Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

Heikkilä, Elena; Gurtovenko, Andrey A.; Martinez‐Seara, Hector; Häkkinen, Hannu; Vattulainen, Ilpo; Akola, Jaakko

doi:10.1016/j.bpj.2012.11.3668

Cited by 3 publications

(3 citation statements)

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“…However, there are currently few studies reporting atomically detailed binding and conformational changes of biomolecules or nucleic acids with cationic dendrimers 21 or nanoparticles. 22 Here, we report the results of first comprehensive all-atom molecular dynamics (MD) simulation study of the binding of cationic functionalized gold nanoparticles to 30 base pairs (bp) double stranded DNA or RNA. Atomistic MD simulations were chosen to provide unbiased details of NP binding as a dynamic process as well as detailed characterization of a final nucleic acid conformation.…”

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confidence: 99%

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

Nash

Singh

et al. 2015

ACS Nano

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The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

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confidence: 99%

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

Nash

Singh

et al. 2015

ACS Nano

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“…In this configuration, the NP charged terminal ligands interact with the zwitterionic headgroups of the membrane [38,52]. Coarse-grained simulations predict a reversible adsorption state, where the The picture of the penetration mechanism of amphiphilic MUS:OT AuNPs is now precise thanks to molecular dynamics (MD) studies employing all-atom and coarse-grained force fields [30,39,52,53], which revealed a multi-step process going through at least three different metastable stages (Figure 1b) [38]. In the first stage, the so-called "adsorbed state", the NP adheres to the external surface of the bilayer.…”

Section: Amphiphilic Gold Nanoparticles and Amphiphilic Peptides: A D...mentioning

confidence: 99%

Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions

et al. 2022

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Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy‑driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials—such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer—can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.

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“…8,9 The optimization of the size, charge, and functionalization of the NPs for specific applications can greatly benefit computer modeling. 10 Recently, atomistic molecular dynamics (MD) simulations of gold NPs (AuNPs) covalently functionalized with charged groups 11,12 have highlighted the role played by solvents and counterions, which form intimately assembled complexes with the NPs and mediate their interactions. Ionicstrength-dependent electrostatics was also confirmed as the main determinant of complexation of AuNPs with nanomaterials and biological molecules.…”

Section: ■ Introductionmentioning

confidence: 99%

Deconstructing Electrostatics of Functionalized Metal Nanoparticles from Molecular Dynamics Simulations

Bini,

Tozzini,

Brancolini

2023

J. Phys. Chem. B

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Gold nanoparticles (NPs) with different surface functionalizations can selectively interact with specific proteins, allowing a wide range of possible applications in biotechnology and biomedicine. To prevent their tendency to aggregate and to modulate their interaction with charged biomolecules or substrates (e.g., for biosensing applications), they can be functionalized with charged groups, introducing a mutual interaction which can be modulated by changing the ionic strength of the solvent. In silico modeling of these systems is often addressed with low-resolution models, which must account for these effects in the, often implicit, solvent representation. Here, we present a systematic conformational dynamic characterization of ligand-coated gold nanoparticles with different sizes, charges, and functionalizations by means of atomistic molecular dynamics simulations. Based on these, we deconstruct their electrostatic properties and propose a general representation of their average-long-range interactions extendable to different sizes, charges, and ionic strengths. This study clarifies in detail the role of the different features of the NP (charge, size, structure) and of the ionic strength in determining the details of the interparticle interaction and represents the first step toward a general strategy for the parametrization of NP coarse-grained models able to account for varying ionic strengths.

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Atomistic Simulations of Functional Gold Nanoparticles Au144(Sr)60 Interacting with Membranes

Cited by 3 publications

References 0 publications

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics

Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions

Deconstructing Electrostatics of Functionalized Metal Nanoparticles from Molecular Dynamics Simulations

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