Molecular Conformational Changes Research Articles

The construction of a FRET assembly by using gold nanoclusters and carbon dots and their application as a ratiometric probe for cysteine detection

Förster resonance energy transfer (FRET) is a powerful tool to study single molecular conformation and/or distance changes between two fluorophores, which is mainly depended on the combinations and spatial distance between the donor and acceptor. The present study has built a FRET assembly by using gold nanoclusters capped by glutathione (AuNCs@GSH) and carbon dots (CDs) prepared by polyethyleneimine (PEI) through supramolecular interactions. The assembly is characterized in detail by employing Zeta potential, UV–vis absorption and fluorescence spectra, the luminescent decay curves and TEM images, which indicate the AuNCs are adhered to the surface of CDs. In addition, the transfer efficiency between them has been calculated to be 65.7%, which is sufficient enough for practical applications, and particularly, the quantum yield (QY) of AuNCs@GSH is increased from 3.07% to 5.35% via the assembly. Moreover, the FRET assembly is used as a ratiometric probe for cysteine detection in showing a limit of detection (LOD) at 100 nM, a very high selectivity to cysteine among amino acids as well as a strong anti-interference on them, especially, it was feasible for cysteine detection in fetal calf serum, which showed very high potential in the diagnose of cysteine-related disease.

Unlocking the secrets of mutable collagenous tissue

The mutable collagenous tissue (MCT) of echinoderms (e.g. sea cucumbers, starfish and sea urchins) is unique because of its ability to ‘switch’ mechanical states rapidly and reversibly – from stiff to soft and vice versa. This kind of tissue in humans, for example, in skin, tendons and ligaments, does not have this property. So what are the molecular-level secrets by which MCT achieves this transformative ability? New real-time ultrastructural investigations are beginning to shed light on this question. Synchrotron X-ray measurements of dynamic molecular conformational changes point to the key factor being the gel-like matrix between the collagen fibrils. These findings could have applications for developing treatments for collagen-based disorders.

Inhibition of P-Glycoprotein Mediated Efflux in Caco-2 Cells by Phytic Acid.

Phytic acid (IP6) is a natural phosphorylated inositol, which is abundantly present in most cereal grains and seeds. This study investigated the effects of IP6 regulation on P-glycoprotein (P-gp) and its potential mechanisms using in situ and in vitro models. The effective permeability of the typical P-gp substrate rhodamine 123 (R123) in colon was significantly increased from (1.69 ± 0.22) × 10-5 cm/s in the control group to (3.39 ± 0.417) × 10-5 cm/s (p < 0.01) in the 3.5 mM IP6 group. Additionally, IP6 can concentration-dependently decrease the R123 efflux ratio in both Caco-2 and MDCK II-MDR1 cell monolayers and increase intracellular R123 accumulation in Caco-2 cells. Furthermore, IP6 noncompetitively inhibited P-gp by impacting R123 efflux kinetics. The noncompetitive inhibition of P-gp by IP6 was likely due to decreases in P-gp ATPase activity and P-gp molecular conformational changes induced by IP6. In summary, IP6 is a promising P-gp inhibitor candidate.

An organoferroelasticity driven by molecular conformational change.

A single crystal of adipic acid shows twinning ferroelasticity by the reversible molecular conformational change. The flexible nature of components in molecular solids raises the efficiency of energy dissipation using organoferroelasticity.

Preparation of Cell-free Synthesized Proteins Selectively Double Labeled for Single-molecule FRET Studies.

Single-molecule FRET (smFRET) is a powerful tool to investigate molecular structures and conformational changes of biological molecules. The technique requires protein samples that are site-specifically equipped with a pair of donor and acceptor fluorophores. Here, we present a detailed protocol for preparing double-labeled proteins for smFRET studies. The protocol describes two cell-free approaches to achieve a selective label scheme that allows the highest possible accuracy in inter-dye distance determination.

