Solvent Effects on Kinetic Mechanisms of Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations

Fu, Iris W.; Markegard, Cade B.; Nguyen, Hung D.

doi:10.1021/la503399x

Cited by 54 publications

(53 citation statements)

References 71 publications

(153 reference statements)

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“…Similarly, a study utilizing the ePRIME force field 24 to CG PAs reported a spherical micelle to rod shape nanostructure transformation. 27 Within this study, with increasing hydrophobicity strength as low, moderate and high, three clusters were observed—random clusters, cylindrical nanofibers and elongated micelles.…”

Section: Simulations Of Peptide-amphiphile Self-assembliesmentioning

confidence: 59%

“…With increasing hydrophobicity, first spherical micelles form which later merge to form cylindrical nanofibers and elongated micelles. Adapted with permission from ref 27. Copyright (2015) American Chemical Society.…”

Section: Figurementioning

confidence: 99%

“…Multiple computational studies have utilized both all-atomistic (AA) and coarse-grained (CG) molecular dynamics (MD) simulation techniques to explore both the self-assembly of short peptide sequences 7 as well as PAs 23,27 and the resulting stability of the assemblies. MD uses the classical Newtonian equations of motion to calculate the dynamic behaviour of the system.…”

Section: Introductionmentioning

confidence: 99%

“…For example, the MARTINI 44 force field is a widely used CG tool for simulations of lipids, proteins and carbohydrates, as well as short peptide sequences 45–47 and PAs 23,32 . Two other CG force fields recently used for PA simulations are the Shinoda-DeVane-Klein (SDK) force field 43,48,49 as well as ePRIME, 24 an extension of PRIME (Protein Intermediate Resolution Model), 50 which was developed by Fu et al 24,27,28 to CG their PA monomer, Palmitoyl-VVVAAAEEE. However, CG MD simulations of such large systems have their own challenges which include: i) the accuracy of the force field for PAs, ii) loss of detailed chemical resolution with CG modelling, and iii) ability to computationally characterize structure and properties of these assemblies to compare with experimental results, validate computational force fields, and establish a feedback loop between experiment and computation.…”

Section: Introductionmentioning

confidence: 99%

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Molecular simulations of peptide amphiphiles

et al. 2017

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This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles, and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process. Furthermore, these computational methods provide the ability to computationally probe the structure of these supramolecular assemblies at the molecular level, which is a challenge experimentally. Herein, we briefly highlight progress in the areas of all-atomistic and coarse-grained simulation studies investigating the self-assembly process of short peptides and peptide amphiphiles. We also discuss recent all-atomistic and coarse-grained simulations of the self-assembly of a drug-amphiphile into elongated filaments. Next, we discuss how these computational methods can provide further insight on the pathway of cylindrical nanofiber formation and predict their biocompatibility by studying the interaction of these peptide-amphiphile nanostructures with model cell membranes.

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Section: Simulations Of Peptide-amphiphile Self-assembliesmentioning

confidence: 59%

Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular simulations of peptide amphiphiles

et al. 2017

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“…The assembly was found to occur via a multistep process with transient intermediates ultimately leading to stable nanostructures. Different kinetic mechanisms were compared on the basis of solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interaction, and aggregate size (Fu et al, 2015). Comparatively, only few simulation studies have been reported on the loading/release of drugs in amphiphilic peptides.…”

Section: F4h5k15 F8h5k15 F12h5k15 F16h5k15mentioning

confidence: 99%

Computational Amphiphilic Materials for Drug Delivery

Thota

Jiang

2015

Front. Mater.

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Amphiphilic materials can assemble into a wide variety of morphologies and have emerged as a novel class of candidates for drug delivery. Along with a large number of experiments reported, computational studies have also been conducted in this field. At an atomistic/molecular level, computations can facilitate quantitative understanding of experimental observations and secure fundamental interpretation of underlying phenomena. This review summarizes the recent computational studies on amphiphilic copolymers and peptides for drug delivery. Atom-resolution and time-resolved insights are provided from bottom-up to microscopically elucidate the mechanisms of drug loading/release, which are indispensable in the rational screening and design of new amphiphiles for high-efficacy drug delivery.

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Simulations of morphology control of self‐assembled amphiphilic surfactants

Zhu

Tree

2023

Journal of Polymer Science

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One of the grand challenges of amphiphilic self‐assembly is the design of ordered structures whose morphology or shape can be explicitly and dynamically controlled by adjusting the properties of the amphiphiles or their surroundings. Such a capacity would enable researchers to create synthetic systems with functionality that meets or exceeds biological cells, and provide a robust platform for a broad range of engineering applications such as artificial tissues, drug delivery, and separation membranes. Despite significant progress, important fundamental questions remain unanswered, due in part to the limited resolution and the restricted parameter spaces that are readily accessible in experiments. Computational studies thus provide an important complement to experiments, enabling in‐depth insight into underlying mechanisms and an exploration of the parameter spaces for behavior that has not yet been achieved in experiments. In this review, we briefly introduce fundamental concepts and pertinent experiments related to dynamic shape modulation in self‐assembled amphiphiles. Then, in the bulk of the review, we survey the most influential simulation studies that investigate and identify approaches to control the self‐assembled shape of amphiphiles, with an emphasis on kinetic and mechanical effects. Finally, we conclude with a perspective on future research directions in this exciting field.

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Solvent Effects on Kinetic Mechanisms of Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations

Cited by 54 publications

References 71 publications

Molecular simulations of peptide amphiphiles

Molecular simulations of peptide amphiphiles

Computational Amphiphilic Materials for Drug Delivery

Simulations of morphology control of self‐assembled amphiphilic surfactants

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