Quantitative analysis of biochemical processes in living cells at a single-molecule level: a case of olaparib–PARP1 (DNA repair protein) interactions

A. Karpińska, M. Pilz, J. Buczkowska, P. J. Żuk, K. Kucharska, G. Magiera, K. Kwapiszewska, and R. Hołyst

Analyst, 2021,146, 7131-7143

Quantitative description of biochemical processes inside living cells and at single-molecule levels remains a challenge at the forefront of modern instrumentation and spectroscopy. This paper demonstrates such single-cell, single-molecule analyses performed to study the mechanism of action of olaparib – an up-to-date, FDA-approved drug for germline-BRCA mutated metastatic breast cancer. We characterized complexes formed with PARPi-FL – fluorescent analog of olaparib in vitro and in cancer cells using the advanced fluorescent-based method: Fluorescence Correlation Spectroscopy (FCS) combined with a length-scale dependent cytoplasmic/nucleoplasmic viscosity model. We determined in vitro olaparib–PARP1 equilibrium constant (6.06 × 108 mol L−1). In the cell nucleus, we distinguished three states of olaparib: freely diffusing drug (24%), olaparib–PARP1 complex (50%), and olaparib–PARP1–RNA complex (26%). We show olaparib accumulation in 3D spheroids, where intracellular concentration is twofold higher than in 2D cells. Moreover, olaparib concentration was tenfold higher (506 nmol L−1vs. 57 nmol L−1) in cervical cancer (BRCA1 high abundance) than in breast cancer cells (BRCA1 low abundance) but with a lower toxic effect. Thus we confirmed that the amount of BRCA1 protein in the cells is a better predictor of the therapeutic effect of olaparib than its penetration into cancer tissue. Our single-molecule and single-cell approach give a new perspective of drug action in living cells. FCS provides a detailed in vivo insight, valuable in drug development and targeting.

Thermodynamics of stationary states of the ideal gas in a heat flow

Robert Hołyst, Karol Makuch, Anna Maciołek, Paweł J. Żuk

There is a long-standing question, to whether and to what extent it is possible to describe nonequilibrium systems in stationary states in terms of global thermodynamic functions. The positive answers have been obtained only for isothermal systems or systems with small temperature differences. We formulate the first and second laws of thermodynamics for stationary states of the ideal gas system subjected to heat flow arbitrarily far from equilibrium. We show rigorously that U satisfies the following equation dU=T∗dS∗−pdV for a constant number of particles, irrespective of the shape of the container, boundary conditions, size of the system, or mode of heat transfer into the system. We calculate a non-equilibrium entropy S∗ and T∗ explicitly. The theory reduces to equilibrium thermodynamics when heat flux goes to zero.

Protein induced lipid demixing in homogeneous membranes

B. H. Stumpf, P. Nowakowski, C. Eggeling, A. Maciołek, and A. S. Smith

Phys. Rev. Research 3, L042013 – Published 29 October 2021

Specific lipid environments are necessary for the establishment of protein signaling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of lipid membranes. The coupling between a local composition and a local thickness of the membrane induces lipid domains around inclusions with hydrophobic mismatch, even for temperatures above the miscibility critical point of the membrane. The model qualitatively explains the experimentally observed formation of lipid domains induced by anchoring of reconstituted actin in flat supported lipid bilayers.

Protein induced lipid demixing in homogeneous membranes

Stumpf, B. H., Nowakowski, P., Eggeling, C., Maciołek, A., & Smith, A.-S.

Phys. Rev. Research 3, L042013

Specific lipid environments are necessary for the establishment of protein signaling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of lipid membranes. The coupling between a local composition and a local thickness of the membrane induces lipid domains around inclusions with hydrophobic mismatch, even for temperatures above the miscibility critical point of the membrane. The model qualitatively explains the experimentally observed formation of lipid domains induced by anchoring of reconstituted actin in flat supported lipid bilayers.

Continuous nonequilibrium transition driven by heat flow

Yirui Zhang, Marek Litniewski, Karol Makuch, Paweł J. Żuk, Anna Maciołek, and Robert Hołyst

Phys. Rev. E 104, 024102

We discovered an out-of-equilibrium transition in the ideal gas between two walls, divided by an inner, adiabatic, movable wall. The system is driven out-of-equilibrium by supplying energy directly into the volume of the gas. At critical heat flux we have found a continuous transition to the state with a low-density, hot gas on one side of the movable wall and a dense, cold gas on the other side. Molecular dynamic simulations of the soft-sphere fluid confirm the existence of the transition in the interacting system. We introduce a stationary state Helmholtz-like function whose minimum determines the stable positions of the internal wall. This transition can be used as a paradigm of transitions in stationary states and the Helmholtz-like function as a paradigm of the thermodynamic description of these states.

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.

Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA

K. Kucharska, M. Pilz, K. Bielec, T. Kalwarczyk, P. Kuźma and R. Hołyst

Molecules 2021, 26(12), 3748

The oxazole yellow dye, YOYO-1 (a symmetric homodimer), is a commonly used molecule for staining DNA. We applied the brightness analysis to study the intercalation of YOYO-1 into the DNA. We distinguished two binding modes of the dye to dsDNA: mono-intercalation and bis-intercalation. Bis-intercalation consists of two consecutive mono-intercalation steps, characterised by two distinct equilibrium constants (with the average number of base pair per binding site equals 3.5): K1=3.36±0.43×107M−1 and K2=1.90±0.61×105M−1, respectively. Mono-intercalation dominates at high concentrations of YOYO-1. Bis-intercalation occurs at low concentrations.

Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis

A. Agasty, A. Wisniewska, T. Kalwarczyk, K. Koynov, and R. Holyst

ACS Appl. Polym. Mater. 2021, 3, 5, 2813–2822

The effective viscosity in polymer solutions probed by diffusion of nanoparticles depends on their size. It is a well-defined function of the probe size, the radius of gyration, mesh size (correlation length), activation energy, and its parameters. As the nanoparticle’s size exceeds the radius of gyration of polymer coils, the effective viscosity approaches its macroscopic limiting value. Here, we apply the equation for effective viscosity in the macroscopic limit to the following polymer solutions: hydroxypropyl cellulose (HPC) in water, polymethylmethacrylate (PMMA) in toluene, and polyacrylonitrile (PAN) in dimethyl sulfoxide (DMSO). We compare them with previous data for PEG/PEO in water and PDMS in ethyl acetate. We determine polymer parameters from the measurements of the macroscopic viscosity in a wide range of average polymer molecular weights (24–300 kg/mol), temperatures (283–303 K), and concentrations (0.005–1.000 g/cm3). In addition, the polydispersity of polymers is taken into account in the appropriate molecular weight averaging functions. We provide the model applicable for the study of nanoscale probe diffusion in polymer solutions and macroscopic characterization of different polymer materials via rheological measurements.

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.

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