Cytoplasmic viscosity near the cell plasma membrane: measurement by evanescent field frequency-domain microfluorimetry

Julolidine-based small molecular probes for fluorescence imaging of RNA in live cells

Intracellular RNA imaging with organic small molecular probes has been an intense topic, although the number of such reported dyes, particularly dyes with high quantum yields and long wavelength excitation/emission, is quite limited. The present work reports the design and synthesis of three cationic julolidine-azolium conjugates (OX-JLD, BTZ-JLD and SEZ-JLD) as turn-on fluorescent probes with appreciably high quantum yields and brightness upon interaction with RNA. A structure-efficiency relationship has been established for their potential for the interaction and imaging of intracellular RNA. Given their chemical structure, the free rotation between the donor and the acceptor gets restricted when the probes bind with RNA resulting in strong fluorescence emission towards a higher wavelength upon photoexcitation. A detailed investigation revealed that the photophysical properties and the optical responses of two probes, viz. BTZ-JLD and SEZ-JLD, towards RNA are very promising and qualify them to be suitable candidates for biological studies, particularly for cellular imaging applications. The probes allow imaging of intracellular RNA with prominent staining of nucleoli in live cells under a range of physiological conditions. The results of the cellular digest test established the appreciable RNA selectivity of BTZ-JLD and SEZ-JLD inside the cellular environment. Moreover, a comparison between the relative intensity profile of SEZ-JLD before and after the RNA-digestion test inside the cellular environment indicated that the interference of cellular viscosity in fluorescence enhancement is insignificant, and hence, SEZ-JLD can be used as a cell membrane permeable cationic molecular probe for deep-red imaging of intracellular RNA with a good degree of selectivity.

In Situ Characterization of the Protein Corona of Nanoparticles In Vitro and In Vivo

A new theoretical framework that enables the use of differential dynamic microscopy (DDM) in fluorescence imaging mode to quantify in situ protein adsorption onto nanoparticles (NP) while simultaneously monitoring for NP aggregation is proposed. This methodology is used to elucidate the thermodynamic and kinetic properties of the protein corona (PC) in vitro and in vivo. The results show that protein adsorption triggers particle aggregation over a wide concentration range and that the formed aggregate structures can be quantified using the proposed methodology. Protein affinity for polystyrene (PS) NPs is observed to be dependent on particle concentration. For complex protein mixtures, this methodology identifies that the PC composition changes with the dilution of serum proteins, demonstrating a Vroman effect never quantitatively assessed in situ on NPs. Finally, DDM allows monitoring of the evolution of the PC in vivo. This results show that the PC composition evolves significantly over time in zebrafish larvae, confirming the inherently dynamic nature of the PC. The performance of the developed methodology allows to obtain quantitative insights into nano-bio interactions in a vast array of physiologically relevant conditions that will serve to further improve the design of nanomedicine.

Mechanisms of cellular retention of melanin bound drugs: Experiments and computational modeling

Melanin binding of drugs is known to increase drug concentrations and retention in pigmented eye tissues. Even though the correlation between melanin binding in vitro and exposure to pigmented eye in vivo has been shown, there is a discrepancy between rapid drug release from melanin particles in vitro and the long in vivo retention in the pigmented tissues. We investigated mechanisms and kinetics of pigment-related drug retention experimentally using isolated melanin particles from porcine retinal pigment epithelium and choroid, isolated porcine eye melanosomes, and re-pigmented ARPE-19 cells in a dynamic flow system. The experimental studies were supplemented with kinetic simulations. Affinity and capacity of levofloxacin, terazosin, papaverine, and timolol binding to melanin revealed K_d values of ≈ 50-150 μM and B_max ≈ 40-112 nmol.mg^-1. The drugs were released from melanin in <1 h (timolol) or in 6-12 h (other drugs). The drugs were released slower from the melanosomes than from melanin; the experimental differences ranged from 1.2-fold (papaverine) to 7.4-fold (timolol). Kinetic simulations supported the role of the melanosomal membrane in slowing down the release of melanin binders. In release studies from the pigmented ARPE-19 cells, drugs were released from the cellular melanin to the extracellular space in ≈ 1 day (timolol) and ≈ 11 days (levofloxacin), i.e., much slower than the release from melanin or melanosomes. Simulations of drug release from pigmented cells in the flow system matched the experimental data and enabled further sensitivity analyses. The simulations demonstrated a significant prolongation of drug retention in the cells as a function of decreasing drug permeability in the melanosomal membranes and increasing melanin content in the cells. Overall, we report the impact of cellular factors in prolonging drug retention and release from melanin-containing cells. These data and simulations will facilitate the design of melanin binding drugs with prolonged ocular actions.

The Thermodynamics of Medial Vascular Calcification

Medial vascular calcification (MVC) is a degenerative process that involves the deposition of calcium in the arteries, with a high prevalence in chronic kidney disease (CKD), diabetes, and aging. Calcification is the process of precipitation largely of calcium phosphate, governed by the laws of thermodynamics that should be acknowledged in studies of this disease. Amorphous calcium phosphate (ACP) is the key constituent of early calcifications, mainly composed of Ca2+ and PO4 3- ions, which over time transform into hydroxyapatite (HAP) crystals. The supersaturation of ACP related to Ca2+ and PO4 3- activities establishes the risk of MVC, which can be modulated by the presence of promoter and inhibitor biomolecules. According to the thermodynamic parameters, the process of MVC implies: (i) an increase in Ca2+ and PO4 3- activities (rather than concentrations) exceeding the solubility product at the precipitating sites in the media; (ii) focally impaired equilibrium between promoter and inhibitor biomolecules; and (iii) the progression of HAP crystallization associated with nominal irreversibility of the process, even when the levels of Ca2+ and PO4 3- ions return to normal. Thus, physical-chemical processes in the media are fundamental to understanding MVC and represent the most critical factor for treatments' considerations. Any pathogenetical proposal must therefore comply with the laws of thermodynamics and their expression within the medial layer.

