Influence of molecular rebindings on the reaction rate of complex formation

T. Kalwarczyk, K. Bielec, K. Burdzy and R. Holyst

Phys. Chem. Chem. Phys., 2021

We simulated the Brownian diffusion and reaction-diffusion processes to study molecular rebinding’s influence on the reaction rates of bimolecular reactions. We found that the number of rebindings, Nreb , is proportional to the target’s size and inversely proportional to the diffusion coefficient D and simulation time-step ∆t. We found the proportionality constant close to π−1/2 . We confirmed that the number of rebinding is defined as a ratio of the activation-limited rate constant ka to the diffusion-limited rate constant, kD. We provide the formula describing the reactivity coefficient κ, modelling the transient-native complex transition for the activation-controlled reaction rates. We show that κ is proportional to (D/∆t)1/2 . Finally, we apply our rebinding-including reaction rate model to the real reactions of photoacid dissociation and protein association. Based on literature data for both types of reactions, we found the ∆t time-scale. We show that for the photodissociation of proton, the ∆t is equal to 171±18 fs and the average number of rebindings is approximately equal to 40. For proteins, ∆t is of the order of 100 ps with around 20 rebindings. In both cases the timescale is similar to the timescale of fluctuation of the solvent molecules surrounding the reactants; vibrations and bending in case of photoacid dissociation and diffusional motion for proteins.

Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates

J. S. Al-Otaibi, P. Albrycht, Y. S. Mary, Y. S. Mary & M. Księżopolska-Gocalska

Chemical Papers (2021)

Using nanosized metal substrates, surface-enhanced Raman scattering (SERS) is a tool for improving the Raman signal of biomolecules. For detection, SERS has gained much popularity and an important role in determining chemical composition. In the present study, SERS spectra of 2-methyl-4-(4-methylpiperazin-1-yl)-10H-thieno[2,3-b][1,5]benzodiazepine (olanzapine) (MPTB) were investigated on silver and silver-gold metal substrates (SERSitive, Warsaw, Poland) at different concentrations. Also, different chemical and electronic properties are investigated using DFT calculations. The ring and other functional modes in SERS change in frequency values with variations in intensity for all concentrations. The molecule is oriented in a tilted manner with respect to Ag and Ag-Au.

Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications

N. Kleczewska, P. J. Sikorski, Z. Warminska, L. Markiewicz, R. Kasprzyk, N. Baran, K. Kwapiszewska, A. Karpinska, J. Michalski, R. Holyst, J. Kowalska and J. Jemielity

Chem. Sci., 2021, Accepted Manuscript

Targeting cap-dependent translation initiation is one of experimental approaches that could lead to the development of novel anti-cancer therapies. Synthetic dinucleoside 5’, 5’-triphosphates cap analogs are potent antagonists of eukaryotic translation initiation factor 4E (eIF4E) in vitro and could counteract elevated levels of eIF4E in cancer cells; however, transformation of these compounds into therapeutic agents remains challenging – they do not easily penetrate into cells and are susceptible to enzymatic cleavage. Here, we tested the potential of several small molecule ligands – folic acid, biotin, glucose, and cholesterol – to deliver both hydrolyzable and cleavage-resistant cap analogs into cells. A broad structure-activity relationship (SAR) study using model fluorescent probes and cap-ligand conjugates showed that cholesterol greatly facilitates uptake of cap analogs without disturbing the interactions with eIF4E. The most potent cholesterol conjugate identified showed apoptosis-mediated cytotoxicity towards cancer cells.

Surface enhanced Raman scattering investigation of pioglitazone on silver and silver-gold metal substrates – Experimental analysis and theoretical modelling

P. Albrycht, J. S.Al-Otaibi, Y. Sheena Mary, Y. Shyma Mary, R. Trivei, B. Chakraborty

Journal of Molecular Structure, Available online 30 June 2021, 130992

Surface enhanced Raman scattering (SERS) is a spectroscopic technique for trace analysis where the efficiency depends on the substrate. In the present work, concentration-dependent SERS of pioglitazone (EPMT) in silver and silver-gold substrates are reported. The presence and absence of different SERS peaks between the analyte spectra on silver and silver-gold substrates show that there is an orientation change of the analyte adsorbed depending on the surface-active metal. The density functional theory (DFT) method was used to verify the experimental findings obtained from normal Raman and SERS spectra. Theoretical modeling of EPMT and metal clusters are reported and enhancement factors are found from theoretical and experimental results. In the EPMT-Ag-Ag and EPMT-Ag-Au molecular systems, Frontier molecular orbital’s (FMO’s) results highlight charge transfers from Ag-Ag/Ag-Au clusters to the molecule. Furthermore, the SERS enhancement factor values show that EPMT is chemisorbed.

