Molecular Dynamics Simulations as a Tool for Accurate Determination of Surfactant Micelle Properties

Faramarzi, Sadegh; Bonnett, Brittany; Scaggs, Carl A.; Hoffmaster, Ashley; Grodi, Danielle; Harvey, Erica; Mertz, Blake

doi:10.1021/acs.langmuir.7b02666

Cited by 38 publications

(38 citation statements)

References 58 publications

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“…Likewise, the proposed capacity of micelles to undergo fission is supported by studies on the influence of micelle constituents on micellar morphology, stability, deformation, and disruption [65,66,67]. In the abovementioned studies, the in silico results are often compared with experimental information as exemplified [68], providing validation to the computational approaches.…”

Section: Molecular Dynamics Of Micelles and Mixed Micellesmentioning

confidence: 99%

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Kahana

Lancet

2019

Life

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Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

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Section: Molecular Dynamics Of Micelles and Mixed Micellesmentioning

confidence: 99%

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Kahana

Lancet

2019

Life

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“…Apart from an excellent performance in terms of surface tension, foamability, and detergency, APG are environmentally friendly, biodegradable, and low-toxic surfactants. Thereby, they can be used for various applications such as drug carriers, intranasal adjuvants, silk degumming agents, and in oil recovery and sludge anaerobic fermentation (Ahmad et al, 2014;Faramarzi et al, 2017;Karam et al, 2017;Wang and Zhang, 2017;Wu et al, 2017;Xiao et al, 2017;Zhou et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…They could be categorized as ecologically safe sugar-based surfactants (Ahmad et al, 2014;Aripin et al, 2012;Karam et al, 2017;Zhao et al, 2017). From a chemical point of view, alkyl D-maltosides are stable under neutral and alkaline conditions because they are comprised of bulkier and rigid sugar headgroups and flexible alkyl chain tail groups connected via an ether linkage rather than an ester linkage or an amide linkage (Faramarzi et al, 2017). Therefore, they have a wide range of applications and development in food, cosmetic, pharmaceutical industries, and scientific research (de Foresta et al, 2011;Jastrzebska et al, 2006;Ni et al, 2011;Pillion et al, 2002;Raman et al, 2006;Rifkin et al, 2011;Santonicola et al, 2008; Supporting information Additional supporting information may be found online in the Supporting Information section at the end of the article.…”

Section: Introductionmentioning

confidence: 99%

Solution Properties of Alkyl β‐D‐Maltosides

Zhencao

Chen

et al. 2019

J Surfact & Detergents

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Alkyl β‐D‐maltosides are an important class of sugar‐based nonionic surfactants and have been widely studied. Nevertheless, it is still necessary to investigate further their amphiphilic structure‐surface property relationships. In this article, we reported a series of properties of synthetic alkyl β‐D‐maltosides (6a–6i, n = 6–18) including their hydrophilic–lipophilic balance (HLB) number, water solubility, hygroscopicity, moisture‐retention capacity, foaming ability, surface tension, thermotropic phase behavior, and skin irritation. Their HLB number and water solubility decreased with increasing alkyl chain length. Hexyl β‐D‐maltoside exhibited the strongest hygroscopicity and moisture‐retention capacity. Decyl β‐D‐maltoside and dodecyl β‐D‐maltoside possessed excellent foaming power and foaming stability. Furthermore, the critical micelle concentration (CMC) of alkyl β‐D‐maltoside (6a–6g, n = 6–14) and their surface tension at CMC decreased with increasing alkyl chain length. At last, alkyl β‐D‐maltosides (6a–6g) should be considered as safe surfactants by the skin irritation assessment.

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“…The moments of inertia of the ellipsoid calculated from a, b, and c were comparable to those reported in recent simulation studies. 58 for Fos10, 379 Å 3 for Fos14, and 488 Å 3 for DHPC.…”

Section: All-atom MD Simulations Of Pure Micellesmentioning

confidence: 97%

“…A pure micelle has been typically approximated as an "ordinary" ellipsoid. [56][57][58] As observed in recent cryo-EM experiments, 3-6 micelle shape can be deformed in the presence of membrane proteins, resulting in a flat region near the micelle center where the protein is contained. Both simple and deformed shapes can be described with the super-ellipsoid function:…”

Section: Approximation Of Micelle Shapementioning

confidence: 99%

Implicit micelle model for membrane proteins using super-ellipsoid approximation

Mori

Sugita

2019

Preprint

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Surfactant micelles are often utilized as membrane mimetics for structure determination and functional analysis of membrane proteins. Although curved-surface effects of the micelle can perturb their structure, it is difficult to assess such effects and membrane mimetic artifacts by experimental and theoretical methods. Here, we propose an implicit micelle model (IMIC) to be used in molecular dynamics (MD) simulations of membrane proteins. IMIC is an extension of the IMM1 implicit membrane model by introducing a super-ellipsoid approximation to represent the curved-surface effects. Most of the parameters for IMIC are obtained from all-atom explicit solvent MD simulations of twelve membrane proteins in various micelles. In simulations of the HIV envelop protein gp41, M13 major coat protein gp8, and amyloid precursor protein (APP) dimer, curved-surface and compact hydrophobic-core effects are exhibited. The MD simulations with IMIC provide accurate structure predictions of membrane proteins in various micelle environments quickly with smaller computational cost than that necessary for explicit solvent/micelle model. Recent development of automated system builders, such as CHARMM-GUI Micelle builder, 26makes it easy to model a protein-micelle complex for all-atom MD simulations in explicit solvent and micelle. One difficulty, though, is that the aggregation number of surfactant around the protein is usually unknown, and there is limited experimental data available in this regard. [27][28][29][30] To avoid this problem, protocols for the spontaneous formation of the protein-micelle complex have been proposed, where the MD simulation starts from a random distribution of surfactants in the simulation box. [31][32][33] Since such simulations require long relaxation times (typically, several hundred nanoseconds), course-grained models or implicit water models have been employed to enhance

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Molecular Dynamics Simulations as a Tool for Accurate Determination of Surfactant Micelle Properties

Cited by 38 publications

References 58 publications

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Solution Properties of Alkyl β‐D‐Maltosides

Implicit micelle model for membrane proteins using super-ellipsoid approximation

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