Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics.

In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.

CNT effective interfacial energy and pre-exponential kinetic factor from measured NaCl crystal nucleation time distributions in contracting microdroplets.

Nucleation, the birth of a stable cluster from a disorder, is inherently stochastic. Yet up to date, there are no quantitative studies on NaCl nucleation that accounts for its stochastic nature. Here, we report the first stochastic treatment of NaCl-water nucleation kinetics. Using a recently developed microfluidic system and evaporation model, our measured interfacial energies extracted from a modified Poisson distribution of nucleation time show an excellent agreement with theoretical predictions. Furthermore, analysis of nucleation parameters in 0.5, 1.5, and 5.5 pl microdroplets reveals an interesting interplay between confinement effects and shifting of nucleation mechanisms. Overall, our findings highlight the need to treat nucleation stochastically rather than deterministically to bridge the gap between theory and experiment.

Evaporation Dynamics of Sessile Saline Microdroplets in Oil.

The occurrence of concentration and temperature gradients in saline microdroplets evaporating directly in air makes them unsuitable for nucleation studies where homogeneous composition is required. This can be addressed by immersing the droplet in oil under regulated humidity and reducing the volume to the picoliter range. However, the evaporation dynamics of such a system is not well understood. In this work, we present evaporation models applicable for arrays of sessile microdroplets with dissolved solute submerged in a thin layer of oil. Our model accounts for the variable diffusion distance due to the presence of the oil film separating the droplet and air, the variation of the solution density and water activity due to the evolving solute concentration, and the diffusive interaction between neighboring droplets. Our model shows excellent agreement with experimental data for both pure water and NaCl solution. With this model, we demonstrate that assuming a constant evaporation rate and neglecting the diffusive interactions can lead to severe inaccuracies in the measurement of droplet concentration, particularly during nucleation experiments. Given the significance of droplet evaporation in a wide array of scientific and industrial applications, the models and insights presented herein would be of great value to many fields of interest.

Nucleation in sessile saline microdroplets: induction time measurement via deliquescence-recrystallization cycling.

Induction time, a measure of how long one will wait for nucleation to occur, is an important parameter in quantifying nucleation kinetics and its underlying mechanisms. Due to the stochastic nature of nucleation, efficient methods for measuring large numbers of independent induction times are needed to ensure statistical reproducibility. In this work, we present a novel approach for measuring and analyzing induction times in sessile arrays of microdroplets via deliquescence/recrystallization cycling. With the help of a recently developed image analysis protocol, we show that the interfering diffusion-mediated interactions between microdroplets can be eliminated by controlling the relative humidity, thereby ensuring independent nucleation events. Moreover, possible influence of heterogeneities, impurities, and memory effect appear negligible as suggested by our 2-cycle experiment. Further statistical analysis (k-sample Anderson-Darling test) reveals that upon identifying possible outliers, the dimensionless induction times obtained from different datasets (microdroplet lines) obey the same distribution and thus can be pooled together to form a much larger dataset. The pooled dataset showed an excellent fit with the Weibull function, giving a mean supersaturation at nucleation of 1.61 and 1.85 for the 60 pL and 4 pL microdroplets respectively. This confirms the effect of confinement where smaller systems require higher supersaturations to nucleate. Both the experimental method and the data-treatment procedure presented herein offer promising routes in the study of fundamental aspects of nucleation kinetics, particularly confinement effects, and are adaptable to other salts, pharmaceuticals, or biological crystals of interest.

Preparation of alginate hydrogel microparticles by gelation introducing cross-linkers using droplet-based microfluidics: a review of methods.

This review examines the preparation of alginate hydrogel microparticles by using droplet-based microfluidics, a technique widely employed for its ease of use and excellent control of physicochemical properties, with narrow size distribution. The gelation of alginate is realized "on-chip" and/or "off-chip", depending on where cross-linkers are introduced. Various strategies are described and compared. Microparticle properties such as size, shape, concentration, stability and mechanical properties are discussed. Finally, we consider future perspectives for the preparation of hydrogel microparticles and their potential applications.

Advances in the Use of Microfluidics to Study Crystallization Fundamentals.

This review compares droplet-based microfluidic systems used to study crystallization fundamentals in chemistry and biology. An original high-throughput droplet-based microfluidic platform is presented. It uses nanoliter droplets, generates a chemical library, and directly solubilizes powder, thus economizing both material and time. It is compatible with all solvents without the need for surfactant. Its flexibility permits phase diagram determination and crystallization studies (screening and optimizing experiments) and makes it easy to use for nonspecialists in microfluidics. Moreover, it allows concentration measurement via ultraviolet spectroscopy and solid characterization via X-ray diffraction analysis.

