Understanding and Designing the Gold–Bio Interface: Insights from Simulations

Abstract

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Antimicrobial Metal Nanomaterials: From Passive to Stimuli‐Activated Applications

“…For example, a 2016 review highlighted the challenges and achievements of modeling gold nanoparticles and materials at biological interfaces. [ 153 ] It is therefore critical that accurate, compatible models for relevant microbial components and models of relevant nanomaterials, ions, and ROS molecules be obtained. Once this is achieved, the effects of metal nanomaterials on bacterial and fungal cell walls and membranes, ion and ROS interactions, and passive antimicrobial activity of nanomaterials should be open avenues for investigation via MD‐based computational methods.…”

Scaffolds as Structural Tools for Bone-Targeted Drug Delivery

“…As a matter of fact, MARTINI force field has been employed to simulate not only lipid membranes but also entire lipid particles ( Figure 2 B) [ 158 , 159 ]. Thanks to the detail at atomic scale provided by microscale models, systems like gold nanoparticles ( Figure 2 D) [ 160 , 161 , 162 , 163 ] have been also investigated through MD-based methods [ 164 ]. The aim of the simulations is to investigate the dynamic behavior at particle/environment interface, such as protein adsorption or the effect of decorating groups at particle surface.…”

The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations

“…[68] There is also a growing research interest in understanding the complex physicochemical phenomena occurring at the Au-bio interface, and the following perspective outlines the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems. [12] We recently applied computer simulations to investigate the facet-dependent conformational changes of another amyloidogenic protein, human amylin, on AuNPs, and their role in fibril formation. [84] Human amylin (IAPP) is responsible for glycemic regulation in our body, however, like the other amyloid proteins, it can self-assemble and form fibrils which are involved in the pathogenesis of type II diabetes.…”

“…While advances in experimental techniques are constantly probing ever-smaller length-scales and ever-shorter timescales, computational modelling is still widely recognised as an invaluable and complementary approach to systematically investigate the detailed mechanisms of nanoscale biological phenomena at atomistic and electronic resolutions. [10][11][12] Despite the exponential increase in computer power [13] there is no single molecular modelling approach, with the electronic structure calculations and classical all-atom and coarse-grained molecular dynamics (MD) simulations commonly used separately or in combination to describe complex biomolecular events at different length and timescales. Indeed, a multiscale modelling approach is required to obtain a comprehensive physicochemical description of multistage protein aggregation processes and, further, to design fibril inhibiting compounds and/or external stimuli.…”