scholarly journals Computational Investigations of a pH-Induced Structural Transition in a CTAB Solution with Toluic Acid

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6978
Author(s):  
Tingyi Wang ◽  
Hui Yan ◽  
Li Lv ◽  
Yingbiao Xu ◽  
Lingyu Zhang ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Carboxyl Groups ◽  
Electrostatic Repulsion ◽  
Structural Transitions ◽  
Density Distributions ◽  
Cylindrical Micelles ◽  
Spherical Micelles ◽  
Aqueous Surfactants ◽  
Dynamics Simulations ◽  
Almost All

In this work, molecular dynamics simulations were performed to study the pH-induced structural transitions for a CTAB/p-toluic acid solution. Spherical and cylindrical micelles were obtained for aqueous surfactants at pH 2 and 7, respectively, which agrees well with the experimental observations. The structural properties of two different micelles were analyzed through the density distributions of components and the molecular orientations of CTA+ and toluic acid inside the micelles. It was found that the bonding interactions between CTA+ and toluic in spherical and cylindrical micelles are very different. Almost all the ionized toluic acid (PTA−) in the solution at pH 7 was solubilized into the micelles, and it was located in the CTA+ headgroups region. Additionally, the bonding between surfactant CTA+ and PTA− was very tight due to the electrostatic interactions. The PTA− that penetrated into the micelles effectively screened the electrostatic repulsion among the cationic headgroups, which is considered to be crucial for maintaining the cylindrical micellar shape. As the pH decreased, the carboxyl groups were protonated. The hydration ability of neutral carboxyl groups weakened, resulting in deeper penetration into the micelles. Meanwhile, their bonding interactions with surfactant headgroups also weakened. Accompanied by the strengthen of electrostatic repulsion among the positive headgroups, the cylindrical micelle was broken into spherical micelles. Our work provided an atomic-level insights into the mechanism of pH-induced structural transitions of a CTAB/p-toluic solution, which is expected to be useful for further understanding the aggregate behavior of mixed cationic surfactants and aromatic acids.

Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Allison Edwards ◽  
Abdolreza Javidialesaadi ◽  
Katie Weigandt ◽  
George Stan ◽  
Charles Eads
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Nmr Relaxation ◽  
Cross Relaxation ◽  
Relaxation Rates ◽  
Surfactant Micelles ◽  
Cylindrical Micelles ◽  
Spherical Micelles ◽  
Dynamics Simulations ◽  
Relative Motions

We study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining high field (600 and 700 MHz) NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. For spherical micelles, but not for cylindrical micelles, cross relaxation rates are positive only for surfactant alkyl tail atoms connected to the hydrophilic head group. All cross relaxation rates are negative for cylindrical micelles. This effect is reproducible either by changing composition (ratios of the nonionic surfactants) or changing temperature of a single surfactant in order to change the micelle shape. We validate the micelle shape by SANS and use the results as a guide for our simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms. Results indicate that relative motions of nearby atoms are liquid-like, in agreement with 13C T1 measurements, though constrained by micelle morphology. Relative motions of distant atoms have slower components because the relative changes in distances and angles are smaller when the moving atoms are further apart. The slow, long-range motions appear to be responsible for the predominantly negative cross relaxation rates observed in NOESY spectra. The densities of atoms from positions 1 and 2 in the boundary region are lower in spherical micelles compared to cylindrical micelles. Correspondingly, motions in this region are less constrained by micelle morphology in the spherical compared to the cylindrical cases. The two effects of morphology lead to the unusual occurrence of positive cross relaxation involving positions 1 and 2 for spheres.

Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Allison Edwards ◽  
Abdolreza Javidialesaadi ◽  
Katie Weigandt ◽  
George Stan ◽  
Charles Eads
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Nmr Relaxation ◽  
Cross Relaxation ◽  
Relaxation Rates ◽  
Surfactant Micelles ◽  
Cylindrical Micelles ◽  
Spherical Micelles ◽  
Dynamics Simulations ◽  
Relative Motions

We study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining high field (600 and 700 MHz) NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. For spherical micelles, but not for cylindrical micelles, cross relaxation rates are positive only for surfactant alkyl tail atoms connected to the hydrophilic head group. All cross relaxation rates are negative for cylindrical micelles. This effect is reproducible either by changing composition (ratios of the nonionic surfactants) or changing temperature of a single surfactant in order to change the micelle shape. We validate the micelle shape by SANS and use the results as a guide for our simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms. Results indicate that relative motions of nearby atoms are liquid-like, in agreement with 13C T1 measurements, though constrained by micelle morphology. Relative motions of distant atoms have slower components because the relative changes in distances and angles are smaller when the moving atoms are further apart. The slow, long-range motions appear to be responsible for the predominantly negative cross relaxation rates observed in NOESY spectra. The densities of atoms from positions 1 and 2 in the boundary region are lower in spherical micelles compared to cylindrical micelles. Correspondingly, motions in this region are less constrained by micelle morphology in the spherical compared to the cylindrical cases. The two effects of morphology lead to the unusual occurrence of positive cross relaxation involving positions 1 and 2 for spheres.