Crystallization via tubing microfluidics permits both in situ and ex situ X-ray diffraction.

A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.

Localizing and inducing primary nucleation.

Do the differing properties of materials influence their nucleation mechanisms? We present different experimental approaches to study and control nucleation, and shed light on some of the factors affecting the nucleation process.

Wetting properties and critical micellar concentration of benzalkonium chloride mixed in sodium hypochlorite.

INTRODUCTION: The purposes of the present study were to (1) assess the effect of the addition of benzalkonium chloride to sodium hypochlorite on its wetting properties, contact angle, and surface energy; (2) determine the critical micellar concentration of benzalkonium chloride in sodium hypochlorite; and (3) investigate the influence of addition of benzalkonium chloride on the free chlorine level, cytotoxicity, and antiseptic properties of the mixture. METHODS: Solutions of benzalkonium chloride, with concentrations ranging from 0%-1%, were mixed in 2.4% sodium hypochlorite and tested as follows. The wetting properties were investigated by measuring the contact angle of the solutions on a nondehydrated dentin surface by using the static sessile drop method. The pending drop technique was subsequently used to determine the surface energy of the solutions. The critical micellar concentration of benzalkonium chloride mixed in sodium hypochlorite was calculated from the data. When 2.4% NaOCl was mixed with benzalkonium chloride at the critical micellar concentration, 3 parameters were tested: free chloride content, cytotoxicity, and antibacterial effects against Enterococcus faecalis. RESULTS: The contact angle (P < .001) as well as the surface energy (P < .001) significantly decreased with increasing benzalkonium chloride concentrations. The critical micellar concentration of benzalkonium chloride in sodium hypochlorite was 0.008%. At this concentration, the addition of benzalkonium chloride had no effect on the free chlorine content, cytotoxicity, or antibacterial efficiency of the mixture. CONCLUSIONS: The addition of benzalkonium chloride to sodium hypochlorite at the critical micellar concentration reduced the contact angle by 51.2% and the surface energy by 53.4%, without affecting the free chloride content, cytotoxicity, or antibacterial properties of the mixture.

Practical physics behind growing crystals of biological macromolecules.

The aim of this review is to provide biocrystallographers who intend to tackle protein-crystallization with theory and practical examples. Crystallization involves two separate processes, nucleation and growth, which are rarely completely unconnected. Here we give theoretical background and concrete examples illustrating protein crystallization. We describe the nucleation of a new phase, solid or liquid, and the growth and transformation of existing crystals obtained by primary or secondary nucleation or by seeding. Above all, we believe that a thorough knowledge of the phase diagram is vital to the selection of starting position and path for any crystallization experiment.

Are conductance plateaus independent events in atomic point contact measurements? A statistical approach.

Conductance-elongation curves of gold atomic wires are measured using a scanning tunneling microscope break junction technique at room temperature. Landauer's conductance plateaus are individually identified and statistically analyzed. Both the probabilities to observe and the lengths of the two last plateaus (at conductance values close to 2e(2)/h and 4e(2)/h) are studied. All results converge to show that the occurrences of these two conductance plateaus on a conductance-elongation curve are statistically independent events.

2D aggregation and selective desorption of nanoparticle probes: a new method to probe DNA mismatches and damages.

A 2D colorimetric DNA sensor is reported based on the 2D aggregation of oligonucleotide-modified gold nanoparticle probes resulting from the molecular hybridization between these latest and their complementary single stranded DNA targets. To increase their mobility the nanoparticles are adsorbed on a fluid lipid bilayer, itself supported on a substrate. The hybridization between the target and the mobile nanoparticle probes creates links between the nanoparticles resulting in the formation of nanoparticle aggregates in the plane of the substrate. This aggregation is detected using a new method based on the selective desorption of non-aggregated nanoparticles. The addition of dextran sulfate induces the substitution of non-aggregated gold nanoparticles while aggregated ones are stable on the substrate. We show that this detection method is highly specific and allows the detection of DNA mismatches and damages.

DNA detection method based on the two-dimensional aggregation and selective desorption of nanoparticle probes.

A label-free two-dimensional colorimetric DNA sensor is reported. This sensor is based on the 2D aggregation of oligonucleotide-modified gold nanoparticle probes induced by the molecular hybridization of single-stranded oligonucleotide probes and their complementary single-stranded DNA targets. To detect the aggregation, we have developed a new detection method based on the selective desorption of nonaggregated nanoparticles. We will show here that this detection method is highly specific and allows the quantification of the DNA targets.