The cytoplasmic matrix: its volume and surface area and the diffusion of molecules through it

Molecular Crowding: Physiologic Sensing and Control

The cytoplasm is densely packed with molecules that contribute to its nonideal behavior. Cytosolic crowding influences chemical reaction rates, intracellular water mobility, and macromolecular complex formation. Overcrowding is potentially catastrophic; to counteract this problem, cells have evolved acute and chronic homeostatic mechanisms that optimize cellular crowdedness. Here, we provide a physiology-focused overview of molecular crowding, highlighting contemporary advances in our understanding of its sensing and control. Long hypothesized as a form of crowding-induced microcompartmentation, phase separation allows cells to detect and respond to intracellular crowding through the action of biomolecular condensates, as indicated by recent studies. Growing evidence indicates that crowding is closely tied to cell size and fluid volume, homeostatic responses to physical compression and desiccation, tissue architecture, circadian rhythm, aging, transepithelial transport, and total body electrolyte and water balance. Thus, molecular crowding is a fundamental physiologic parameter that impacts diverse functions extending from molecule to organism.

A comparative modeling study of the mitochondrial function of the proximal tubule and thick ascending limb cells in the rat kidney

To reabsorb >99% of the glomerular filtrate, the metabolic demand of the kidney is high. Interestingly, renal blood flow distribution exhibits marked inhomogeneity, with typical tissue oxygen tension (Po2) of 50-60 mmHg in the well-perfused cortex and 10-20 mmHg in the inner medulla. Cellular fluid composition and acidity also varies substantially. To understand how different renal epithelial cells adapt to their local environment, we have developed and applied computational models of mitochondrial function of proximal convoluted tubule cell (baseline Po2 = 50 mmHg, cytoplasmic pH = 7.20) and medullary thick ascending limb (mTAL) cell (baseline Po2 = 10 mmHg, cytoplasmic pH = 6.85). The models predict key cellular quantities, including ATP generation, P/O (phosphate/oxygen) ratio, proton motive force, electrical potential gradient, oxygen consumption, the redox state of key electron carriers, and ATP consumption. Model simulations predict that close to their respective baseline conditions, the proximal tubule and mTAL mitochondria exhibit qualitatively similar behaviors. Nonetheless, because the mTAL mitochondrion has adapted to a much lower Po2, it can sustain a sufficiently high ATP production at Po2 as low as 4-5 mmHg, whereas the proximal tubule mitochondria would not. Also, because the mTAL cytosol is already acidic under baseline conditions, the proton motive force (pmf) exhibits higher sensitivity to further acidification. Among the different pathways that lead to oxidative phosphorylation impairment, the models predict that both the proximal tubule and mTAL mitochondria are most sensitive to reductions in Complex III activity.NEW & NOTEWORTHY Tissue fluid composition varies substantially within the mammalian kidney. The renal cortex is well perfused and pH neutral, whereas some medullary regions are hypoxic and acidic. How do these environments affect the mitochondrial function of proximal convoluted tubule and medullary thick ascending limb cells, which reside in the cortex and medulla, respectively? This computational modeling study demonstrates that these mitochondria can adapt to their contrasting environments and exhibit different sensitivities to perturbations to local environments.

Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.

A dual initiator approach for oxygen tolerant RAFT polymerization

Reversible-deactivation radical polymerizations are privileged approaches for the synthesis of functional and hybrid materials. A bottleneck for conducting these processes is the need to maintain oxygen free conditions. Herein we report a broadly applicable approach to "polymerize through" oxygen using the synergistic combination of two radical initiators having different rates of homolysis. The in situ monitoring of the concentrations of oxygen and monomer simultaneously provided insight into the function of the two initiators and enabled the identification of conditions to effectively remove dissolved oxygen and control polymerization under open-to-air conditions. By understanding how the surface area to volume ratio of reaction vessels influence open-to-air polymerizations, well-defined polymers were produced using acrylate, styrenic, and methacrylate monomers, which each represent an expansion of scope for the "polymerizing through" oxygen approach. Demonstration of this method in tubular reactors using continuous flow chemistry provided a more complete structure-reactivity understanding of how reaction headspace influences PTO RAFT polymerizations.

