Conformational Order Research Articles

Study of the interactions of gold nanoparticles functionalized with aminolevulinic acid in membrane models

Gold nanoparticles have been intensively studied in cancer therapy to improve drug release, increasing therapeutic action and reducing adverse effects. The interaction between gold nanoparticles and cell membranes can give information about the cell internalization. In this study, gold nanoparticles with aminolevulinic acid (5-ALA) were synthesized using the photoreduction method (5-ALA: AuNPs). The prodrug 5-ALA is responsible for protoporphyrin IX synthesis inside the cell and allows the use of therapies as photodynamic and sonodynamic therapies. The cytotoxicity test was performed on a breast cancer tumor line (MCF-7), and high Content Screening assay was applied to evaluate the entry of nanoparticles into cells. DPPS Langmuir monolayers were assembled at the air/water interface and employed as a simplified membrane model for half of a tumorigenic cell membrane. We assessed the molecular interactions between 5-ALA: AuNPs and phospholipids using tensiometry (π-A isotherms) and vibrational spectroscopy (PM-IRRAS) experiments. We found that the functionalized gold nanoparticles strongly interact with DPPS polar head groups (especially phosphate and carbonyl), changing the phospholipid hydration and leading to a general decrease in the monolayer conformational order. This work then probes that specific interaction between 5-ALA: AuNPs and the negatively charged phospholipid can be assessed using Langmuir monolayers as simplified biomembrane models.

Conformational preferences of diallylamine: A rotational spectroscopic and theoretical study.

The conformational space of diallylamine (DAA) was investigated using rotational spectroscopy from 7 to 19 GHz aided by quantum chemical calculations. Extensive conformational searches using density functional theory B3LYP-D3(BJ) and the ab initio MP2 method with the aug-cc-pVTZ basis set identified a total of 42 minima for DAA within ∼22 kJ mol-1. This reveals a strikingly rich conformational landscape for this secondary amine with two equivalent substituents. Experimentally, transitions belonging to four low energy conformers (I, II, III, and IV) were unequivocally assigned in the rotational spectrum, and their patterns were confirmed by the presence of the hyperfine structure owing to the 14N quadrupolar nucleus. The relative intensities of the observed transitions suggest a conformational energy ordering of I < II < III < IV. Natural bond orbital and non-covalent interaction calculations reveal that the geometric preferences for the observed conformers are governed by an interplay of subtle attractive interactions (including hyperconjugation involving the lone pair at nitrogen) and repulsive effects.

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains.

Native states of folded proteins are characterized by a large ensemble of conformations whose relative populations and interconversion dynamics determine the functional output. This is more apparent in transcription factors that have evolved to be inherently sensitive to small perturbations, thus fine-tuning gene expression. To explore the extent to which such functional features are imprinted on the folding landscape of transcription factor ligand-binding domains (LBDs), we characterize paralogous LBDs of the nuclear receptor (NR) family employing an energetically detailed and ensemble-based Ising-like statistical mechanical model. We find that the native ensembles of the LBDs from glucocorticoid receptor, PPAγ, and thyroid hormone receptor display a remarkable diversity in the width of the native wells, the number and nature of partially structured states, and hence the degree of conformational order. Monte Carlo simulations employing the full state representation of the ensemble highlight that many of the functional conformations coexist in equilibrium, whose relative populations are sensitive to both temperature and the strength of ligand binding. Allosteric modulation of the degree of structure at a coregulator binding site on ligand binding is shown to arise via a redistribution of populations in the native ensembles of glucocorticoid and PPAγ LBDs. Our results illustrate how functional requirements can drive the evolution of conformationally diverse native ensembles in paralogs.

Ion conformation and orientational order in a dicationic ionic liquid crystal studied by solid-state nuclear magnetic resonance spectroscopy

