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Molecular Simulations of Functionalized Nanoscale Materials
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Molecular Simulations of Functionalized Nanoscale Materials

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 (30 April 2022) | Viewed by 19069

Special Issue Editors

Dr. Paul Mulheran

E-Mail Website
Guest Editor
Department of Chemical and Process Engineering, University of Strathclyde, Glasgow G1 1XJ, UK
Interests: protein adsorption; protein aggregation and amyloid formation; modelling and simulation; nanotechnology; antibodies; biopolymers; diagnostics; xerogels and porous materials
Dr. Giorgia Brancolini

E-Mail Website
Co-Guest Editor
Consiglio Nazionale delle Ricerche, CNR NANO - Institute Nanoscience, Center S3, via G. Campi 213/A, 41125 Modena, Italy
Interests: multiscale simulations of biomolecule/nanomaterial interfaces; nanoscale biosensor; surface functionalization; molecular dynamics; coarse grained models; amyloid proteins; functionalized metal nanoparticles

Special Issue Information

Dear Colleagues,

Well-designed molecular simulations can give atomistic insight into the interactions between a biomolecule and an inorganic/organic surface, revealing details that cannot be accessed through experiment alone. In turn, experiments can validate some key aspects of the simulation to build confidence in the theoretical predictions. This synergy between experiment and simulation can be harnessed to optimize the design of functionalized nanoscale systems, and indeed provide rational design tools to create new technologies.

In this Special Issue, we bring together research at the interface between modelling and experiment, where molecular simulation plays an important role in the scientific discovery and development of functionalized nanoscale materials. The systems of interest include, amongst others:

  • Targeted drug delivery;
  • Novel therapeutics and vaccines;
  • Imaging and diagnostics;
  • Biosensors;
  • Industrial catalysis.

Full papers and short communications covering methodological and theoretical aspects, as well as interdisciplinary approaches underlying the potential interpretation of experimental data and applications are all welcome.

Dr. Paul Mulheran
Guest Editor
Dr. Giorgia Brancolini
Co-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

  • proteins
  • nanostructures
  • surface functionalization
  • molecular dynamics simulations
  • biosensors
  • biointerfaces
  • Brownian dynamics
  • coarse-grained models

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Published Papers (6 papers)

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Research

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17 pages, 4944 KiB  
Article
Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study
by Mohammed A. H. Farouq, Karina Kubiak-Ossowska, Mohammed M. Al Qaraghuli, Valerie A. Ferro and Paul A. Mulheran
Int. J. Mol. Sci. 2022, 23(9), 4832; https://doi.org/10.3390/ijms23094832 - 27 Apr 2022
Viewed by 1664
Abstract
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development [...] Read more.
Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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18 pages, 9366 KiB  
Article
Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle–Protein Conjugates for Biosensing
by Giorgia Brancolini, Vincent M. Rotello and Stefano Corni
Int. J. Mol. Sci. 2022, 23(4), 2368; https://doi.org/10.3390/ijms23042368 - 21 Feb 2022
Cited by 7 | Viewed by 2800
Abstract
Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or [...] Read more.
Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP–GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold–sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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14 pages, 3497 KiB  
Article
Simulating Peptide Monolayer Formation: GnRH-I on Silica
by Neret Pujol-Navarro, Karina Kubiak-Ossowska, Valerie Ferro and Paul Mulheran
Int. J. Mol. Sci. 2021, 22(11), 5523; https://doi.org/10.3390/ijms22115523 - 24 May 2021
Cited by 1 | Viewed by 1941
Abstract
Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for [...] Read more.
Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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17 pages, 3101 KiB  
Article
Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex
by Sutapa Dutta, Stefano Corni and Giorgia Brancolini
Int. J. Mol. Sci. 2021, 22(7), 3624; https://doi.org/10.3390/ijms22073624 - 31 Mar 2021
Cited by 18 | Viewed by 4077
Abstract
Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and [...] Read more.
Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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12 pages, 4552 KiB  
Article
Disclosing the Interaction of Gold Nanoparticles with Aβ(1–40) Monomers through Replica Exchange Molecular Dynamics Simulations
by Francesco Tavanti, Alfonso Pedone and Maria Cristina Menziani
Int. J. Mol. Sci. 2021, 22(1), 26; https://doi.org/10.3390/ijms22010026 - 22 Dec 2020
Cited by 19 | Viewed by 3167
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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Review

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19 pages, 2206 KiB  
Review
Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications
by Sutapa Dutta, Stefano Corni and Giorgia Brancolini
Int. J. Mol. Sci. 2022, 23(3), 1484; https://doi.org/10.3390/ijms23031484 - 27 Jan 2022
Cited by 11 | Viewed by 3859
Abstract
Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for [...] Read more.
Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from “substrate–receptor–analyte” conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule–surface complex formation as a whole. Full article
(This article belongs to the Special Issue Molecular Simulations of Functionalized Nanoscale Materials)
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