Theoretical study on mesoscopic-size impurity effects in the charge separation process of organic photocells.

A bulk-heterojunction structure is often employed to develop high-performance organic photocells, in which the donor and acceptor regions are complexly intertwined. In such situations, mesoscopic-scale islands and peninsulas that compose the donor materials may be formed in the acceptor region. Alternatively, the donor region may extend deeply into the acceptor region. This yields mesoscopic-size impurities that can create obstacles in the charge separation (exciton dissociation) process of organic photocells and prevents the dissociation of excitons (electron-hole pairs). We previously reported on the effect of the cooperative behavior between the hot charge transfer (CT) state and the dimensional (entropy) effect on the charge separation process. In this paper, we discuss the mesoscopic-scale impurity effect on the charge separation process in PCBM acceptor models by considering the hot CT state and dimensional effects. In addition, we discuss atomic-scale effects such as molecular distortions and conformation changes using molecular dynamics (MD) simulations.

A multi-scale approach to describe electrical impulses propagating along actin filaments in both intracellular and in vitro conditions.

An accurate and efficient characterization of the polyelectrolyte properties for cytoskeleton filaments are key to the molecular understanding of electrical signal propagation, bundle and network formation, as well as their potential nanotechnological applications. In this article, we introduce an innovative multi-scale approach able to account for the atomistic details of a protein molecular structure, its biological environment, and their impact on electrical impulses propagating along wild type actin filaments. The formulation includes non-trivial contributions to the ionic electrical conductivity and capacitance coming from the diffuse part of the electrical double layer of G-actins. We utilize this monomer characterization in a non-linear inhomogeneous transmission line prototype model to account for the monomer–monomer interactions, dissipation and damping perturbations along the filament length. A novel, simple, accurate, approximate analytic expression has been obtained for the transmission line model. Our results reveal the propagation of electrical signal impulses in the form of solitons for the range of voltage stimulus and electrolyte solutions typically present for intracellular and in vitro conditions. The approach predicts a lower electrical conductivity with higher linear capacitance and non-linear accumulation of charge for intracellular conditions. Our results show a significant influence of the voltage input on the electrical impulse shape, attenuation and kern propagation velocity. The filament is able to sustain the soliton propagation at almost constant kern velocity for the in vitro condition, whereas the intracellular condition displays a remarkable deceleration. Additionally, the solitons are narrower and travel faster at higher voltage input. As a unique feature, this multi-scale theory is able to account for molecular structure conformation (mutation) and biological environment (protonations/deprotonations) changes often present in pathological conditions. It is also applicable to other highly charged rod-like polyelectrolytes with relevance in biomedicine and biophysics.

Impact of ultrasound pretreatment on hydrolysate and digestion products of grape seed protein

The effects of ultrasound pretreatment with different working modes, including mono frequency ultrasound (MFU), simultaneous dual frequency ultrasound (SDFU) and alternate dual frequency ultrasound (ADFU) using energy-gather counter flow ultrasound equipment, on the degree of hydrolysis (DH) of grape seed protein (GSP) hydrolysate and IC50 of GSP digestion products were studied. Amino acid composition analysis (AACA), ultraviolet–visible (UV) spectroscopy and atomic force microscopy (AFM) of GSP with different ultrasound pretreatments were measured. The results showed that MFU, SDFU and ADFU pretreatments improved the DH and reduced the IC50 of GSP significantly (P < .05). The MFU of 20 kHz and SDFU of 20/40 kHz showed higher ACE inhibitory activity within the MFU and SDFU groups, respectively. ADFU of 20/35 kHz produced the highest ACE inhibitory activity among the three working modes (MFU, SDFU and ADFU). AACA showed that all the working modes of the ultrasound pretreatment could increase the amount of hydrophobic amino acids and the total amino acids. The changes in UV spectra and amino acid analysis indicated the unfolding of protein structure and exposure of more hydrophobic groups by SDFU and ADFU pretreatments. AFM analysis of the GSP indicated that the microstructures were destroyed and the particle size reduced after dual-frequency ultrasound pretreatments. Therefore, energy-gather counter flow ultrasound pretreatment is an effective method to improve the DH and reducing the IC50 due to the changes of molecular conformation and effects on the microstructure by sonochemistry of GSP. In conclusion, it is necessary to select the frequency and working modes of ultrasound pretreatment for the preparation of ACE inhibitory peptide of GSP.