Ionic liquids crystals belong to a special class of ionic liquids that exhibit thermotropic liquid-crystalline behavior. Recently, dicationic ionic liquid crystals have been reported with a cation containing two single-charged ions covalently linked by a spacer. In ionic liquid crystals, electrostatic and hydrogen bonding interactions in ionic sublayer and van der Waals interaction in hydrophobic domains are the main forces contributing to the mesophase stabilization and determining the molecular orientational order and conformation. How these properties in dicationic materials are compared to those in conventional monocationic analogs? We address this question using a combination of advanced NMR methods and DFT analysis. Dicationic salt 3,3′-(1,6-hexanediyl)bis(1-dodecylimidazolium)dibromide was studied. Local bond order parameters of flexible alkyl side chains, linker chain, and alignment of rigid polar groups were analyzed. The dynamic spacer effectively “decouples” the motion of two ionic moieties. Hence, local order and alignment in dicationic mesophase were similar to those in analogous single-chain monocationic salts. Bond order parameters in the side chains in the dicationic smectic phase were found consistently lower compared to double-chain monocationic analogs, suggesting decreasing contribution of van der Waals forces. Overall dication reorientation in the smectic phase was characterized by low values of orientational order parameter S. With increased interaction energy in the polar domain the layered structure is stabilized despite less ordered dications. The results emphasized the trends in the orientational order in ionic liquid crystals and contributed to a better understanding of interparticle interactions driving smectic assembly in this and analogous ionic mesogens.

Conformation, and Charge Tunneling through Molecules in SAMs.

This paper demonstrates that the molecular conformation (in addition to the composition and structure) of molecules making up self-assembled monolayers (SAMs) influences the rates of charge tunneling (CT) through them, in molecular junctions of the form AuTS/S(CH2)2CONR1R2//Ga2O3/EGaIn, where R1 and R2 are alkyl chains of different length. The lengths of chains R1 and R2 were selected to influence the conformations and conformational homogeneity of the molecules in the monolayer. The conformations of the molecules influence the thickness of the monolayer (i.e. tunneling barrier width) and their rectification ratios at ±1.0 V. When R1 = H, the molecules are well ordered and exist predominantly in trans-extended conformations. When R1 is an alkyl group (e.g., R1 ≠ H), however, their conformations can no longer be all-trans-extended, and the molecules adopt more gauche dihedral angles. This change in the type of conformation decreases the conformational order and influences the rates of tunneling. When R1 = R2, the rates of CT decrease (up to 6.3×), relative to rates of CT observed through SAMs having the same total chain lengths, or thicknesses, when R1 = H. When R1 ≠ H ≠ R2, there is a weaker correlation (relative to that when R1 = H or R1 = R2) between current density and chain length or monolayer thickness, and in some cases the rates of CT through SAMs made from molecules with different R2 groups are different, even when the thicknesses of the SAMs (as determined by XPS) are the same. These results indicate that the thickness of a monolayer composed of insulating, amide-containing alkanethiols does not solely determine the rate of CT, and rates of charge tunneling are influenced by the conformation of the molecules making up the junction.

Holographic conformal order in supergravity

We explore the embedding of the phenomenological holographic models describing thermal relativistic ordered conformal phases in R2,1 in SUGRA/String theory. The dual black branes in a Poincare patch of asymptotically AdS4 have “hair” — a condensate of the order parameter for the broken symmetry. In a gravitational dual the order parameter for a spontaneous symmetry breaking is represented by a bulk scalar field with a nontrivial potential. To construct the ordered conformal phases perturbatively we introduce a phenomenological deformation parameter in the scalar potential. We find that while the ordered phases exist for different values of the deformation parameter, they disappear before the deformation is removed, in one case once the potential is precisely as in the top-down holography. While the holographic models with the conformal ordered phases considered here are in the String theory swampland, it remains an open question whether the presence of conformal ordered phases is a genuine swampland principle.

Chirped W-shape bright, dark and other solitons solutions of a conformable fractional nonlinear Schrödinger’s equation in nonlinear optics

In this work, two types of integration architecture, namely the sine-Gordon expansion and modified $$\exp (-\psi (\xi )$$ -expansion function methods are used for constructing chirped W-shape bright, dark and other solitons solutions to perturbed nonlinear Schrodinger’s equation with conformable fractional order. The paper addresses optical solitons which are serviced in fields of nonlinear optics. As results, various types of new chirped soliton solutions and other solitons solutions not yet reported in the literature are obtained. These solutions associated with their chirp are included dark, bright optical solitons, hyperbolic, periodic and other types of solitons solutions. Moreover, some graphical representations were done successfully to stress out the virtue of the fractional order derivative.

Domains 12 to 16 of tropoelastin promote cell attachment and spreading through interactions with glycosaminoglycan and integrins alphaV and alpha5beta1.

