi 213, 41125 Modena, Italy
Interests: computational chemistry; protein–nanoparticle interactions; amorphous materials; molecular dynamics

Special Issue Information

Dear Colleagues,

Nanoparticles are undergoing 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 future use 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 understanding of the mechanisms that govern the interatomic interactions between nanoparticles and biological molecules.

Experimental analysis and computer simulations elucidate the molecular mechanisms of specific interactions and the dynamics that nanoparticles induce on biological molecules upon binding from different points of view.

This Special Issue will cover 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, experimental and theoretical aspects and interdisciplinary approaches underlying the potential interpretation of experimental data and applications are all welcome.

Prof. Dr. Maria Cristina Menziani
Dr. Francesco Tavanti
Guest Editors

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
  • nanoparticles
  • structure–function relationships
  • advanced molecular modelling techniques
  • self-assembly
  • molecular dynamics simulations
  • chemoinformatics
  • nanomedicine
  • proteins
  • drug delivery
  • machine learning

Published Papers (6 papers)

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Research

31 pages, 7405 KiB  
Article
Light Tailoring: Impact of UV-C Irradiation on Biosynthesis, Physiognomies, and Clinical Activities of Morus macroura-Mediated Monometallic (Ag and ZnO) and Bimetallic (Ag–ZnO) Nanoparticles
by Sumaira Anjum, Amna Komal Khan, Anza Qamar, Noor Fatima, Samantha Drouet, Sullivan Renouard, Jean Philippe Blondeau, Bilal Haider Abbasi and Christophe Hano
Int. J. Mol. Sci. 2021, 22(20), 11294; https://doi.org/10.3390/ijms222011294 - 19 Oct 2021
Cited by 10 | Viewed by 2817
Abstract
A nano-revolution based on the green synthesis of nanomaterials could affect all areas of human life, and nanotechnology represents a propitious platform for various biomedical applications. During the synthesis of nanoparticles, various factors can control their physiognomies and clinical activities. Light is one [...] Read more.
A nano-revolution based on the green synthesis of nanomaterials could affect all areas of human life, and nanotechnology represents a propitious platform for various biomedical applications. During the synthesis of nanoparticles, various factors can control their physiognomies and clinical activities. Light is one of the major physical factors that can play an important role in tuning/refining the properties of nanoparticles. In this study, biocompatible monometallic (AgNPs and ZnONPs) and bimetallic Ag–ZnONPs (0.1/0.1 and 0.1/0.5) were synthesized under UV-C light irradiation from the leaf extract of Morus macroura, which possesses enriched TPC (4.238 ± 0.26 mg GAE/g DW) and TFC (1.073 ± 0.18 mg QE/g DW), as well as strong FRSA (82.39%). These green synthesized NPs were evaluated for their anti-diabetic, anti-glycation, and biocompatibility activities. Furthermore, their anti-cancerous activity against HepG2 cell lines was assessed in terms of cell viability, production of reactive oxygen/nitrogen species, mitochondrial membrane potential, and apoptotic caspase-3/7 expression and activity. Synthesized NPs were characterized by techniques including ultraviolet-visible spectroscopy, SEM, EDX, FTIR, and XRD. UV-C mediated monometallic and bimetallic NPs showed well-defined characteristic shapes with a more disperse particle distribution, definite crystalline structures, and reduced sizes as compared to their respective controls. In the case of clinical activities, the highest anti-diabetic activity (67.77 ± 3.29% against α-amylase and 35.83 ± 2.40% against α-glucosidase) and anti-glycation activity (37.68 ± 3.34% against pentosidine-like AGEs and 67.87 ± 2.99% against vesperlysine-like AGEs) was shown by UV-C mediated AgNPs. The highest biocompatibility (IC50 = 14.23 ± 1.68 µg/mL against brine shrimp and 2.48 ± 0.32% hemolysis of human red blood cells) was shown by UV-C mediated ZnONPs. In the case of anti-cancerous activities, the lowest viability (23.45 ± 1.40%) with enhanced ROS/NOS production led to a significant disruption of mitochondrial membrane potential and greater caspase-3/7 gene expression and activity by UV-C mediated bimetallic Ag–ZnONPs (0.1/0.5). The present work highlights the positive effects of UV-C light on physico-chemical physiognomies as well as the clinical activities of NPs. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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17 pages, 9723 KiB  
Article
A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations
by Congcong Li, Zhongkui Lu, Min Wang, Siao Chen, Lu Han and Weiwei Han
Int. J. Mol. Sci. 2021, 22(19), 10813; https://doi.org/10.3390/ijms221910813 - 06 Oct 2021
Cited by 3 | Viewed by 1896
Abstract
Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this [...] Read more.
Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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15 pages, 8525 KiB  
Article
Silver Nanoparticles as a Tool for the Study of Spontaneous Aggregation of Immunoglobulin Monoclonal Free Light Chains
by Anna Lizoń, Joanna Tisończyk, Marta Gajewska and Ryszard Drożdż
Int. J. Mol. Sci. 2021, 22(18), 9703; https://doi.org/10.3390/ijms22189703 - 08 Sep 2021
Cited by 2 | Viewed by 2177
Abstract
Some misfolded proteins, e.g., immunoglobulin monoclonal free light chains (FLC), tend to form fibrils. Protein deposits in tissue may lead to amyloidosis and dysfunction of different organs. There is currently no technique allowing for the identification of FLC that are prone to aggregate. [...] Read more.