Finite element analysis of the influence of cyclic strain on cells anchored to substrates with varying properties

The response of cytoskeleton to mechanical cues plays a pivotal role in understanding several aspects of cellular growth, migration, and cell-cell and cell-matrix interactions under normal and diseased conditions. Finite element analysis (FEA) has become a powerful computational technique to study the response of cytoskeleton in the maintenance of overall cellular mechanics. With the revelation of role of external mechanical microenvironment on cell mechanics, FEA models have also been developed to simulate the effect of substrate stiffness on the mechanical properties of cancer cells. However, the models developed so far model cellular response under static mode, whereas in physiological condition, cells always experience dynamic loading conditions. To develop a more accurate model of cell-extracellular matrix (ECM) interactions, this paper models the cytoskeleton and other parts of the cell by beam and solid elements respectively, assuming spherical morphology of the cell. The stiffness and roughness of extracellular matrix were varied. Furthermore, static and dynamic sinusoidal loads were applied through a flat plate indenter on the cell along with providing sinusoidal strain at the substrate. It is observed that due to axial loading, cell reaches a plastic region, and when the sinusoidal loading is added to the axial load, the cell experiences permanent deformation. Degradation of the cytoskeleton elements and a physiologically more relevant spherical cap shape of the cell were also considered during the analysis. This study suggests that asperity topology of the substrate and indirect cyclic load can play a significant role in the shape alterations and motion of a cell.

Evaluation of quasi-static and dynamic nanomechanical properties of bone-metastatic breast cancer cells using a nanoclay cancer testbed

In recent years, there has been increasing interest in investigating the mechanical properties of individual cells to delineate disease mechanisms. Reorganization of cytoskeleton facilitates the colonization of metastatic breast cancer at bone marrow space, leading to bone metastasis. Here, we report evaluation of mechanical properties of two breast cancer cells with different metastatic ability at the site of bone metastases, using quasi-static and dynamic nanoindentation methods. Our results showed that the significant reduction in elastic modulus along with increased liquid-like behavior of bone metastasized MCF-7 cells was induced by depolymerization and reorganization of F-actin to the adherens junctions, whereas bone metastasized MDA-MB-231 cells showed insignificant changes in elastic modulus and F-actin reorganization over time, compared to their respective as-received counterparts. Taken together, our data demonstrate evolution of breast cancer cell mechanics at bone metastases.

Blends of neem oil based polyesteramide as nanofiber mats to control Culicidae

Mosquitoes act as vectors for several disease-causing microorganisms and pose a threat to mankind by transmitting various diseases. There are different conventional methods to repel or kill these mosquitoes for avoiding susceptibility against infections. However, to overcome the difficulties with conventional methods, new advanced materials are being studied. For the first time, we report developing a nanofiber mat with a controlled release of insecticide to repel or detain the mosquitoes. Briefly, various blend compositions were prepared by manipulating the ratio of neem oil-based polyesteramide (PEA) and polycaprolactone (PCL) immobilized with insecticide, transfluthrin (Tf). The blend solutions were electrospun to get non-woven nanofiber mats, and these nanomaterials were characterized by various spectroscopic techniques to understand their physicochemical properties. The surface morphology was analyzed using environmental scanning electron microscopy (E-SEM), and the diameter of the nanofibers was in the range of 200 to 450 nm. Further, thermal and mechanical properties were evaluated to understand the stability of nanofiber mats. In vitro drug release studies of nanofiber mat PPT-1335 showed controlled and sustained release of Tf, with ∼35% of Tf released in 24 h. However, a film of the same composition (PPT-1335) showed ∼5% of Tf release within 24 h. Moreover, in vivo bio-efficacy studies suggested the mortality of mosquitoes was about 50% with PP-133, which was further increased to 100% within 12 h in the presence of Tf (PPT-1335). However, 60% mortality of mosquitoes was observed with the film of PPT-1335. Hence, the nanofiber mat showed better efficacy against mosquitoes as compared to the film of the same composition. The degradation studies under various conditions revealed biocompatibility of the developed nanofiber mats with the ecosystem.

Electrospun nanofiber mats immobilized with transfluthrin to control mosquitoes.