Elastin is an extracellular matrix component with key structural and biological roles in elastic tissues. Interactions between resident cells and tropoelastin, the monomer of elastin, underpin elastin's regulation of cellular processes. However, the nature of tropoelastin-cell interactions and the contributions of individual tropoelastin domains to these interactions are only partly elucidated. In this study, we identified and characterized novel cell-adhesive sites in the tropoelastin N-terminal region between domains 12 and 16. We found that this region interacts with αV and α5β1 integrin receptors, which mediate cell attachment and spreading. A peptide sequence from within this region, spanning domains 14 to mid-domain 16, binds heparan sulfate through electrostatic interactions with peptide lysine residues and induces conformational ordering of the peptide. We propose that domains 14-16 direct initial cell attachment through cell-surface heparan sulfate glycosaminoglycans, followed by αV and α5β1 integrin-promoted attachment and spreading on domains 12-16 of tropoelastin. These findings advance our mechanistic understanding of elastin matrix biology, with the potential to enhance tissue regenerative outcomes of elastin-based materials.

Abundant wave solutions of conformable space-time fractional order Fokas wave model arising in physical sciences

The higher dimensional Fokas equation is the integrable expansion of the Kadomtsev-Petviashvili (KP) and Davey-Stewartson (DS) equations. The Fokas model has an important role in wave theory, to describe the physical phenomena of waves on the surface and inside the water. This article deals with the (4+1)-dimensional conformable space-time fractional-order Fokas partial differential equation. Two efficient methods, namely the generalized exp(-ϕ(ξ))-expansion and improved F-expansion methods, are formulated for conformable fractional-order partial differential equation and new wave structures of fractional order Fokas model are constructed. The different kinds of new solitons are achieved such as bright soliton, dark soliton, Kink and anti-kink solitons, periodic solitary waves, and traveling waves. These new soliton waves are constructed at some values of fractional order α and using different parametric values of the methods by using the software package Mathematica. Newly obtained soliton solutions are compared with the available soliton solutions with different fractional derivatives in the literature. Some of the achieved results are explained 2D and 3D graphically. The new results interpreting that these obtained solutions can be a part, to complete the family of solutions and considered methods are effective, simple, and easy to use. Furthermore, this paper gives an idea, how can reduce the conformable fractional order higher dimensional partial differential equation into an ODE of one variable to obtain the exact solutions. These results and methods can be help to investigate the other higher-dimensional conformable fractional-order models which appear in nonlinear wave theory such as optics, quantum gases, hydrodynamics, photonics, plasmas, and solid-state physics.

Fate of the conformal order

We use holographic correspondence to study transport of the conformal plasma in ${\mathbb{R}}^{2,1}$ in a phase with a spontaneously broken global ${\mathbb{Z}}_{2}$ symmetry. The dual black branes in a Poincare patch of asymptotically ${\mathrm{AdS}}_{4}$ have ``hair''---a condensate of the order parameter for the broken symmetry. This hair affects both the hydrodynamic and the nonhydrodynamic quasinormal modes of the black branes. Nonetheless, the shear viscosity of the conformal order is universal, the bulk viscosity vanishes and the speed of the sound waves is ${c}_{s}^{2}=\frac{1}{2}$. We compute the low-lying spectrum of the nonhydrodynamic modes. We identify a quasinormal mode associated with the fluctuations of the ${\mathbb{Z}}_{2}$ order parameter with the positive imaginary part. The presence of this mode in the spectrum renders the holographic conformal order perturbatively unstable. Correspondingly, the dual black branes violate the correlated stability conjecture.

Comparison of dynamical behavior between fractional order delayed and discrete conformable fractional order tumor-immune system

In this paper, we analyze the dynamical behavior of the delayed fractional-order tumor model with Caputo sense and discretized conformable fractional-order tumor model. The model is constituted with the group of nonlinear differential equations having effector and tumor cells. First of all, stability and bifurcation analysis of the delayed fractional-order tumor model in the sense of Caputo fractional derivative is studied, and the existence of Hopf bifurcation depending on the time delay parameter is proved by using center manifold and bifurcation theory. Applying the discretization process based on using the piecewise constant arguments to the conformable version of the model gives a two-dimensional discrete system. Stability and Neimark–Sacker bifurcation analysis of the discrete system are demonstrated using the Schur-Cohn criterion and projection method. This study reveals that the delay parameterτin the model with Caputo fractional derivative and the discretization parameterhin the discrete-time conformable fractional-order model have similar effects on the dynamical behavior of corresponding systems. Moreover, the effect of the order of fractional derivative on the dynamical behavior of the systems is discussed. Finally, all results obtained are interpreted biologically, and numerical simulations are presented to illustrate and support theoretical results.