Vapour–liquid interfacial properties of n-alkanes

The vapour–liquid interfacial properties of linear alkanes (n-hexane, n-heptane, n-octane, n-nonane, and n-decane) were studied via the square gradient theory (SGT) and by molecular dynamics (MD) simulations. The objectives were the determination of interfacial density profiles, surface tensions, molecular orientations, and conformations via order parameters and radii of gyration, the self-diffusion coefficients and free energy profiles. The Soave-Redlich-Kwong (SRK) and Perturbed-Chain SAFT (PC-SAFT) equations of state (EoSs) were combined with SGT to correlate experimental surface tensions and to predict density profiles. SGT-EoSs and MD interfacial density profiles and interface thicknesses are very similar, especially at low reduced temperatures. MD simulations revealed that not only does the density change throughout the interface but also the average molecular orientation and conformation change. The interface can be roughly divided into three main regions: around the Gibbs dividing surface the molecules, on average, lie at the interface; and in the two regions close to the bulk phases they favour a non-parallel orientation. With respect to the self-diffusion coefficients, three different zones were also observed: close to the bulk phases, the diffusivity is a nonlinear function of the local density, whereas in the middle zone it is linear and coincides with the quasi-linear portion of the density profile. Free energy profiles were obtained via umbrella sampling technique, showing an increase of energy at the interfacial region. These profiles show a similar behaviour as the density profiles.

Wettability of Al2O3 Surface by Organic Molecules: Insights from Molecular Dynamics Simulation.

We use molecular dynamics (MD) simulations to investigate the wettability of Al2O3 (0001) by organic molecules. Diffusion coefficients estimated for organic molecules are clearly correlated with the contact angles observed experimentally. The results of the MD simulations suggest that molecular flexibility influences wettability. In other words, wettability owing to flexible molecules, such as an epoxy tridecamer, improves with increasing temperature because the interaction between the droplet and the surface increases due to changes in molecular conformation. Conversely, for phenylene sulfide tetramer, wettability does not change with temperature because of the molecular rigidity. In addition, for epoxy monomers, we analyze the different molecular structures responsible for modifying the droplet-surface interaction. For hydrogens in aromatic rings and in methyl groups, the interaction with the surface clearly decreases with increasing temperature.

On–Off Mechano-responsive Switching of ESIPT Luminescence in Polymorphic N-Salicylidene-4-amino-2-methylbenzotriazole

We report the synthesis of a luminescent N-salicylidene aniline derivative, N-salicylidene-4-amino-2-methylbenzotriazole (1), and the study of its polymorphism and photophysical properties. Three phases showing yellow (1-Y), orange (1-O), and red (1-R) fluorescence have been isolated and characterized by thermal and single crystal X-ray analysis. The photoluminescence results from excited-state intramolecular proton transfer process and the quantum yield is strongly dependent on polymorphism (Φ1-Y = 0.87, Φ1-O = 0.11, Φ1-R = 0.028). The poorly emitting 1-R can be easily prepared, converted to the bright 1-Y by grinding, and reverted to 1-R through melting and annealing, giving rise to a luminescence on–off mechano-responsive cycle. The different photophysical properties are explained with the variable π-overlap and molecular conformation changes in the three polymorphs, characterized by a very similar crystal packing. By DFT calculations, the absorption properties were explained as dependent on the torsio...

A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms.