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between ¹H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).

Magnetic hyperthermia with ε-Fe2O3 nanoparticles

Biocompatibility restrictions have limited the use of magnetic nanoparticles for magnetic hyperthermia therapy to iron oxides, namely magnetite (Fe₃O₄) and maghemite (γ-Fe₂O₃). However, there is yet another magnetic iron oxide phase that has not been considered so far, in spite of its unique magnetic properties: ε-Fe₂O₃. Indeed, whereas Fe₃O₄ and γ-Fe₂O₃ have a relatively low magnetic coercivity, ε-Fe₂O₃ exhibits a giant coercivity. In this report, the heating power of ε-Fe₂O₃ nanoparticles in comparison with γ-Fe₂O₃ nanoparticles of similar size (∼20 nm) was measured in a wide range of field frequencies and amplitudes, in uncoated and polymer-coated samples. It was found that ε-Fe₂O₃ nanoparticles primarily heat in the low-frequency regime (20-100 kHz) in media whose viscosity is similar to that of cell cytoplasm. In contrast, γ-Fe₂O₃ nanoparticles heat more effectively in the high frequency range (400-900 kHz). Cell culture experiments exhibited no toxicity in a wide range of nanoparticle concentrations and a high internalization rate. In conclusion, the performance of ε-Fe₂O₃ nanoparticles is slightly inferior to that of γ-Fe₂O₃ nanoparticles in human magnetic hyperthermia applications. However, these ε-Fe₂O₃ nanoparticles open the way for switchable magnetic heating owing to their distinct response to frequency.

Helical nanobots as mechanical probes of intra- and extracellular environments

A rheological probe that can measure mechanical properties of biological milieu at well-defined locations with high spatial resolution, on a time scale faster than most biological processes, can further improve our understanding of how living systems operate and behave. Here, we demonstrate nanorobots actively driven in realistic ex vivo biological systems for fast mechanical measurements with high spatial accuracy. In the various demonstrations of magnetic nanobots as mechanical probes, we report the first direct observation of the internalization of probes by a living cell, the accurate measurement of the 'fluid phase' cytoplasmic viscosity of ~200 cP for a HeLa cell, demonstration of intracellular measurements in cells derived from human patients; all of which establish the strength of this novel technique for measurements in both intra- and extracellular environments.

Vesicle Shrinking and Enlargement Play Opposing Roles in the Release of Exocytotic Contents

For decades, two fusion modes were thought to control hormone and transmitter release essential to life; one facilitates release via fusion pore dilation and flattening (full collapse), and the other limits release by closing a narrow fusion pore (kiss-and-run). Using super-resolution stimulated emission depletion (STED) microscopy to visualize fusion modes of dense-core vesicles in neuroendocrine cells, we find that facilitation of release is mediated not by full collapse but by shrink fusion, in which the Ω-profile generated by vesicle fusion shrinks but maintains a large non-dilating pore. We discover that the physiological osmotic pressure of a cell squeezes, but does not dilate, the Ω-profile, which explains why shrink fusion prevails over full collapse. Instead of kiss-and-run, enlarge fusion, in which Ω-profiles grow while maintaining a narrow pore, slows down release. Shrink and enlarge fusion may thus account for diverse hormone and transmitter release kinetics observed in secretory cells, previously interpreted within the full-collapse/kiss-and-run framework.

The ERC1 scaffold protein implicated in cell motility drives the assembly of a liquid phase

Several cellular processes depend on networks of proteins assembled at specific sites near the plasma membrane. Scaffold proteins assemble these networks by recruiting relevant molecules. The scaffold protein ERC1/ELKS and its partners promote cell migration and invasion, and assemble into dynamic networks at the protruding edge of cells. Here by electron microscopy and single molecule analysis we identify ERC1 as an extended flexible dimer. We found that ERC1 scaffolds form cytoplasmic condensates with a behavior that is consistent with liquid phases that are modulated by a predicted disordered region of ERC1. These condensates specifically host partners of a network relevant to cell motility, including liprin-α1, which was unnecessary for the formation of condensates, but influenced their dynamic behavior. Phase separation at specific sites of the cell periphery may represent an elegant mechanism to control the assembly and turnover of dynamic scaffolds needed for the spatial localization and processing of molecules.

Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements

A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell's heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with previous reports of cytoplasmic viscosity in E. coli. The results of these TRLD studies in E. coli (1) provide a measurement of myoglobin mobility in the cytoplasm, (2) taken together with in vitro TRLD studies yield new insights into the nature of the cytoplasmic environment in cells, and (3) demonstrate the feasibility of TRLD as a probe of intracellular viscosity.

Impact of ConcanavalinA affinity in the intracellular fate of Protein Corona on Glucosamine Au nanoparticles

Biological fate and toxicity of nanoparticles (NPs) are connected to the interaction between NPs and the protein corona (PC) spontaneously forming around NPs in biological matrixes. PC is a dynamic entity that confers biological identity to NPs. In this work, fluorescence cross-correlation spectroscopy (FCCS) is used to study the impact of specific interactions between the NP surface and proteins on the intracellular fate of PC. The stability of the PC formed around glucosamide-functionalized Au-NPs from ConcanavalinA (ConA) or Bovine Serum Albumin (BSA) is characterized by FCCS. The NPs show higher affinity for ConA and competitive assays show that ConA easily exchanges BSA. A549 cells are exposed to glucosamide-functionalized Au-NPs with preformed ConA and BSA PCs. Intracellularly the frequency of cross-correlation for Au NPs with ConA PC remains constant to a 70% value until 24 h while for BSA it decreases to a 15% during the same period. FCCS measurements in several locations in the cell point out a different level of aggregation for the NPs with either ConA or BSA PCs. Our results show that the affinity of NPs functionalized with a ligand with affinity for a specific protein in bulk is retained intracellularly influencing NP fate and translocation.