Complex modulus and compliance for airway smooth muscle cells

A cell can be described as a complex viscoelastic material with structural relaxations that is modulated by thermal and chemically nonequilibrium processes. Tissue morphology and function rely upon cells' physical responses to mechanical force. We measured the frequency-dependent mechanical relaxation response of adherent human airway smooth muscle cells under adenosine triphosphate (ATP) depletion and normal ATP conditions. The frequency dependence of the complex compliance J^{*} and modulus G^{*} was measured over the frequencies 10^{-1}<f<10^{3} Hz at selected temperatures between 4<T<54^{∘}C. Our results show characteristic relaxation features which can be interpreted by the mode-coupling theory (MCT) of viscoelastic liquids. We analyze the shape of the spectra in terms of a so-called A_{4} scenario with logarithmic scaling laws. Characteristic timescales τ_{β} and τ_{α} appear with corresponding energy barriers E_{β}≈(10-20)k_{B}T and E_{α}≈(20-30)k_{B}T. We demonstrate that cells are close to a glass transition. We find that the cell becomes softer around physiological temperatures, where its surface structure is more liquid-like with a plateau modulus around 0.1-0.8 kPa compared with the more solid-like interior cytoskeletal structures with a plateau modulus 1-15 kPa. Corresponding values for the viscosity are 10^{2}-10^{3} Pa s for the surface structures closer to the membrane and 10^{4}-10^{6} Pa s for the core cytoskeletal structures.

Transforming Complexity to Simplicity: Protein-Like Nanotransformer for Improving Tumor Drug Delivery Programmatically

It was difficult for nanodrugs to simultaneously meet the contradictory requirements of prolonged circulation time, augmented cellular uptake, rapid lysosome escape, precise drug release, and tumor penetration in tumor drug delivery. We prepared a nanotransformer (DTIG) through assembling doxorubicin, tannic acid, and indocyanine green to overcome this dilemma. Hydrophilic DTIG showed prolonged blood circulation time. Besides, DTIG could be efficiently internalized by tumor cells through transforming into hydrophobic particles in an acidic tumor microenvironment. Subsequently, oversized hydrophobic particles were further formed in acidic lysosomes to escape from it through rupturing the lysosome. These hydrophobic DTIGs could rapidly revert to a smaller hydrophilic nanoassembly and release the payloads in cytoplasm. Similar to denaturation and renaturation of protein, these high-efficiency instantaneous transformations were activated by proton. Besides, photothermal therapy of DTIG promoted drug penetration efficiency in tumor. This optimized drug delivery process of DTIG finally offered potent antitumor efficacy and an obvious advantage on prognosis.

A model of mitochondrial O2 consumption and ATP generation in rat proximal tubule cells

Oxygen tension in the kidney is mostly determined by O2 consumption (Qo2), which is, in turn, closely linked to tubular Na+ reabsorption. The objective of the present study was to develop a model of mitochondrial function in the proximal tubule (PT) cells of the rat renal cortex to gain more insight into the coupling between Qo2, ATP formation (GATP), ATP hydrolysis (QATP), and Na+ transport in the PT. The present model correctly predicts in vitro and in vivo measurements of Qo2, GATP, and ATP and Pi concentrations in PT cells. Our simulations suggest that O2 levels are not rate limiting in the proximal convoluted tubule, absent large metabolic perturbations. The model predicts that the rate of ATP hydrolysis and cytoplasmic pH each substantially regulate the GATP-to-Qo2 ratio, a key determinant of the number of Na+ moles actively reabsorbed per mole of O2 consumed. An isolated increase in QATP or in cytoplasmic pH raises the GATP-to-Qo2 ratio. Thus, variations in Na+ reabsorption and pH along the PT may, per se, generate axial heterogeneities in the efficiency of mitochondrial metabolism and Na+ transport. Our results also indicate that the GATP-to-Qo2 ratio is strongly impacted not only by H+ leak permeability, which reflects mitochondrial uncoupling, but also by K+ leak pathways. Simulations suggest that the negative impact of increased uncoupling in the diabetic kidney on mitochondrial metabolic efficiency is partly counterbalanced by increased rates of Na+ transport and ATP consumption. This model provides a framework to investigate the role of mitochondrial dysfunction in acute and chronic renal diseases.

Automated Strong Cation-Exchange Cleanup To Remove Macromolecular Crowding Agents for Protein Hydrogen Exchange Mass Spectrometry

