Recent Advances in Simulation Studies on the Protein Corona DOI Creative Commons
Hwankyu Lee

Pharmaceutics, Journal Year: 2024, Volume and Issue: 16(11), P. 1419 - 1419

Published: Nov. 6, 2024

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on nanoparticle surface, known "protein corona". Since corona influences size, shape, and surface properties nanoparticles, it can modulate their circulating lifetime, cytotoxicity, targeting efficiency. Therefore, understanding mechanism formation at atomic scale is crucial, which has become possible due to advances in computer power simulation methodologies. This review covers following topics: (1) structure, dynamics, composition nanoparticles; (2) effects concentration ionic strength formation; (3) particle morphology, (4) interactions among lipids, membranes, with corona. For each topic, mesoscale, coarse-grained, all-atom molecular dynamics simulations since 2020 are discussed. These not only successfully reproduce experimental observations but also provide physical insights into formation. In particular, these findings be applied manipulate that target specific cells, aiding rational design nanomedicines for delivery applications.

Language: Английский

Impact of Glycosylation of Apolipoprotein D on Its Interaction with Gold Nanoparticles: Insights from Molecular Dynamics Simulations DOI

Xiaolei Li,

Zengshuai Yan,

Yu‐qiang Ma

et al.

ACS Applied Materials & Interfaces, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 7, 2025

Efficient delivery of nanoparticles (NPs) as carriers for biochemical substances is crucial in various biomedical applications. In this study, we systematically investigate the interactions between glycosylated and nonglycosylated forms Apolipoprotein D (ApoD) with gold (AuNPs) functionalized different polymer coatings, including polyethylene glycol (PEG) zwitterionic polymers. Using all-atom molecular dynamics simulations, demonstrate that glycosylation significantly enhances adsorption behavior ApoD on AuNP surfaces, extent enhancement being dependent type (especially charge property) coatings. Notably, while polymers exhibit strong resistance to protein their form, antifouling capability diminished when present. Further, our findings reveal not only strengthens binding energy proteins but also alters hydration at NP–protein interface. Overall, study provides a deeper understanding role modulating protein–nanoparticle interactions, which essential design more effective nanomaterials precision medicine.

Language: Английский

Citations

1
Effects of Bare and PEG Coated Gold Nanoparticles on RRM2 Protein: A Pathway Analysis and MD Simulations Approach DOI
Ajit Kumar Singh, Anupam Nath Jha

BioNanoScience, Journal Year: 2025, Volume and Issue: 15(2)

Published: April 8, 2025

Language: Английский

Citations

0
Size-Dependent Interactions of Degraded PET Nanoparticles with Human Serum Albumin: Thermodynamic and Molecular Insights DOI Creative Commons
Tomasz Pańczyk, Paweł Wolski, Krzysztof Nieszporek

et al.

The Journal of Physical Chemistry B, Journal Year: 2025, Volume and Issue: unknown

Published: April 28, 2025

This study examines the interaction between degraded polyethylene terephthalate (PET) nanoparticles and human serum albumin (HSA), focusing on effects of nanoparticle size surface modifications resulting from degradation. PET degradation, induced via shock compression in water, leads to significant chemical alterations, including formation hydroxyl, carboxyl, carbonyl groups. These influence hydrophilicity their binding behavior with HSA. The production involves subjecting pristine controlled an aqueous environment, which initiates reactions similar those that may occur during degradation process is characterized by a progressive breakdown polymer chains, leading increase functionalized groups enhanced hydrophilicity. performed analysis chemistry reveals introduction oxygen-containing alters properties nanoparticles, making them more prone hydrogen bonding water molecules while simultaneously reducing affinity for HSA binding. Molecular dynamics simulations, umbrella sampling, weighted histogram are employed investigate thermodynamic aspects PET-HSA interactions. identifies preferred sites HSA, revealing preferentially bind Domain I III Interaction energy demonstrates larger exhibit stronger binding, whereas small have significantly reduced energies, indicating higher likelihood desorption. Further structural using root-mean-squared deviation (RMSD) fluctuation (RMSF) confirms does not alter HSA's secondary structure. However, increases hydrophilicity, weakening adsorption onto Large strongly bound, remain unbound, raising concerns regarding potential toxicity due free migration bloodstream. findings provide crucial insights into biological implications role determining interactions, contributions nanoplastic toxicity.

Language: Английский

Citations

0
Free energy calculations in biomolecule-nanomaterial interactions DOI Creative Commons

Hongze Fu,

Yinbang Zhu,

Qu Chen

et al.

Frontiers in Physics, Journal Year: 2024, Volume and Issue: 12

Published: Sept. 13, 2024

In computational chemistry and molecular modeling, the interactions between biomolecules (BMs) nanomaterials (NMs) play a crucial role in various physical biological processes, have significant implications material discovery development. While there is extensive literature on free energy calculations for drug-target interactions, reviews specifically addressing BM-NM are relatively scarce. This manuscript aims to fill this gap by presenting comprehensive overview of most widely used well-established methods calculations. It provides detailed analysis advantages limitations these discusses their applicability systems. work intended offer insights into serve as guide future research field.

Language: Английский

Citations

2
Recent Advances in Simulation Studies on the Protein Corona DOI Creative Commons
Hwankyu Lee

Pharmaceutics, Journal Year: 2024, Volume and Issue: 16(11), P. 1419 - 1419

Published: Nov. 6, 2024

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on nanoparticle surface, known "protein corona". Since corona influences size, shape, and surface properties nanoparticles, it can modulate their circulating lifetime, cytotoxicity, targeting efficiency. Therefore, understanding mechanism formation at atomic scale is crucial, which has become possible due to advances in computer power simulation methodologies. This review covers following topics: (1) structure, dynamics, composition nanoparticles; (2) effects concentration ionic strength formation; (3) particle morphology, (4) interactions among lipids, membranes, with corona. For each topic, mesoscale, coarse-grained, all-atom molecular dynamics simulations since 2020 are discussed. These not only successfully reproduce experimental observations but also provide physical insights into formation. In particular, these findings be applied manipulate that target specific cells, aiding rational design nanomedicines for delivery applications.

Language: Английский

Citations

1