Room-temperature in-cell EPR spectroscopy: alpha-Synuclein disease variants remain intrinsically disordered in the cell

Human alpha-Synuclein (aS), implicated in Parkinson's disease, adopts a rich variety of different conformations depending on the macromolecular context. In order to unravel its pathophysiological role, monitoring its intracellular conformational state and identifying differences for the disease variants is crucial. Here, we present an intracellular spectroscopy approach based on a systematic spin-labeling site-scan in combination with intracellular electron paramagnetic resonance spectroscopy determining conformations on a molecular scale. A quantitative and model-based data analysis revealed that the vast majority of aS, be it wild-type or disease variants A30P or A53T, exists in the monomeric intrinsically disordered form in the cell.

Characterization of Cell Membrane Permeability In Vitro Part I: Transport Behavior Induced by Single-Pulse Electric Fields

Most experimental studies of electroporation focus on permeabilization of the outer cell membrane. Some experiments address delivery of ions and molecules into cells that should survive; others focus on efficient killing of the cells with minimal temperature rise. A basic method for quantifying electroporation effectiveness is measuring the membrane's diffusive permeability. More specifically, comparisons of membrane permeability between electroporation protocols often rely on relative fluorescence measurements, which are not able to be directly connected to theoretical calculations and complicate comparisons between studies. Here we present part I of a 2-part study: a research method for quantitatively determining the membrane diffusive permeability for individual cells using fluorescence microscopy. We determine diffusive permeabilities of cell membranes to propidium for electric field pulses with durations of 1 to 1000 μs and strengths of 170 to 400 kV/m and show that diffusive permeabilities can reach 1.3±0.4×10-8 m/s. This leads to a correlation between increased membrane permeability and eventual propidium uptake. We also identify a subpopulation of cells that exhibit a delayed and significant propidium uptake for relatively small single pulses. Our results provide evidence that cells, especially those that uptake propidium more slowly, can achieve large permeabilities with a single electrical pulse that may be quantitatively measured using standard fluorescence microscopy equipment and techniques.

Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments

Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.

Cytoplasmic transport and nuclear import of plasmid DNA

Productive transfection and gene transfer require not simply the entry of DNA into cells and subsequent transcription from an appropriate promoter, but also a number of intracellular events that allow the DNA to move from the extracellular surface of the cell into and through the cytoplasm, and ultimately across the nuclear envelope and into the nucleus before any transcription can initiate. Immediately upon entry into the cytoplasm, naked DNA, either delivered through physical techniques or after disassembly of DNA-carrier complexes, associates with a large number of cellular proteins that mediate subsequent interactions with the microtubule network for movement toward the microtubule organizing center and the nuclear envelope. Plasmids then enter the nucleus either upon the mitotic disassembly of the nuclear envelope or through nuclear pore complexes in the absence of cell division, using a different set of proteins. This review will discuss our current understanding of these pathways used by naked DNA during the transfection process. While much has been elucidated on these processes, much remains to be discerned, but with the development of a number of model systems and approaches, great progress is being made.

Mapping Cell Membrane Fluctuations Reveals Their Active Regulation and Transient Heterogeneities

Shape fluctuations of the plasma membrane occur in all cells, are incessant, and are proposed to affect membrane functioning. Although studies show how membrane fluctuations are affected by cellular activity in adherent cells, their spatial regulation and the corresponding change in membrane mechanics remain unclear. In this article, we study how ATP-driven activities and actomyosin cytoskeleton impact basal membrane fluctuations in adherent cells. Using interference imaging, we map height fluctuations within single cells and compare the temporal spectra with existing theoretical models to gain insights about the underlying membrane mechanics. We find that ATP-dependent activities enhance the nanoscale z fluctuations but stretch out the membrane laterally. Although actin polymerization or myosin-II activity individually enhances fluctuations, the cortex in unperturbed cells stretches out the membrane and dampens fluctuations. Fitting with models suggest this dampening to be due to confinement by the cortex. However, reduced fluctuations on mitosis or on ATP-depletion/stabilization of cortex correlate with increased tension. Both maps of fluctuations and local temporal autocorrelation functions reveal ATP-dependent transient short-range (<2 μm) heterogeneities. Together, our results show how various ATP-driven processes differently affect membrane mechanics and hence fluctuations, while creating distinct local environments whose functional role needs future investigation.

Time-Resolved Linear Dichroism Measurements of Carbonmonoxy Myoglobin as a Probe of the Microviscosity in Crowded Environments

The distribution of viscosities in living cells is heterogeneous because of the different sizes and natures of macromolecular components. When thinking about protein folding/function processes in such an environment, the relevant (micro)viscosity at the micrometer length scale is necessarily distinguished from the bulk (macro)viscosity. The concentration dependencies of microviscosities are determined by a number of factors, such as electrostatic interactions, van der Waals forces, and excluded volume effects. To explore such factors, the rotational diffusion time of myoglobin in the presence of varying concentrations of macromolecules that differ in molecular weight (dextran 6000, 10 000, and 70 000), shape (dextran versus Ficoll), size, and surface charge is measured with time-resolved linear dichroism spectroscopy. The results of these studies offer simple empirically determined linear and exponential functions useful for predicting microviscosities as a function of concentration for these macromolecular crowders that are typically used to study crowding effects on protein folding. To understand how relevant these microviscosity measurements are to intracellular environments, the TRLD results are discussed in the context of studies that measure viscosity in cells.