Measuring amide hydrogen exchange (HX) of intrinsically disordered proteins (IDPs) in solutions containing high concentrations of macromolecular crowding agents would give new insights into the structure and dynamics of these proteins under crowded conditions. High concentrations of artificial crowders, required to simulate cellular crowding, introduce overwhelming interferences to mass spectrometry (MS) analysis. We have developed a fully automated, dual-stage online cleanup that uses strong cation-exchange (SCX) followed by reversed-phase desalting to remove Ficoll, a synthetic polymer, for HX-MS analysis of proteins under crowded conditions. We tested the efficiency of our method by measuring the HX-MS signal intensities of myoglobin peptides from crowded samples containing 300 g L^-1 Ficoll and from uncrowded samples. Although there was loss of abundance relative to uncrowded myoglobin analyzed using conventional HX-MS, 97% coverage of the myoglobin sequence was still obtained. Control HX-MS experiments using unstructured peptides labeled at pD 4.0 under crowded and uncrowded conditions confirmed that Ficoll does not alter chemical exchange and that the same extent of HX is achieved in uncrowded solutions as in solutions containing 300 g L^-1 of predeuterated Ficoll. We validated our method by measuring HX of CBP, the intrinsically disordered nuclear coactivator binding domain of CREB binding protein (UniProt CBP_MOUSE P45481 ), residues 2059-2117, at pD 6.5 under crowded and uncrowded conditions. Ficoll induced both protection and deprotection from HX in different regions of CBP, with the greatest deprotection occurring at the edges of helices. These results are consistent with previous observation of IDPs under the influence of synthetic polymers.

A mathematical model of Aurora B activity in prophase and metaphase

Aurora B kinase is a protein that controls several processes in mitosis when it is found associated with INCENP, Survivin and Borealin in a complex known as the Chromosomal Passenger Complex. Aurora B in complex with INCENP is phosphorylated on three sites, resulting in the full activation of Aurora B. In prophase and metaphase, Aurora B is activated at centromeres, the region of chromatin linking sister chromatids, due to an autophosphorylation mechanism, and it has been hypothesised that Aurora B is activated throughout the cytoplasm due to its concentration at centromeres. In this article, we first develop a time-dependent model of Aurora B activation that does not incorporate spatial variation. This model is used to demonstrate the various qualitative behaviours that the activation of Aurora B is capable of displaying for different model parameters. Next, we develop a spatio-temporal model of Aurora B activation that includes diffusion of soluble Aurora B and binding of Aurora B to immobile centromeric binding sites. This model describes the activation of Aurora B throughout the cytoplasm due to its concentration-dependent activation at centromeres. The models demonstrate the effects that a soluble phosphatase concentration, multisite phosphorylation and diffusion have on the activation of Aurora B.

A novel bio-functional material based on mammalian cell aggresomes

Aggresomes are protein aggregates found in mammalian cells when the intracellular protein degradation machinery is over-titered. Despite that they abound in cells producing recombinant proteins of biomedical and biotechnological interest, the physiological roles of these protein clusters and the functional status of the embedded proteins remain basically unexplored. In this work, we have determined for the first time that, like in bacterial inclusion bodies, deposition of recombinant proteins into aggresomes does not imply functional inactivation. As a model, human α-galactosidase A (GLA) has been expressed in mammalian cells as enzymatically active, mechanically stable aggresomes showing higher thermal stability than the soluble GLA version. Since aggresomes are easily produced and purified, we propose these particles as novel functional biomaterials with potential as carrier-free, self-immobilized catalyzers in biotechnology and biomedicine.

Enzyme kinetics and transport in a system crowded by mobile macromolecules

The dynamics of an elastic network model for the enzyme 4-oxalocrotonate tautomerase is studied in a system crowded by mobile macromolecules, also modeled by elastic networks.

Diffusion coefficients of endogenous cytosolic proteins from rabbit skinned muscle fibers

Efflux time courses of endogenous cytosolic proteins were obtained from rabbit psoas muscle fibers skinned in oil and transferred to physiological salt solution. Proteins were separated by gel electrophoresis and compared to load-matched standards for quantitative analysis. A radial diffusion model incorporating the dissociation and dissipation of supramolecular complexes accounts for an initial lag and subsequent efflux of glycolytic and glycogenolytic enzymes. The model includes terms representing protein crowding, myofilament lattice hindrance, and binding to the cytomatrix. Optimization algorithms returned estimates of the apparent diffusion coefficients, D(r,t), that were very low at the onset of diffusion (∼10(-10) cm(2) s(-1)) but increased with time as cytosolic protein density, which was initially high, decreased. D(r,t) at later times ranged from 2.11 × 10(-7) cm(2) s(-1) (parvalbumin) to 0.20 × 10(-7) cm(2) s(-1) (phosphofructose kinase), values that are 3.6- to 12.3-fold lower than those predicted in bulk water. The low initial values are consistent with the presence of complexes in situ; the higher later values are consistent with molecular sieving and transient binding of dissociated proteins. Channeling of metabolic intermediates via enzyme complexes may enhance production of adenosine triphosphate at rates beyond that possible with randomly and/or sparsely distributed enzymes, thereby matching supply with demand.

