Kinetics of protein-release by an aptamer-based DNA nanodevice

A recently introduced DNA nanodevice can be used to selectively bind or release the protein thrombin triggered by DNA effector strands. The release process is not well described by simple first or second order reaction kinetics. Here, fluorescence resonance energy transfer and fluorescence correlation spectroscopy experiments are used to explore the kinetics of the release process in detail. To this end the influence of concentration variations and also of temperature is determined. The relevant kinetic parameters are extracted from these experiments and the kinetic behavior of the system is simulated numerically using a set of rate equations. The hydrodynamic radii of the aptamer device alone and bound to thrombin are determined as well as the dissociation constant for the aptamer device-thrombin complex. The results from the experiments and a numerical simulation support the view that the DNA effector strand first binds to the aptamer device followed by the displacement of the protein.     

Molecular switching on surfaces

Molecular switching has established itself as a key functionality of building blocks developed for addressable materials and surfaces over the last two decades. Many challenges in their use and characterisation have been presented by the wide variation in interfaces studied, these ranging from truly single-molecule devices to two-dimensional self-assembled monolayers and thin films that bridge the gap between surface and macroscopically bulk materials (polymers, MOFs, COFs), and further still to other interfaces (solid–liquid, liquid–air, etc.). The low number density of molecules on monolayer-coated interfaces as well as in thin films, for example, presents substantial challenges in the characterisation of the composition of modified interfaces. The switching of molecular structure with external stimuli such as light and electrode potential adds a further layer of complexity in the characterisation of function. Such characterisation “in action” is necessary to correlate macroscopic phenomena with changes in molecular structure. In this review, key classes of molecular switches that have been applied frequently to interfaces will be discussed in the context of the techniques and approaches used for their operando characterisation. In particular, we will address issues surrounding the non-innocence of otherwise information-rich techniques and show how model – non-switching – compounds are often helpful in confirming and understanding the limitations and quirks of specific techniques.     

Effects of ultrasound treatment on the morphological characteristics,structures and emulsifying properties of genipin cross-linked myofibrillar protein

Genipin is a natural crosslinker that improves the functional properties of proteins by modifying its structures. This study aimed to investigate the effects of sonication on the emulsifying properties of different genipin concentration-induced myofibrillar protein (MP) cross-linking. The structural characteristics, solubility, emulsifying properties, and rheological properties of genipin-induced MP crosslinking without sonication (Native), sonication before crosslinking (UMP), and sonication after crosslinking (MPU) treatments were determined, and the interaction between genipin and MP were estimated by molecular docking. The results demonstrated that hydrogen bond might be the main forces for genipin binding to the MP, and 0.5 μM/mg genipin was a desirable concentration for protein cross-linking to improve MP emulsion stability. Ultrasound treatment before and after crosslinking were better than Native treatment to improve the emulsifying stability index (ESI) of MP. Among the three treatment groups at the 0.5 μM/mg genipin treatment, the MPU treatment group showed the smallest size, most uniform protein particle distribution, and the highest ESI (59.89%). Additionally, the highest α-helix (41.96%) in the MPU + G5 group may be conducive to the formation of a stable and multilayer oil–water interface. Furthermore, the free groups, solubility, and protein exposure extent of the MPU groups were higher than those of UMP and Native groups. Therefore, this work suggests that the treatment of cross-linking followed by ultrasound (MPU) could be a desirable approach for improving the emulsifying stability of MP.     

Polymer-mediated and ultrasound-assisted crystallization of ropivacaine: Crystal growth and morphology modulation

The objective of this research was to modify the crystal shape and size of poorly water-soluble drug ropivacaine, and to reveal the effects of polymeric additive and ultrasound on crystal nucleation and growth. Ropivacaine often grow as needle-like crystals extended along the a-axis and the shape was hardly controllable by altering solvent types and operating conditions for the crystallization process. We found that ropivacaine crystallized as block-like crystals when polyvinylpyrrolidone (PVP) was used. The control over crystal morphology by the additive was related to crystallization temperature, solute concentration, additive concentration, and molecular weight. SEM and AFM analyses were performed providing insights into crystal growth pattern and cavities on the surface induced by the polymeric additive. In ultrasound-assisted crystallization, the impacts of ultrasonic time, ultrasonic power, and additive concentration were investigated. The particles precipitated at extended ultrasonic time exhibited plate-like crystals with shorter aspect ratio. Combined use of polymeric additive and ultrasound led to rice-shaped crystals, which the average particle size was further decreased. The induction time measurement and single crystal growth experiments were carried out. The results suggested that PVP worked as strong nucleation and growth inhibitor. Molecular dynamics simulation was performed to explore the action mechanism of the polymer. The interaction energies between PVP and crystal faces were calculated, and mobility of the additive with different chain length in crystal-solution system was evaluated by mean square displacement. Based on the study, a possible mechanism for the morphological evolution of ropivacaine crystals assisted by PVP and ultrasound was proposed.     

Molecular-dynamics of a 2D Model of the Shape Memory Effect

This work investigates the thermodynamic properties of a qualitative atomistic model for austenite–martensite transitions. The model, still in 2D, employs Lennard-Jones potentials for the determination of the atomic interactions. By use of two atom species it is possible to identify three stable lattice structures in 2D, interpreted as austenite and two variants of martensite. The model is described in the first part of the work [6] in detail. The present work studies the thermodynamic properties of the model concerning a small, 2-dimensional test assembly consisting of 41 atoms. The phase stability is investigated by exploitation of the condition of minimal free energy. The free energy is calculated from the thermal equation of state, which is measured in numerical tensile tests. In the second part of this work a chain of eleven 41-atom assemblies is investigated. The chain is interpreted as an idealized larger body, where the individual crystallites represent crystallographic layers allowing for the creation of micro structure. By use of tensile tests at various temperature conditions we sketch how such chain may exhibit quasi-plasticity, pseudo-elasticity and the shape memory effect.     