Modelling ionic channels represents a fundamental step towards developing biologically detailed neuron models. Until recently, the voltage-gated ion channels have been mainly modelled according to the formalism introduced by the seminal works of Hodgkin and Huxley (HH). However, following the continuing achievements in the biophysical and molecular comprehension of these pore-forming transmembrane proteins, the HH formalism turned out to carry limitations and inconsistencies in reproducing the ion-channels electrophysiological behaviour. At the same time, Markov-type kinetic models have been increasingly proven to successfully replicate both the electrophysiological and biophysical features of different ion channels. However, in order to model even the finest non-conducting molecular conformational change, they are often equipped with a considerable number of states and related transitions, which make them computationally heavy and less suitable for implementation in conductance-based neurons and large networks of those. In this purely modelling study we develop a Markov-type kinetic model for all human voltage-gated sodium channels (VGSCs). The model framework is detailed, unifying (i.e., it accounts for all ion-channel isoforms) and computationally efficient (i.e. with a minimal set of states and transitions). The electrophysiological data to be modelled are gathered from previously published studies on whole-cell patch-clamp experiments in mammalian cell lines heterologously expressing the human VGSC subtypes (from NaV1.1 to NaV1.9). By adopting a minimum sequence of states, and using the same state diagram for all the distinct isoforms, the model ensures the lightest computational load when used in neuron models and neural networks of increasing complexity. The transitions between the states are described by original ordinary differential equations, which represent the rate of the state transitions as a function of voltage (i.e., membrane potential). The kinetic model, developed in the NEURON simulation environment, appears to be the simplest and most parsimonious way for a detailed phenomenological description of the human VGSCs electrophysiological behaviour.

Learning surface molecular structures via machine vision

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Conformational Effect of Polymorphic Terfluorene on Photophysics, Crystal Morphologies, and Lasing Behaviors

Molecular conformation is an important factor in flexible organic molecules and deeply influences their physical and chemical properties. Here, a model fluorene trimer, 2,2′:7′,2″-ter(9,9-dimethylfluorene) (TDMeF), was designed and synthesized to investigate the effect of conformational diversity of oligofluorene on the morphologies of microcrystals and photophysical properties. Single crystal X-ray diffraction analysis indicates that TDMeF has four polymorphs with different molecular conformations, and crystalline polymorphism is first observed in oligofluorenes. Moreover, the slight change in molecular conformation leads to form different crystal morphologies, namely, ribbon and rodlike microcrystals, in virtue of different intermolecular interactions. Finally, although both microcrystals display deep blue lasing behaviors, the rodlike microcrystal shows a threshold of 114 W/cm2, which is twice times lower than that of the ribbon-like one due to the effect of molecular orientation and optical microcavity.

Förster resonance energy transfer: Role of diffusion of fluorophore orientation and separation in observed shifts of FRET efficiency.

Förster resonance energy transfer (FRET) is a widely used single-molecule technique for measuring nanoscale distances from changes in the non-radiative transfer of energy between donor and acceptor fluorophores. For macromolecules and complexes this observed transfer efficiency is used to infer changes in molecular conformation under differing experimental conditions. However, sometimes shifts are observed in the FRET efficiency even when there is strong experimental evidence that the molecular conformational state is unchanged. We investigate ways in which such discrepancies can arise from kinetic effects. We show that significant shifts can arise from the interplay between excitation kinetics, orientation diffusion of fluorophores, separation diffusion of fluorophores, and non-emitting quenching.

Relation between molecular electronic structure and nuclear spin-induced circular dichroism

The recently theoretically described nuclear spin-induced circular dichroism (NSCD) is a promising method for the optical detection of nuclear magnetization. NSCD involves both optical excitations of the molecule and hyperfine interactions and, thus, it offers a means to realize a spectroscopy with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state. The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes are discussed. The results underline NSCD spectroscopy as a plausible tool with a power for the identification of not only different molecules, but their specific structures as well.