Evaluating the performance of time-gated live-cell microscopy with lanthanide probes

Probes and biosensors that incorporate luminescent Tb(III) or Eu(III) complexes are promising for cellular imaging because time-gated microscopes can detect their long-lifetime (approximately milliseconds) emission without interference from short-lifetime (approximately nanoseconds) fluorescence background. Moreover, the discrete, narrow emission bands of Tb(III) complexes make them uniquely suited for multiplexed imaging applications because they can serve as Förster resonance energy transfer (FRET) donors to two or more differently colored acceptors. However, lanthanide complexes have low photon emission rates that can limit the image signal/noise ratio, which has a square-root dependence on photon counts. This work describes the performance of a wide-field, time-gated microscope with respect to its ability to image Tb(III) luminescence and Tb(III)-mediated FRET in cultured mammalian cells. The system employed a UV-emitting LED for low-power, pulsed excitation and an intensified CCD camera for gated detection. Exposure times of ∼1 s were needed to collect 5-25 photons per pixel from cells that contained micromolar concentrations of a Tb(III) complex. The observed photon counts matched those predicted by a theoretical model that incorporated the photophysical properties of the Tb(III) probe and the instrument's light-collection characteristics. Despite low photon counts, images of Tb(III)/green fluorescent protein FRET with a signal/noise ratio ≥ 7 were acquired, and a 90% change in the ratiometric FRET signal was measured. This study shows that the sensitivity and precision of lanthanide-based cellular microscopy can approach that of conventional FRET microscopy with fluorescent proteins. The results should encourage further development of lanthanide biosensors that can measure analyte concentration, enzyme activation, and protein-protein interactions in live cells.

Aging-related viscoelasticity variation of tendon stem cells (TSCs) characterized by quartz thickness shear mode (TSM) resonators

Aging not only affects the whole body performance but also alters cellular biological properties, including cell proliferation and differentiation. This study was designed to determine the effect of aging on the mechanical properties of tendon stem cells (TSCs), a newly discovered stem cell type in tendons, using quartz thickness shear mode (TSM) resonators. TSCs were isolated from both old and young rats, and allowed to grow to confluency on the surface of TSM resonators. The admittance spectrums of TSM with TSC monolayer were acquired, and a series of complex shear modulus G' + jG″ as well as average thickness hTSC were calculated based on a two-layer-loading transmission line model (TLM) for TSM resonator sensor. The results showed an overall increase in G', G″ and hTSC during aging process. Specifically, the storage modulus G' of aging TSCs was over ten times than that of young, revealing an important increase in stiffness of aging TSCs. Additionally, through phase-contrast and scanning electronic microscopy, it was shown that aging TSCs were large, flat and heterogeneous in morphologies while young TSCs were uniformly elongated. Increased cell size and irregular cell shape might be associated with the dense cytoskeleton organization, which could lead to an increase in both stiffness and viscosity. These results are in agreement with previously published data using different measurement methods, indicating TSM resonator sensor as a promising tool to measure the mechanical properties of cells.

Mechanical properties of respiratory muscles

Striated respiratory muscles are necessary for lung ventilation and to maintain the patency of the upper airway. The basic structural and functional properties of respiratory muscles are similar to those of other striated muscles (both skeletal and cardiac). The sarcomere is the fundamental organizational unit of striated muscles and sarcomeric proteins underlie the passive and active mechanical properties of muscle fibers. In this respect, the functional categorization of different fiber types provides a conceptual framework to understand the physiological properties of respiratory muscles. Within the sarcomere, the interaction between the thick and thin filaments at the level of cross-bridges provides the elementary unit of force generation and contraction. Key to an understanding of the unique functional differences across muscle fiber types are differences in cross-bridge recruitment and cycling that relate to the expression of different myosin heavy chain isoforms in the thick filament. The active mechanical properties of muscle fibers are characterized by the relationship between myoplasmic Ca2+ and cross-bridge recruitment, force generation and sarcomere length (also cross-bridge recruitment), external load and shortening velocity (cross-bridge cycling rate), and cross-bridge cycling rate and ATP consumption. Passive mechanical properties are also important reflecting viscoelastic elements within sarcomeres as well as the extracellular matrix. Conditions that affect respiratory muscle performance may have a range of underlying pathophysiological causes, but their manifestations will depend on their impact on these basic elemental structures.

Influence of semiflexible structural features of actin cytoskeleton on cell stiffness based on actin microstructural modeling

A new actin cytoskeleton microstructural model based on the semiflexible polymer nature of the actin filament is proposed. The relationship between the stretching force and the mechanical properties of cells was examined. Experiments on deforming hematopoietic cells with distinct primitiveness from normal and leukemic sources were conducted via optical tweezer manipulation at single-cell level. The modeling results were demonstrated to be in good agreement with the experimental data. We characterized how the structural properties of the actin cytoskeleton, such as prestress, density of cross-links, and actin concentration, affect the mechanical behavior of cells based on the proposed model. Increasing prestress, actin concentration, and density of cross-links reduced cell deformation, and the cell also exhibited strain stiffening behavior with an increase in the stretching force. Compared with existing models, the proposed model exhibits a distinct feature in probing the influence of semiflexible polymer nature of the actin filament on cell mechanical behavior.

Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments

Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined.

Functionalized nanosystems for targeted mitochondrial delivery

Mitochondrial dysfunction including oxidative stress and DNA mutations underlies the pathology of various diseases including Alzheimer's disease and diabetes, necessitating the development of mitochondria targeted therapeutic agents. Nanotechnology offers unique tools and materials to target therapeutic agents to mitochondria. As discussed in this paper, a variety of functionalized nanosystems including polymeric and metallic nanoparticles as well as liposomes are more effective than plain drug and non-functionalized nanosystems in delivering therapeutic agents to mitochondria. Although the field is in its infancy, studies to date suggest the superior therapeutic activity of functionalized nanosystems for treating mitochondrial defects.

Unified regression model of binding equilibria in crowded environments

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment.

Brownian motion of polyphosphate complexes in yeast vacuoles: characterization by fluorescence microscopy with image analysis

In the vacuoles of Saccharomyces cerevisiae yeast cells, vividly moving insoluble polyphosphate complexes (IPCs) <1 microm size, stainable by a fluorescent dye, 4',6-diamidino-2-phenylindole (DAPI), may appear under some growth conditions. The aim of this study was to quantitatively characterize the movement of the IPCs and to evaluate the viscosity in the vacuoles using the obtained data. Studies were conducted on S. cerevisiae cells stained by DAPI and fluorescein isothyocyanate-labelled latex microspheres, using fluorescence microscopy combined with computer image analysis (ImageJ software, NIH, USA). IPC movement was photorecorded and shown to be Brownian motion. On latex microspheres, a methodology was developed for measuring a fluorescing particle's two-dimensional (2D) displacements and its size. In four yeast cells, the 2D displacements and sizes of the IPCs were evaluated. Apparent viscosity values in the vacuoles of the cells, computed by the Einstein-Smoluchowski equation using the obtained data, were found to be 2.16 +/- 0.60, 2.52 +/- 0.63, 3.32 +/- 0.9 and 11.3 +/- 1.7 cP. The first three viscosity values correspond to 30-40% glycerol solutions. The viscosity value of 11.3 +/- 1.7 cP was supposed to be an overestimation, caused by the peculiarities of the vacuole structure and/or volume in this particular cell. This conclusion was supported by the particular quality of the Brownian motion trajectories set in this cell as compared to the other three cells.

A numerical model of cellular blebbing: a volume-conserving, fluid-structure interaction model of the entire cell

In animal cells, blebs are smooth, quasi-hemispherical protrusions of the plasma membrane that form when a section of the membrane detaches from the underlying actin cytoskeleton and is inflated by flowing cytosol. The mechanics behind this common cellular activity are not yet clear. As a first step in the development of a full computational framework, we present a numerical model of overall cell behavior based upon the interaction between a background Newtonian-fluid cytosol and elastic structures modeling the membrane and filaments. The detailed micromechanics of the cytoskeletal network are the subject of future work. Here, the myosin-driven contraction of the actin network is modeled through stressed elastic filaments. Quantitative models of cytoskeletal micromechanics and biochemistry require accurate estimates of local stress and flow conditions. The main contribution of this paper is the development of a computationally efficient fluid-structure interaction model based on operator splitting, to furnish this data. Cytosol volume conservation (as supported by experimental evidence) is enforced through an intermediate energy minimization step. Realistic bleb formation and retraction is observed from this model, offering an alternative formulation to positing complex continuum behavior of the cytoplasm (e.g. poroelastic model of Charras et al., 2008).

Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

The intracellular environment imposes a variety of constraints on biochemical reaction systems that can substantially change reaction rates and equilibria relative to an ideal solution-based environment. One of the most notable features of the intracellular environment is its dense macromolecular crowding, which, among many other effects, tends to strongly enhance binding and assembly reactions. Despite extensive study of biochemistry in crowded media, it remains extremely difficult to predict how crowding will quantitatively affect any given reaction system due to the dependence of the crowding effect on numerous assumptions about the reactants and crowding agents involved. We previously developed a two dimensional stochastic off-lattice model of binding reactions based on the Green's function reaction dynamics method in order to create a versatile simulation environment in which one can explore interactions among many parameters of a crowded assembly system. In the present work, we examine interactions among several critical parameters for a model dimerization system: the total concentration of reactants and inert particles, the binding probability upon a collision between two reactant monomers, the mean time of dissociation reactions, and the diffusion coefficient of the system. Applying regression models to equilibrium constants across parameter ranges shows that the effect of the total concentration is approximately captured by a low-order nonlinear polynomial model, while the other three parameter effects are each accurately captured by a linear model. Furthermore, validation on tests with multi-parameter variations reveals that the effects of these parameters are separable from one another over a broad range of variation in all four parameters. The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved.

Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics

The environment inside a living cell is dramatically different from that found in in vitro models, presenting a problem for computational models of biochemistry that are only beginning to capture these differences. This deviation between idealized in vitro models and more realistic intracellular conditions is particularly problematic for models of molecular self-assembly, but also specifically hard to address because the large sizes and long assembly times of biological self-assembly systems force the use of highly simplified models. We have developed a prototype of a molecular self-assembly simulator based on the Green's function reaction dynamics (GFRD) model to achieve more realistic models of assembly in the crowded conditions of the cell without unduly sacrificing tractability. We tested the model on a simple representation of dimer assembly in a two-dimensional space. Our simulations verify that the model is computationally efficient, provides a realistic quantitative model of reaction kinetics in uncrowded conditions, and exhibits expected excluded volume effects under conditions of high crowding. This work confirms the effectiveness of the GFRD technique for more realistic coarse-grained modeling of self-assembly in crowded conditions and helps lay the groundwork for exploring the effects of in vivo crowding on more complex assembly systems.