Brownian Dynamics simulation of reversible polymeric networks

In this paper we describe the construction of a Brownian Dynamics simulation of reversibly cross-linked networks. The simulation differs from existing analytical approaches and computer simulations of networks in the sense that we also take the topology of the network into account. The motion of the junction points between different molecules is not prescribed but is calculated from a force balance. This makes it possible to measure the effect of network reorganisations on the stress relaxation. The response of networks to shear flow is measured and analysed in terms of transient network theory and within the framework of linear viscoelasticity. It is shown that the average motion of the junction is affine but that there is a long time diffusive process around the affine path. It was found that, even in systems with Gaussian chains and fixed association and disociation rates, a shear thickening of the viscosity and primary normal stress coefficient can occur. The reason was found to be that dangling segments are recaptured by the network before they had the opportunity to fully relax to the equilibrium state where the probability of reattachment to the network increases linearly with the length of a segment. Due to this mechanism the fraction of long segments present in the network is increased. This explanation of shear thickening seems to be consistent with experimental findings.     

DNA molecular configurations in flows near adsorbing and nonadsorbing surfaces

We investigate experimentally -phage and T2-coliphage DNA molecules near both non-adsorbing glass and adsorbing 3-aminopropyltriethoxysilane (APTES)-coated glass surfaces in a simple steady shearing flow generated by a torsional flow cell. The DNA molecular deformations near the surface are found to be considerably weaker than in bulk flow at the same shear rate. This affects the DNA molecules deposition and stretching on the adsorbing surface. Surprisingly, for a simple shearing flow in the torsional shearing device, the observed stretch, for molecules both near (<10 µm) the surface and adsorbed to it, is much less than predicted by simulations.     

Modeling the dynamic behavior of shape memory alloys

The paper studies the single degree of freedom vibration of a rigid mass suspended by a thin-walled shape memory alloy tube under torsional loading. The behavior is analyzed for the cases of quasiplasticity (low temperatures) and pseudoelasticity (high temperatures) on the basis of an improved version of the Müller–Achenbach model. To illustrate the strong hysteresis-induced damping capacity and the non-linear vibration characteristics, both, free and forced vibrations are considered in the first part of the paper. This is done on the basis of an isothermal version of the model, while the second part of the paper focuses on the effect of non-constant temperature caused by the rate-dependent release and absorption of latent heats.     

Dynamic theory for smectic A liquid crystals

A dynamic continuum theory is presented for smectic A liquid crystals in which the usual director n and unit layer normal a do not always necessarily coincide. Most previous dynamic continuum theories equate n with a; the theory developed in this article allows n and a to differ in non-equilibrium situations, work that has been motivated by the recent investigations by Auernhammer et al. (Rheol. Acta 39, 215–222, 2000; Phys. Rev. E 66, 061707, 2002) and Soddemann et al. (Eur. Phys. J. E 13, 141–151, 2004). The usual Oseen constraint () for smectics is not imposed upon the unit normal a. Permeation is also included. After a summary of the complete dynamic equations, an application is given via an example which shows that planar aligned layers of smectic A subjected to an arbitrary periodic disturbance are linearly stable.      

Molecular characterization,modeling and docking of CYP107CB2 from Bacillus lehensis G1, an alkaliphile

Cytochrome P450s are a superfamily of heme monooxygenases which catalyze a wide range of biochemical reactions. The reactions involve the introduction of an oxygen atom into an inactivated carbon of a compound which is essential to produce an intermediate of a hydroxylated product. The diversity of chemical reactions catalyzed by cytochrome P450s has led to their increased demand in numerous industrial and biotechnology applications. A recent study showed that a gene sequence encoding a CYP was found in the genome of Bacillus lehensis G1, and this gene shared structural similarity with the bacterial vitamin D hydroxylase (Vdh) from Pseudonocardia autotrophica. The objectives of present study was to mine, for a novel CYP from a new isolate B. lehensis G1 alkaliphile and determine the biological properties and functionalities of CYP in this bacterium. Our study employed the usage of computational methods to search for the novel CYP from CYP structural databases to identify the conserved pattern, functional domain and sequence properties of the uncharacterized CYP from B. lehensis G1. A computational homology model of the protein’s structure was generated and a docking analysis was performed to provide useful structural knowledge on the enzyme’s possible substrate and their interaction. Sequence analysis indicated that the newly identified CYP, termed CYP107CB2, contained the fingerprint heme binding sequence motif FxxGxxxCxG at position 336-345 as well as other highly conserved motifs characteristic of cytochrome P450 proteins. Using docking studies, we identified Ser-79, Leu-81, Val-231, Val-279, Val-383, Ala-232, Thr-236 and Thr-283 as important active site residues capable of stabilizing interactions with several potential substrates, including vitamin D₃, 25-hydroxyvitamin D₃ and 1α-hydroxyvitamin D₃, in which all substrates docked proximally to the enzyme’s heme center. Biochemical analysis indicated that CYP107CB2 is a biologically active protein to produce 1α,25-dihydroxyvitamin D₃ from 1α-hydroxyvitamin D₃. Based on these results, we conclude that the novel CYP107CB2 identified from B. lehensis G1 is a putative vitamin D hydroxylase which is possibly capable of catalyzing the bioconversion of parental vitamin D₃ to calcitriol, or related metabolic products.