Nanoscale monolayer adsorption of polyelectrolytes at the solid/liquid interface observed by quartz crystal microbalance

The adsorption properties of cationic polyelectrolytes (poly (diallyl dimethylammonium chloride) (PDDA) and poly (allylamine hydrochloride) (PAH)) on solid surfaces were observed using quartz crystal microbalance. The response of adsorption was different with the change of polyelectrolyte solution concentration and pH value. The influence of pH value on the PDDA adsorption process is inconspicuous, while PAH shows strong dependence on the pH value. Furthermore, the change of molecular conformation of polyelectrolyte molecule is the main factor that affects the adsorption properties and structures.

Gene-Transformation-Induced Changes in Chemical Functional Group Features and Molecular Structure Conformation in Alfalfa Plants Co-Expressing Lc-bHLH and C1-MYB Transcriptive Flavanoid Regulatory Genes: Effects of Single-Gene and Two-Gene Insertion.

Alfalfa (Medicago sativa L.) genotypes transformed with Lc-bHLH and Lc transcription genes were developed with the intention of stimulating proanthocyanidin synthesis in the aerial parts of the plant. To our knowledge, there are no studies on the effect of single-gene and two-gene transformation on chemical functional groups and molecular structure changes in these plants. The objective of this study was to use advanced molecular spectroscopy with multivariate chemometrics to determine chemical functional group intensity and molecular structure changes in alfalfa plants when co-expressing Lc-bHLH and C1-MYB transcriptive flavanoid regulatory genes in comparison with non-transgenic (NT) and AC Grazeland (ACGL) genotypes. The results showed that compared to NT genotype, the presence of double genes (Lc and C1) increased ratios of both the area and peak height of protein structural Amide I/II and the height ratio of α-helix to β-sheet. In carbohydrate-related spectral analysis, the double gene-transformed alfalfa genotypes exhibited lower peak heights at 1370, 1240, 1153, and 1020 cm−1 compared to the NT genotype. Furthermore, the effect of double gene transformation on carbohydrate molecular structure was clearly revealed in the principal component analysis of the spectra. In conclusion, single or double transformation of Lc and C1 genes resulted in changing functional groups and molecular structure related to proteins and carbohydrates compared to the NT alfalfa genotype. The current study provided molecular structural information on the transgenic alfalfa plants and provided an insight into the impact of transgenes on protein and carbohydrate properties and their molecular structure’s changes.

Alkylated pectin: Molecular characterization, conformational change and gel property

The molecular characterization, conformational change and gel property of alkylated pectins (ALP) prepared by chemical covalent binding with different alkyl chains (C6, C12, or C18) at different degrees of substitution (DS) (1.35, 2.90 or 4.53) were investigated. Molecular weight of ALP was affected by degradation, alkylation and aggregation. The conformation parameter α (obtained from Rg vs Mw) and ρ (Rg/Rh) both indicated that original pectin (HMP) and ALP with the lowest DS and the shortest alkyl chain had random coil conformation, while ALP with the greater DS and longer chain had sphere conformation in 0.1 M NaCl. In addition, we observed that the gel strength of ALP with higher DS and longer chain length was higher than HMP, and they were significantly positively correlated with the conformation parameter Mw.

SERS Measurement of Cysteamine Molecules Stretched by the Electromagnetophoretic Force.

The role of an external force on chemical equilibria is an important subject in mechanobiochemistry. The effect of an electromagnetophoretic force for the stretching of cysteamine molecules was examined by using SERS spectrometry. Polystyrene particles modified with cysteamine were bound to silver nanoparticles adsorbed on the wall of a silica capillary cell. Under a constant magnetic field, when an electric current was applied to the conductive medium in the capillary, the shift of SERS bands and the increase of the trans/gauche ratio of cysteamine were observed, suggesting a molecular conformation change of cysteamine due to the stretching force.