Biological cell-based screening for scientific membranal and cytoplasmatic markers using dielectric spectroscopy

Dielectric spectroscopy (DS) of living biological cells is based on the analysis of cells suspended in a physiological medium. It provides knowledge of the polarization-relaxation response of the cells to external electric field as function of the excitation frequency. This response is strongly affected by both structural and molecular properties of the cells and, therefore, can reveal rare insights into cell physiology and behaviour. This study demonstrates the mapping potential of DS after cytoplasmic and membranal markers for cell-based screening analysis. The effect of membrane permittivity and cytoplasm conductivity was examined using tagged MBA and MDCK cell lines respectively. The comparison of the dielectric spectra of tagged and native cell lines reveals clear differences between the cells. In addition, the differences in the matching dielectric properties of the cells were discovered. Those findings support the high distinction resolution and sensitivity of DS after fine molecular and cellular changes, and hence, highlight the high potential of DS as non invasive screening tool in cell biology research.

Intracellular trafficking of plasmids for gene therapy: mechanisms of cytoplasmic movement and nuclear import

Under physiologically relevant conditions, the levels of non-viral gene transfer are low at best. The reason for this is that many barriers exist for the efficient transfer of genes to cells, even before any gene expression can occur. While many transfection strategies focus on DNA condensation and overcoming the plasma membrane, events associated with the intracellular trafficking of the DNA complexes have not been as extensively studied. Once internalized, plasmids must travel potentially long distances through the cytoplasm to reach their next barrier, the nuclear envelope. This review summarizes the current progress on the cytoplasmic trafficking and nuclear transport of plasmids used for gene therapy applications. Both of these processes utilize specific and defined mechanisms to facilitate movement of DNA complexes through the cell. The continued elucidation and exploitation of these mechanisms will lead to improved strategies for transfection and successful gene therapy.

Retracted article: In-cell protein dynamics

The native intracellular environment of proteins is crowded with metabolites and macromolecules. However, most biophysical information concerning proteins is acquired in dilute solution. To determine whether there are differences in dynamics, nuclear magnetic resonance spectroscopy can be used to measure 15N relaxation in uniformly 15N-enriched apocytochrome b5 inside living Escherichia coli and in dilute solution. Such data can then be used to compare the fast backbone dynamics of the partially folded protein in cells to its dynamics in dilute solution by using Lipari-Szabo analysis. It appears that the intracellular environment does not alter the protein's structure, or significantly change its fast dynamics. Specifically, the cytosol does not change the amplitude of fast backbone motions, but does increase the average timescale of these motions, most likely due to the increase in viscosity of the cytosol.

In-cell NMR spectroscopy

The role of a protein inside a cell is determined by both its location and its conformational state. Although fluorescence techniques are widely used to determine the cellular localization of proteins in vivo, these approaches cannot provide detailed information about a protein's three-dimensional state. This gap, however, can be filled by NMR spectroscopy, which can be used to investigate both the conformation as well as the dynamics of proteins inside living cells. In this chapter we describe technical aspects of these "in-cell NMR" experiments. In particular, we show that in the case of (15)N-labeling schemes the background caused by labeling all cellular components is negligible, while (13)C-based experiments suffer from high background levels and require selective labeling schemes. A correlation between the signal-to-noise ratio of in-cell NMR experiments with the overexpression level of the protein shows that the current detection limit is 150-200 muM (intracellular concentration). We also discuss experiments that demonstrate that the intracellular viscosity is not a limiting factor since the intracellular rotational correlation time is only approximately two times longer than the correlation time in water. Furthermore, we describe applications of the technique and discuss its limitations.

Fluorescence imaging with two-photon evanescent wave excitation

We demonstrate broad-field, non-scanning, two-photon excitation fluorescence (2PEF) close to a glass/cell interface by total internal reflection of a femtosecond-pulsed infrared laser beam. We exploit the quadratic intensity dependence of 2PEF to provide non-linear evanescent wave (EW) excitation in a well-defined sample volume and to eliminate scattered background excitation. A simple model is shown to describe the resulting 2PEF intensity and to predict the effective excitation volume in terms of easily measurable beam, objective and interface properties. We demonstrate non-linear evanescent wave excitation at 860 nm of acridine orange-labelled secretory granules in live chromaffin cells, and excitation at 900 nm of TRITC-phalloidin-actin/GPI-GFP double-labelled fibroblasts. The confined excitation volume and the possibility of simultaneous multi-colour excitation of several fluorophores make EW 2PEF particularly advantageous for quantitative microscopy, imaging biochemistry inside live cells, or biosensing and screening applications in miniature high-density multi-well plates.

The effect of temperature on membrane hydraulic conductivity

The objective of this study was to use the temperature dependence of water permeability to suggest the physical mechanisms of water transport across membranes of osmotically slowly responding cells and to demonstrate that insight into water transport mechanisms in these cells may be gained from easily performed experiments using an electronic particle counter. Osmotic responses of V-79W Chinese hamster fibroblast cells were measured in hypertonic solutions at various temperatures and the membrane hydraulic conductivity was determined. The results were fit with the general Arrhenius equation with two free parameters, and also fit with two specific membrane models each having only one free parameter. Data from the literature including that for human bone marrow stem cells, hamster pancreatic islets, and bovine articular cartilage chondrocytes were also examined. The results indicated that the membrane models could be used in conjunction with measured permeability data at different temperatures to investigate the method of water movement across various cell membranes. This approach for slower responding cells challenges the current concept that the presence of aqueous pores is always accompanied by an osmotic water permeability value, P(f)>0.01 cm/s. The possibility of water transport through aqueous pores in lower-permeability cells is proposed.