Infinitely Many Positive Solutions for an Iterative System of Conformable Fractional Order Dynamic Boundary Value Problems on Time Scales

In this paper, we establish infinitely many positive solutions for the iterative system of conformable fractional order dynamic equations on time scales $$ \begin{aligned} &\mathcal{T}_α^{\Delta}\big[\mathcal{T}_β^{\Delta}\big(\vartheta_\mathtt{n}(t)\big)\big]=\varphi(t)\mathtt{f}_\mathtt{n}\left(\vartheta_{\mathtt{n}+1}(t)\right),~t\in(0,1)_\mathbb{T},~1

Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation

The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM. However, their biological role and properties are poorly defined. In this study, we investigated the role of GIPCs in membrane organization. Because GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of trihydroxylated long chain bases and 2-hydroxylated very long-chain fatty acids up to 26 carbon atoms. The glycan head groups of the GIPCs from monocots and dicots were analyzed by gas chromatograph–mass spectrometry, revealing different sugar moieties. Multiple biophysics tools, namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR, and molecular modeling, were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the different phytosterols species, and regulate the gel-to-fluid phase transition during temperature variations. These results unveil the multiple roles played by GIPCs in the plant PM.

Crystallization behavior of poly(lactic acid) and its blends

Poly(lactic acid) (PLA) is one of the most interesting bio-based biodegradable alternatives, with great promise to replace petroleum-based plastics. However, the intrinsic slow crystallization ability of PLA restricts its extensive applications. In this perspective, we highlight some recent advances in PLA crystallization, including nucleation by self-assembly nucleating agents, self-nucleation (or memory effect), conformational ordering in the very early stage of crystallization, crystal nucleation investigated by fast scanning calorimetry (Flash DSC), crystallization under flow, and pressure fields, and crystallization of enantiomeric blends. Finally, major challenges and future perspectives are proposed.

Modifiye Edilmiş Coulomb Potansiyelli Conformable Sturm-Liouville Problemi

In this paper, Conformable derivative order version of the Sturm-Liouville problem having modified Coulomb potential is obtained. The studied system proves the shape of the conformable derivative general statement of the Sturm-Liouville operator with boundary conditions. Furthermore, real of eigenvalues and α-orthogonal of eigenfunctions have been proved for the problem considered. Additionally, the representation of the solution of the Sturm-Liouville problem having modified Coulomb potential is found. The results are shown comparatively by figures.

What Is the Assembly Pathway of a Conjugated Polymer From Solution to Thin Films?

The hierarchical assembly of conjugated polymers has gained much attention due to its critical role in determining optical/electrical/mechanical properties. The hierarchical morphology encompasses molecular-scale intramolecular conformation (torsion angle, chain folds) and intermolecular ordering (π–π stacking), mesoscale domain size, orientation and connectivity, and macroscale alignment and (para)crystallinity. Such complex morphology in the solid state is fully determined by the polymer assembly pathway in the solution state, which, in turn, is sensitively modulated by molecular structure and processing conditions. However, molecular pictures of polymer assembly pathways remain elusive due to the lack of detailed structural characterizations in the solution state and the lack of understanding on how various factors impact the assembly pathways. In this mini-review, we present possible assembly pathways of conjugated polymers and their characteristics across length scales. Recent advances in understanding and controlling of assembly pathways are highlighted. We also discuss the current gap in our knowledge of assembly pathways, with future perspectives on research needed on this topic.