Cryo-TEM of CTAB micelles and microemulsions

1988 ◽  
Vol 46 ◽  
pp. 112-113
Author(s):  
Phillip K. Vinson
Keyword(s):  
Mean Curvature ◽  
Surfactant Concentration ◽  
Phase Region ◽  
Water Soluble ◽  
Ionic Surfactants ◽  
Electrostatic Repulsion ◽  
Micellar Aggregates ◽  
Head Groups ◽  
Cylindrical Micelles ◽  
Spherical Micelles

Single-tailed surfactant molecules in aqueous solutions can associate into several different microstructural forms within a one-phase region of the phase diagram (Fig. 1). The molecules associate into globular aggregates called spherical micelles above a surfactant concentration called the critical micelle concentration, or cmc. At higher surfactant concentrations some surfactants will associate into rod-like micelles called cylindrical micelles. In systems containing ionic surfactants the transition from spherical to cylindrical micelles can be brought about at lower surfactant concentrations by adding an electrolyte. The electrolyte screens the electrostatic repulsion between surfactant head groups and allows formation of the lower mean curvature cylindrical microstructures. Micellar aggregates are equilibrium microstructures in which the nonpolar (often hydrocarbon or fluorocarbon) moieties of the surfactant molecules are shielded from the aqueous medium by the water-soluble moieties of the surfactant molecules. The solubilization of oil into the nonpolar micelle interior produces an aqueous solution of oil swollen micelles, i.e., a microemulsion.

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

scholarly journals Characterization of design grammar of peptides for regulating liquid droplets and aggregates of FUS

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kiyoto Kamagata ◽  
Rika Chiba ◽  
Ichiro Kawahata ◽  
Nanako Iwaki ◽  
Saori Kanbayashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Droplet Formation ◽  
Liquid Droplets ◽  
Proof Of Concept ◽  
Aggregate Formation ◽  
Fused In Sarcoma ◽  
Dynamics Simulations

AbstractLiquid droplets of aggregation-prone proteins, which become hydrogels or form amyloid fibrils, are a potential target for drug discovery. In this study, we proposed an experiment-guided protocol for characterizing the design grammar of peptides that can regulate droplet formation and aggregation. The protocol essentially involves investigation of 19 amino acid additives and polymerization of the identified amino acids. As a proof of concept, we applied this protocol to fused in sarcoma (FUS). First, we evaluated 19 amino acid additives for an FUS solution and identified Arg and Tyr as suppressors of droplet formation. Molecular dynamics simulations suggested that the Arg additive interacts with specific residues of FUS, thereby inhibiting the cation–π and electrostatic interactions between the FUS molecules. Second, we observed that Arg polymers promote FUS droplet formation, unlike Arg monomers, by bridging the FUS molecules. Third, we found that the Arg additive suppressed solid aggregate formation of FUS, while Arg polymer enhanced it. Finally, we observed that amyloid-forming peptides induced the conversion of FUS droplets to solid aggregates of FUS. The developed protocol could be used for the primary design of peptides controlling liquid droplets and aggregates of proteins.

scholarly journals Spatial segregation of mixed-sized counterions in dendritic polyelectrolytes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. S. Kłos ◽  
J. Paturej
Keyword(s):  
Electrostatic Interactions ◽  
Spatial Separation ◽  
Excluded Volume ◽  
The Core ◽  
Bjerrum Length ◽  
Two Component ◽  
Conformational Properties ◽  
Dynamics Simulations ◽  
Two Parameters ◽  
Swelling Factor

AbstractLangevin dynamics simulations are utilized to study the structure of a dendritic polyelectrolyte embedded in two component mixtures comprised of conventional (small) and bulky counterions. We vary two parameters that trigger conformational properties of the dendrimer: the reduced Bjerrum length, $$\lambda _B^*$$ λ B ∗ , which controls the strength of electrostatic interactions and the number fraction of the bulky counterions, $$f_b$$ f b , which impacts on their steric repulsion. We find that the interplay between the electrostatic and the counterion excluded volume interactions affects the swelling behavior of the molecule. As compared to its neutral counterpart, for weak electrostatic couplings the charged dendrimer exists in swollen conformations whose size remains unaffected by $$f_b$$ f b . For intermediate couplings, the absorption of counterions into the pervaded volume of the dendrimer starts to influence its conformation. Here, the swelling factor exhibits a maximum which can be shifted by increasing $$f_b$$ f b . For strong electrostatic couplings the dendrimer deswells correspondingly to $$f_b$$ f b . In this regime a spatial separation of the counterions into core–shell microstructures is observed. The core of the dendrimer cage is preferentially occupied by the conventional ions, whereas its periphery contains the bulky counterions.

scholarly journals Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

2018 ◽  
Author(s):  
Giovanni B. Brandani ◽  
Shoji Takada
Keyword(s):  
Genome Organization ◽  
Electrostatic Interactions ◽  
Defect Formation ◽  
Energy Landscape ◽  
Molecular Machines ◽  
Biological Processes ◽  
Complete Understanding ◽  
Chromatin Remodelers ◽  
Nucleosomal Dna ◽  
Dynamics Simulations

ABSTRACTATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the remodeler overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these important biological processes.

Mechanism for Transition of Reverse Cylindrical Micelles to Spherical Micelles Induced by Diverse Alcohols

Langmuir ◽  
2020 ◽  
Vol 36 (28) ◽  
pp. 8174-8183
Author(s):  
Hwa-Jin Lee ◽  
Hyun-Jin Kim ◽  
Da-Gyun Park ◽  
Kyeong Sik Jin ◽  
Ji Woong Chang ◽  
...  
Keyword(s):  
Cylindrical Micelles ◽  
Spherical Micelles

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

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