Mechanotransduction through the cytoskeleton

We constructed a model cytoskeleton to investigate the proposal that this interconnected filamentous structure can act as a mechano- and signal transducer. The model cytoskeleton is composed of rigid rods representing actin filaments, which are connected with springs representing cross-linker molecules. The entire mesh is placed in viscous cytoplasm. The model eukaryotic cell is submitted to either shock wave-like or periodic mechanical perturbations at its membrane. We calculated the efficiency of this network to transmit energy to the nuclear wall as a function of cross-linker stiffness, cytoplasmic viscosity, and external stimulation frequency. We found that the cytoskeleton behaves as a tunable band filter: for given linker molecules, energy transmission peaks in a narrow range of stimulation frequencies. Most of the normal modes of the network are spread over the same frequency range. Outside this range, signals are practically unable to reach their destination. Changing the cellular ratios of linker molecules with different elastic characteristics can control the allowable frequency range and, with it, the efficiency of mechanotransduction.

In-cell NMR spectroscopy

The recent development of "in-cell NMR" techniques by two independent groups has demonstrated that NMR spectroscopy can be used to characterize the conformation and dynamics of biological macromolecules inside living cells. In this article, we describe different methods and discuss current and future applications as well as critical parameters of this new technique. We show experimental results, compare them with traditional in vitro experiments, and demonstrate that differences between the in vitro and the in vivo state of a macromolecule exist and can be detected and characterized.

Reactive oxidizing species produced near the plasma membrane induce apoptosis in bovine aorta endothelial cells

Many cytotoxic agents initiate apoptosis by generating reactive oxidizing species (ROS). The goal of this study was to determine whether apoptosis could be induced by initial reactions of ROS near the plasma membrane. Bovine aorta endothelial cells (BAEC) were illuminated with evanescent wave visible radiation, which has limited penetration into the basal surface of cells, or by trans-radiation. Imaging of fluorescent dyes localizing in the plasma membrane, mitochondria, or nucleus confirmed that evanescent wave radiation excited only dyes in and near the plasma membrane. Singlet oxygen, an ROS generated by photosensitization, has a very short lifetime, ensuring that it oxidizes molecules residing in or very close to the plasma membrane when evanescent wave radiation is used. Cells with condensed nuclei were considered apoptotic and were quantified after treatment with varying doses of light. Annexin V staining without propidium iodide staining confirmed that these cells were apoptotic. The doses required to induce apoptosis using evanescent wave radiation were 10-fold greater than those needed for trans-irradiation. Quantitative analysis of the evanescent wave penetration into cells supports a mechanism in which the singlet oxygen created near the plasma membrane, rather than at intracellular sites, was responsible for initiation of apoptosis.

Size-dependent DNA mobility in cytoplasm and nucleus

The diffusion of DNA in cytoplasm is thought to be an important determinant of the efficacy of gene delivery and antisense therapy. We have measured the translational diffusion of fluorescein-labeled double-stranded DNA fragments (in base pairs (bp): 21, 100, 250, 500, 1000, 2000, 3000, 6000) after microinjection into cytoplasm and nucleus of HeLa cells. Diffusion was measured by spot photobleaching using a focused argon laser spot (488 nm). In aqueous solutions, diffusion coefficients of the DNA fragments in water (D(w)) decreased from 53 x 10(-8) to 0.81 x 10(-8) cm(2)/s for sizes of 21-6000 bp; D(w) was related empirically to DNA size: D(w) = 4.9 x 10(-6) cm(2)/s.[bp size](-0.72). DNA diffusion coefficients in cytoplasm (D(cyto)) were lower than D(w) and depended strongly on DNA size. D(cyto)/D(w) decreased from 0.19 for a 100-bp DNA fragment to 0.06 for a 250-bp DNA fragment and was <0.01 for >2000 bp. Diffusion of microinjected fluorescein isothiocyanate (FITC) dextrans was faster than that of comparably sized DNA fragments of 250 bp and greater. In nucleus, all DNA fragments were nearly immobile, whereas FITC dextrans of molecular size up to 580 kDa were fully mobile. These results suggest that the highly restricted diffusion of DNA fragments in nucleoplasm results from extensive binding to immobile obstacles and that the decreased lateral mobility of DNAs >250 bp in cytoplasm is because of molecular crowding. The diffusion of DNA in cytoplasm may thus be an important rate-limiting barrier in gene delivery utilizing non-viral vectors.

Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area

Classical biochemistry is founded on several assumptions valid in dilute aqueous solutions that are often extended without question to the interior milieu of intact cells. In the first section of this chapter, we present these assumptions and briefly examine the ways in which the cell interior may depart from the conditions of an ideal solution. In the second section, we summarize experimental evidence regarding the physical properties of the cell cytoplasm and their effect on the diffusion and binding of macromolecules and vesicles. While many details remain to be worked out, it is clear that the aqueous phase of the cytoplasm is crowded rather than dilute, and that the diffusion and partitioning of macromolecules and vesicles in cytoplasm is highly restricted by steric hindrance as well as by unexpected binding interactions. Furthermore, the enzymes of several metabolic pathways are now known to be organized into structural and functional units with specific localizations in the solid phase, and as much as half the cellular protein content may also be in the solid phase.