Adsorption of bacteriophages on polypropylene labware affects the reproducibility of phage research

Ł. Richter, K. Księżarczyk, K. Paszkowska, M. Janczuk-Richter, J. Niedziółka-Jönsson, J. Gapiński, M. Łoś, R. Hołyst & J. Paczesny

Scientific Reports volume 11, Article number: 7387 (2021)

Hydrophobicity is one of the most critical factors governing the adsorption of molecules and objects, such as virions, on surfaces. Even moderate change of wetting angle of plastic surfaces causes a drastic decrease ranging from 2 to 5 logs of the viruses (e.g., T4 phage) in the suspension due to adsorption on polymer vials’ walls. The effect varies immensely in seemingly identical containers but purchased from different vendors. Comparison of glass, polyethylene, polypropylene, and polystyrene containers revealed a threshold in the wetting angle of around 95°: virions adsorb on the surface of more hydrophobic containers, while in more hydrophilic vials, phage suspensions are stable. The polypropylene surface of the Eppendorf-type and Falcon-type can accommodate from around 108 PFU/ml to around 1010 PFU/ml from the suspension. The adsorption onto the container’s wall might result in complete scavenging of virions from the bulk. We developed two methods to overcome this issue. The addition of surfactant Tween20 and/or plasma treatment provides a remedy by modulating surface wettability and inhibiting virions’ adsorption. Plastic containers are essential consumables in the daily use of many bio-laboratories. Thus, this is important not only for phage-related research (e.g., the use of phage therapies as an alternative for antibiotics) but also for data comparison and reproducibility in the field of biochemistry and virology.

Toxicological Responses of α-Pinene-Derived Secondary Organic Aerosol and Its Molecular Tracers in Human Lung Cell Lines

F. Khan, K. Kwapiszewska, Y. Zhang, Y. Chen, A. T. Lambe, A. Kołodziejczyk, N. Jalal, K. Rudzinski, A. Martínez-Romero, R. C. Fry, J. D. Surratt and R. Szmigielski

Chem. Res. Toxicol. 2021, 34, 3, 817–832

Secondary organic aerosol (SOA) is a major component of airborne fine particulate matter (PM2.5) that contributes to adverse human health effects upon inhalation. Atmospheric ozonolysis of α-pinene, an abundantly emitted monoterpene from terrestrial vegetation, leads to significant global SOA formation; however, its impact on pulmonary pathophysiology remains uncertain. In this study, we quantified an increasing concentration response of three well-established α-pinene SOA tracers (pinic, pinonic, and 3-methyl-1,2,3-butanetricarboxylic acids) and a full mixture of α-pinene SOA in A549 (alveolar epithelial carcinoma) and BEAS-2B (bronchial epithelial normal) lung cell lines. The three aforementioned tracers contributed ∼57% of the α-pinene SOA mass under our experimental conditions. Cellular proliferation, cell viability, and oxidative stress were assessed as toxicological end points. The three α-pinene SOA molecular tracers had insignificant responses in both cell types when compared with the α-pinene SOA (up to 200 μg mL–1). BEAS-2B cells exposed to 200 μg mL–1 of α-pinene SOA decreased cellular proliferation to ∼70% and 44% at 24- and 48-h post exposure, respectively; no changes in A549 cells were observed. The inhibitory concentration-50 (IC50) in BEAS-2B cells was found to be 912 and 230 μg mL–1 at 24 and 48 h, respectively. An approximate 4-fold increase in cellular oxidative stress was observed in BEAS-2B cells when compared with untreated cells, suggesting that reactive oxygen species (ROS) buildup resulted in the downstream cytotoxicity following 24 h of exposure to α-pinene SOA. Organic hydroperoxides that were identified in the α-pinene SOA samples likely contributed to the ROS and cytotoxicity. This study identifies the potential components of α-pinene SOA that likely modulate the oxidative stress response within lung cells and highlights the need to carry out chronic exposure studies on α-pinene SOA to elucidate its long-term inhalation exposure effects.

High-Throughput Monitoring of Bacterial Cell Density in Nanoliter Droplets: Label-Free Detection of Unmodified Gram-Positive and Gram-Negative Bacteria

N. Pacocha, J. Bogusławski, M. Horka, K. Makuch, K. Liżewski, M. Wojtkowski, and P. Garstecki

Anal. Chem. 2021, 93, 2, 843–850

Droplet microfluidics disrupted analytical biology with the introduction of digital polymerase chain reaction and single-cell sequencing. The same technology may also bring important innovation in the analysis of bacteria, including antibiotic susceptibility testing at the single-cell level. Still, despite promising demonstrations, the lack of a high-throughput label-free method of detecting bacteria in nanoliter droplets prohibits analysis of the most interesting strains and widespread use of droplet technologies in analytical microbiology. We use a sensitive and fast measurement of scattered light from nanoliter droplets to demonstrate reliable detection of the proliferation of encapsulated bacteria. We verify the sensitivity of the method by simultaneous readout of fluorescent signals from bacteria expressing fluorescent proteins and demonstrate label-free readout on unlabeled Gram-negative and Gram-positive species. Our approach requires neither genetic modification of the cells nor the addition of chemical markers of metabolism. It is compatible with a wide range of bacterial species of clinical, research, and industrial interest, opening the microfluidic droplet technologies for adaptation in these fields.

Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements

G. Bubak, K. Kwapiszewska, T. Kalwarczyk, K. Bielec, T. Andryszewski, M. Iwan, S. Bubak, and R. Hołyst

J. Phys. Chem. Lett. 2021, 12, 1, 294–301

Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure–function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus. Supported by the analysis of electron tomography images, these results advocate the ∼150 nm-wide interchromosomal channels filled with the aqueous diluted protein solution. The nucleus is percolated by these channels to allow various cargos to migrate freely at the nanoscale. We determined the volume of interchromosomal channels in the HeLa cell nucleus to 237 ± 61 fL, which constitutes 34% of the cell nucleus volume. The volume fraction of mobile proteins in channels equals 16% ± 4%, and the concentration is 1 mM.

Charge-, salt- and flexoelectricity-driven anchoring effects in nematics

J. C. Everts and M. Ravnik

Liquid Crystals 2021, 48, 423-435

We investigate the effects of electric double layers and flexoelectricity on the surface anchoring in general nematic fluids. Within a simplified model, we demonstrate for a nematic electrolyte how the surface anchoring strength can be affected by the surface charge, bulk ion concentration and/or flexoelectricity, effectively changing not only the magnitude of the anchoring but also the anchoring type, such as from planar to tilted. In particular, we envisage possible tuning of the anchoring strength by the salt concentration in the regime where sufficiently strong electrostatic anchoring, as controlled by the (screened) surface charge, can compete with the non-electrostatic anchoring. This effect is driven by the competing energetic-torque couplings between nematic director and the emergent electrostatic potential, due to surface charge, ions and flexoelectricity. Our findings propose a way of influencing surface anchoring by using electrostatic effects, which could be used in various aspects, including in the self-assembly of colloidal particles in nematic fluids, optical and display patterns, and sensing.

Anisotropic electrostatic screening of charged colloids in nematic solvents

J. C. Everts, B. Senyuk, H. Mundoor, M. Ravnik and I. I. Smalyukh

Science Advances 2021, 7, 5, eabd0662

The physical behavior of anisotropic charged colloids is determined by their material dielectric anisotropy, affecting colloidal self-assembly, biological function, and even out-of-equilibrium behavior. However, little is known about anisotropic electrostatic screening, which underlies all electrostatic effective interactions in such soft or biological materials. In this work, we demonstrate anisotropic electrostatic screening for charged colloidal particles in a nematic electrolyte. We show that material anisotropy behaves markedly different from particle anisotropy. The electrostatic potential and pair interactions decay with an anisotropic Debye screening length, contrasting the constant screening length for isotropic electrolytes. Charged dumpling-shaped near-spherical colloidal particles in a nematic medium are used as an experimental model system to explore the effects of anisotropic screening, demonstrating competing anisotropic elastic and electrostatic effective pair interactions for colloidal surface charges tunable from neutral to high, yielding particle-separated metastable states. Generally, our work contributes to the understanding of electrostatic screening in nematic anisotropic media.

Ionically Charged Topological Defects in Nematic Fluids

J. C. Everts and M. Ravnik

Phys. Rev. X 2021, 11, 011054

Charge profiles in liquid electrolytes are of crucial importance for applications such as supercapacitors, fuel cells, batteries, or the self-assembly of particles in colloidal or biological settings. However, creating localized (screened) charge profiles in the bulk of such electrolytes generally requires the presence of surfaces—for example, provided by colloidal particles or outer surfaces of the material—which poses a fundamental constraint on the material design. Here, we show that topological defects in nematic electrolytes can perform as regions for local charge separation, forming charged defect cores and, in some geometries, even electric multilayers, as opposed to the electric double layers found in isotropic electrolytes. Using a Landau-de Gennes-Poisson-Boltzmann theoretical framework, we show that ions highly effectively couple with the topological defect cores via ion solvability and with the local director-field distortions of the defects via flexoelectricity. The defect charging is shown for different defect types—lines, points, and walls—using geometries of ionically screened flat isotropic-nematic interfaces, radial hedgehog point defects, and half-integer wedge disclinations in the bulk and as stabilized by (charged) colloidal particles. More generally, our findings are relevant for possible applications where topological defects act as diffuse ionic capacitors or as ionic charge carriers.

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