Some misfolded proteins, e.g., immunoglobulin monoclonal free light chains (FLC), tend to form fibrils. Protein deposits in tissue may lead to amyloidosis and dysfunction of different organs. There is currently no technique allowing for the identification of FLC that are prone to aggregate. The development of such a method would enable the early selection of patients at high risk of developing amyloidosis. The aim of this study was to investigate whether silver nanoparticles (AgNPs) could be a useful tool to study the process of aggregation of FLC and their susceptibility to form the protein deposits. Mixtures of AgNPs and urine samples from patients with multiple myeloma were prepared. To evaluate the aggregation process of nanoparticles coated with proteins, UV-visible spectroscopy, transmission electron microscopy, and the original laser light scattering method were used. It has been shown that some clones of FLC spontaneously triggered aggregation of the nanoparticles, while in the presence of others, the nanoparticle solution became hyperstable. This is probably due to the structure of the chains themselves, unique protein-AgNPs interactions and perhaps correlates with the tendency of some FLC clones to form deposits. Nanoparticle technology has proven to be helpful in identifying clones of immunoglobulin FLC that tend to aggregate. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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24 pages, 3489 KiB  
Article
Fe-N Co-Doped Titanium Dioxide Nanoparticles Induce Cell Death in Human Lung Fibroblasts in a p53-Independent Manner
by Ionela Cristina Nica, Miruna S. Stan, Roua G. Popescu, Nicoleta Nicula, Robert Ducu, Lucian Diamandescu and Anca Dinischiotu
Int. J. Mol. Sci. 2021, 22(17), 9627; https://doi.org/10.3390/ijms22179627 - 06 Sep 2021
Cited by 3 | Viewed by 2173
Abstract
The advancement of nanotechnology in the last decade has developed an abundance of novel and intriguing TiO2-based nanomaterials that are widely used in many sectors, including industry (as a food additive and colorant in cosmetics, paints, plastics, and toothpaste) and biomedicine [...] Read more.
The advancement of nanotechnology in the last decade has developed an abundance of novel and intriguing TiO2-based nanomaterials that are widely used in many sectors, including industry (as a food additive and colorant in cosmetics, paints, plastics, and toothpaste) and biomedicine (photoelectrochemical biosensing, implant coatings, drug delivery, and new emerging antimicrobial agents). Therefore, the increased use of engineered nanomaterials in the industry has raised serious concern about human exposure and their unexpected cytotoxic effects. Since inhalation is considered the most relevant way of absorbing nanomaterials, different cell death mechanisms induced in MRC-5 lung fibroblasts, following the exposure to functionalized TiO2 NPs, were investigated. Long-term exposure to TiO2 nanoparticles co-doped with 1% of iron and nitrogen led to the alteration of p53 protein activity and the gene expression controlled by this suppressor (NF-kB and mdm2), DNA damage, cell cycle disruptions at the G2/M and S phases, and lysosomal membrane permeabilization and the subsequent release of cathepsin B, triggering the intrinsic pathway of apoptosis in a Bax- and p53-independent manner. Our results are of major significance, contributing to the understanding of the mechanisms underlying the interaction of these nanoparticles with in vitro biological systems, and also providing useful information for the development of new photocatalytic nanoparticles that are active in the visible spectrum, but with increased biocompatibility. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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14 pages, 4270 KiB  
Article
Computational Insight on the Interaction of Common Blood Proteins with Gold Nanoparticles
by Francesco Tavanti and Maria Cristina Menziani
Int. J. Mol. Sci. 2021, 22(16), 8722; https://doi.org/10.3390/ijms22168722 - 13 Aug 2021
Cited by 4 | Viewed by 2321
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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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15 pages, 2216 KiB  
Article
Activity of CdTe Quantum-Dot-Tagged Superoxide Dismutase and Its Analysis in Capillary Electrophoresis
by Natalia Zaręba, Łukasz Lewandowski, Dominika Kunachowicz, Rene Kizek and Marta Kepinska
Int. J. Mol. Sci. 2021, 22(11), 6156; https://doi.org/10.3390/ijms22116156 - 07 Jun 2021
Viewed by 2522
Abstract
Quantum dots (QDs) have a broad range of applications in cell biolabeling, cancer treatment, metastasis imaging, and therapeutic drug monitoring. Despite their wide use, relatively little is known about their influence on other molecules. Interactions between QDs and proteins can influence the properties [...] Read more.
Quantum dots (QDs) have a broad range of applications in cell biolabeling, cancer treatment, metastasis imaging, and therapeutic drug monitoring. Despite their wide use, relatively little is known about their influence on other molecules. Interactions between QDs and proteins can influence the properties of both nanoparticles and proteins. The effect of mercaptosuccinic acid-capped CdTe QDs on intercellular copper–zinc superoxide dismutase (SOD1)—one of the main enzymatic antioxidants—was investigated. Incubation of SOD1 with QDs caused an increase in SOD1 activity, unlike in the case of CdCl2, which inhibited SOD1. Moreover, this effect on SOD1 increased with the size and potential of QDs, although the effect became clearly visible in higher concentrations of QDs. The intensity of QD-SOD1 fluorescence, analyzed with the use of capillary electrophoresis with laser-induced fluorescence detection, was dependent on SOD1 concentration. In the case of green QDs, the fluorescence signal decreased with increasing SOD1 concentration. In contrast, the signal strength for Y-QD complexes was not dependent on SOD1 dilutions. The migration time of QDs and their complexes with SOD1 varied depending on the type of QD used. The migration time of G-QD complexes with SOD1 differed slightly. However, in the case of Y-QD complexes with SOD1, the differences in the migration time were not dependent on SOD concentration. This research shows that QDs interact with SOD1 and the influence of QDs on SOD activity is size-dependent. With this knowledge, one might be able to control the activation/inhibition of specific enzymes, such as SOD1. Full article
(This article belongs to the Special Issue Advances in Nanoparticles-Biomolecules Interactions)
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