Diffusion of green fluorescent protein in the aqueous-phase lumen of endoplasmic reticulum

The endoplasmic reticulum (ER) is the major compartment for the processing and quality control of newly synthesized proteins. Green fluorescent protein (GFP) was used as a noninvasive probe to determine the viscous properties of the aqueous lumen of the ER. GFP was targeted to the ER lumen of CHO cells by transient transfection with cDNA encoding GFP (S65T/F64L mutant) with a C-terminus KDEL retention sequence and upstream prolactin secretory sequence. Repeated laser illumination of a fixed 2-micrometers diameter spot resulted in complete bleaching of ER-associated GFP throughout the cell, indicating a continuous ER lumen. A residual amount (<1%) of GFP-KDEL was perinuclear and noncontiguous with the ER, presumably within a pre- or cis-Golgi compartment involved in KDEL-substrate retention. Quantitative spot photobleaching with a single brief bleach pulse indicated that GFP was fully mobile with a t1/2 for fluorescence recovery of 88 +/- 5 ms (SE; 60x lens) and 143 +/- 8 ms (40x). Fluorescence recovery was abolished by paraformaldehyde except for a small component of reversible photobleaching with t1/2 of 3 ms. For comparison, the t1/2 for photobleaching of GFP in cytoplasm was 14 +/- 2 ms (60x) and 24 +/- 1 ms (40x). Utilizing a mathematical model that accounted for ER reticular geometry, a GFP diffusion coefficient of 0.5-1 x 10(-7) cm2/s was computed, 9-18-fold less than that in water and 3-6-fold less than that in cytoplasm. By frequency-domain microfluorimetry, the GFP rotational correlation time was measured to be 39 +/- 8 ns, approximately 2-fold greater than that in water but comparable to that in the cytoplasm. Fluorescence recovery after photobleaching using a 40x lens was measured (at 23 degrees C unless otherwise indicated) for several potential effectors of ER structure and/or lumen environment: t1/2 values (in ms) were 143 +/- 8 (control), 100 +/- 13 (37 degrees C), 53 +/- 13 (brefeldin A), and 139 +/- 6 (dithiothreitol). These results indicate moderately slowed GFP diffusion in a continuous ER lumen.

Rapid diffusion of green fluorescent protein in the mitochondrial matrix

It is thought that the high protein density in the mitochondrial matrix results in severely restricted solute diffusion and metabolite channeling from one enzyme to another without free aqueous-phase diffusion. To test this hypothesis, we measured the diffusion of green fluorescent protein (GFP) expressed in the mitochondrial matrix of fibroblast, liver, skeletal muscle, and epithelial cell lines. Spot photobleaching of GFP with a 100x objective (0.8-micron spot diam) gave half-times for fluorescence recovery of 15-19 ms with >90% of the GFP mobile. As predicted for aqueous-phase diffusion in a confined compartment, fluorescence recovery was slowed or abolished by increased laser spot size or bleach time, and by paraformaldehyde fixation. Quantitative analysis of bleach data using a mathematical model of matrix diffusion gave GFP diffusion coefficients of 2-3 x 10(-7) cm2/s, only three to fourfold less than that for GFP diffusion in water. In contrast, little recovery was found for bleaching of GFP in fusion with subunits of the fatty acid beta-oxidation multienzyme complex that are normally present in the matrix. Measurement of the rotation of unconjugated GFP by time-resolved anisotropy gave a rotational correlation time of 23.3 +/- 1 ns, similar to that of 20 ns for GFP rotation in water. A rapid rotational correlation time of 325 ps was also found for a small fluorescent probe (BCECF, approximately 0.5 kD) in the matrix of isolated liver mitochondria. The rapid and unrestricted diffusion of solutes in the mitochondrial matrix suggests that metabolite channeling may not be required to overcome diffusive barriers. We propose that the clustering of matrix enzymes in membrane-associated complexes might serve to establish a relatively uncrowded aqueous space in which solutes can freely diffuse.

Mapping fluorophore distributions in three dimensions by quantitative multiple angle-total internal reflection fluorescence microscopy

The decay of evanescent field intensity beyond a dielectric interface depends upon beam incident angle, enabling the 3-d distribution of fluorophores to be deduced from total internal reflection fluorescence microscopy (TIRFM) images obtained at multiple incident angles. Instrumentation was constructed for computer-automated multiple angle-TIRFM (MA-TIRFM) using a right angle F2 glass prism (n(r) 1.632) to create the dielectric interface. A laser beam (488 nm) was attenuated by an acoustooptic modulator and directed onto a specified spot on the prism surface. Beam incident angle was set using three microstepper motors controlling two rotatable mirrors and a rotatable optical flat. TIRFM images were acquired by a cooled CCD camera in approximately 0.5 degree steps for >15 incident angles starting from the critical angle. For cell studies, cells were grown directly on the glass prisms (without refractive index-matching fluid) and positioned in the optical path. Images of the samples were acquired at multiple angles, and corrected for angle-dependent evanescent field intensity using "reference" images acquired with a fluorophore solution replacing the sample. A theory was developed to compute fluorophore z-distribution by inverse Laplace transform of angle-resolved intensity functions. The theory included analysis of multiple layers of different refractive index for cell studies, and the anisotropic emission from fluorophores near a dielectric interface. Instrument performance was validated by mapping the thickness of a film of dihexyloxacarbocyanine in DMSO/water (n(r) 1.463) between the F2 glass prism and a plano-convex silica lens (458 mm radius, n(r) 1.463); the MA-TIRFM map accurately reproduced the lens spherical surface. MA-TIRFM was used to compare with nanometer z-resolution the geometry of cell-substrate contact for BCECF-labeled 3T3 fibroblasts versus MDCK epithelial cells. These studies establish MA-TIRFM for measurement of submicroscopic distances between fluorescent probes and cell membranes.