Characterization of a self-assembled monolayer of O-(2-Mercaptoethyl)-O′-methyl-hexa(ethylene glycol) (EG7-SAM) on gold electrodes

The modification of surfaces by polyethylene glycol (EGn) is an approach used to reduce the antifouling effects of these materials in a biological medium. It has been found that the packing density and conformational order of these molecules in the films are crucial for the inhibition of unspecific protein adsorption. In this work, we present a study of the formation and characterization of a self-assembled monolayer of O-(2-Mercaptoethyl)-O′-methyl-hexa(ethylene glycol) (EG7-SAM) on either poly-oriented or Au(111) single crystal surfaces. The final properties of the formed EG7-SAMs are studied by examining the reductive desorption process as well as the electronic and ionic blocking behaviour of these layers, under different experimental conditions, by using cyclic voltammetry and electrochemical impedance spectroscopy. Additional information of the structure, composition and organization is obtained by absorption-reflection infrared and X ray photoelectron spectroscopies and contact angle measurements. In contrast to the behaviour observed with alkanethiols, the EG7-SAM shows the best final organization at a modification time of 1 h. The antifouling properties of this EG7-SAM against the adsorption of the bovine serum albumin protein in a phosphate saline medium, has been evidenced by using the electrochemical quartz crystal microbalance technique.

Fractional convection-dispersion equation with conformable derivative approach

Abstract In this present work, a well-structured and limit-based derivative definition of fractional derivative term, known as conformable derivative, is employed to develop a local generalized form of time variable fractional convection-dispersion equation (FCDE). The fractional models of convection-dispersion equation have been widely established as more authentic mode to characterize the pollutant transport in geological structures. In this work, models are formulated corresponding to spatial dependency of velocity and dispersion coefficient and also for the temporally varying decay rate, that dealt with more realistic phenomenon of the pollutant transport in groundwater reservoir. Due to the non-linearity of the problem, homotopy analysis method (HAM) is adopted to investigate the complex solutions of FCDE. As the FCDE comprises the classical convection-dispersion equation (CDE) as a special case corresponding to the fractional order α = 1 , so the obtained solutions are validated by the corresponding numerical solution and exact analytical solution for α = 1 and solutions are also verified for different fractional values of α . The effect of conformable derivative order α is properly visible over concentration strength. Hence, this investigation helps to interpret the accurate description of time dependent behaviour of contaminant transport in porous structure.

Conformational disorder of organic cations tunes the charge carrier mobility in two-dimensional organic-inorganic perovskites

The chemical nature of the organic cations governs the optoelectronic properties of two-dimensional organic-inorganic perovskites. But its mechanism is not fully understood. Here, we apply femtosecond broadband sum frequency generation vibrational spectroscopy to investigate the molecular conformation of spacer organic cations in two-dimensional organic-inorganic perovskite films and establish a correlation among the conformation of the organic cations, the charge carrier mobility, and broadband emission. Our study indicates that both the mobility and broadband emission show strong dependence on the molecular conformational order of organic cations. The gauche defect and local chain distortion of organic cations are the structural origin of the in-plane mobility reduction and broad emission in two-dimensional organic-inorganic perovskites. Both of the interlayer distance and the conformational order of the organic cations affect the out-of-plane mobility. This work provides molecular-level understanding of the conformation of organic cations in optimizing the optoelectronic properties of two-dimensional organic-inorganic perovskites.

Conformational ordering of intrinsically disordered peptides for targeting translation initiation

BackgroundIntrinsically disordered regions (IDRs) in proteins can regulate their activity by facilitating protein-protein interactions (PPIs) as exemplified in the recruitment of the eukaryotic translation initiation factor 4E (eIF4E) protein by the protein eIF4G. Deregulation of this PPI module is central to a broad spectrum of cancer related malignancies and its targeted inhibition through bioactive peptides is a promising strategy for therapeutic intervention. MethodsWe employed molecular dynamics simulations coupled with biophysical assays to rationally develop peptide derivatives from the intrinsically disordered eIF4G scaffold by incorporating non-natural amino acids that facilitates disorder-to-order transition. ResultsThe conformational heterogeneity of these peptides and the degree of structural reorganization required to adopt the optimum mode of interaction with eIF4E underscores their differential binding affinities. The presence of a pre-structured local helical element in the ensemble of structures was instrumental in the efficient docking of the peptides on to the protein surface. The formation of Y4: P38 hydrogen-bond interaction between the peptide and eIF4E is a rate limiting event in the efficient recognition of the protein since it occurs through the disordered region of the peptide. ConclusionsThese insights were exploited to further design features into the peptide to propagate bound-state conformations in solution which resulted in the generation of a potent eIF4E binder. General significanceThe study illustrates the molecular basis of eIF4E recognition by a disordered epitope from eIF4G and its modulation to generate peptides that can potentially attenuate translation initiation in oncology.