The role of tubulin in the mitochondrial metabolism and arrangement in muscle cells

Tubulin, a well-known component of the microtubule in the cytoskeleton, has an important role in the transport and positioning of mitochondria in a cell type dependent manner. This review describes different functional interactions of tubulin with cellular protein complexes and its functional interaction with the mitochondrial outer membrane. Tubulin is present in oxidative as well as glycolytic type muscle cells, but the kinetics of the in vivo regulation of mitochondrial respiration in these muscle types is drastically different. The interaction between VDAC and tubulin is probably influenced by such factors as isoformic patterns of VDAC and tubulin, post-translational modifications of tubulin and phosphorylation of VDAC. Important factor of the selective permeability of VDAC is the mitochondrial creatine kinase pathway which is present in oxidative cells, but is inactive or missing in glycolytic muscle and cancer cells. As the tubulin-VDAC interaction reduces the permeability of the channel by adenine nucleotides, energy transfer can then take place effectively only through the mitochondrial creatine kinase/phosphocreatine pathway. Therefore, closure of VDAC by tubulin may be one of the reasons of apoptosis in cells without the creatine kinase pathway. An important question in tubulin regulated interactions is whether other proteins are interacting with tubulin. The functional interaction may be direct, through other proteins like plectins, or influenced by simultaneous interaction of other complexes with VDAC.

Solutions are solutions, and gels are almost solutions

Molecular gastronomy is the scientific discipline that looks for mechanisms of phenomena occurring during dish preparation and consumption. Solutions are studied because most foods, being based on animal and plant tissues, are gels, with a liquid fraction and a continuous solid phase. This is why food can be studied in situ using liquid NMR spectroscopy in the frequency domain (isq NMR). Using such tools, processes of the kind F@M → F' @ M' (where F stands for the food matrix, M for its environment, and @ for inclusion) were investigated for various processes as classified using the complex disperse system/non-periodical organization of space formalism (“disperse systems formalism”, DSF). As an application of these studies, “note by note cuisine” was promoted as a new paradigm for culinary activities.

Spatial simulations in systems biology: from molecules to cells

Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.

Macromolecular dynamics in crowded environments

The structural and dynamical properties of macromolecules in confining or crowded environments are different from those in simple bulk liquids. In this paper, both the conformational and diffusional dynamics of globular polymers are studied in solutions containing fixed spherical obstacles. These properties are studied as a function of obstacle volume fraction and size, as well as polymer chain length. The results are obtained using a hybrid scheme that combines multiparticle collision dynamics of the solvent with molecular dynamics that includes the interactions among the polymer monomers and between the polymer beads and obstacles and solvent molecules. The dynamics accounts for hydrodynamic interactions among the polymer beads and intermolecular forces with the solvent molecules. We consider polymers in poor solvents where the polymer chain adopts a compact globular structure in solution. Our results show that the collapse of the polymer chain to a compact globular state is strongly influenced by the obstacle array. A nonmonotonic variation in the radius of gyration with time is observed and the collapse time scale is much longer than that in simple solutions without obstacles. Hydrodynamic interactions are important at low obstacle volume fractions but are screened at high volume fractions. The diffusion of the globular polymer chain among the obstacles is subdiffusive in character on intermediate time scales where the dynamics explores the local structure of the heterogeneous environment. For large polymer chains in systems with high obstacle volume fractions, the chain adopts bloblike conformations that arise from trapping of portions of the chain in voids among the obstacles.

Effects of macromolecular crowding on intracellular diffusion from a single particle perspective

Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60-70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed 'crowded'. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.

Investigating the effects of molecular crowding on Ca2+ diffusion using a particle-based simulation model

Calcium ions (Ca(2+)) are an important second messenger in eucaryotic cells. They are involved in numerous physiological processes which are triggered by calcium signals in the form of local release events, temporal oscillations, or reaction-diffusion waves. The diffusive spread of calcium signals in the cytosol is strongly affected by calcium-binding proteins (buffers). In addition, the cytosol contains a large number of inert molecules and molecular structures which make it a crowded environment. Here, we investigate the effects of such excluded volumes on calcium diffusion in the presence of different kinds of buffers. We find that the contributions in slowing down Ca(2+) diffusion coming from buffering and molecular crowding are not additive, i.e., the reduction in Ca(2+) diffusivity due to crowding and buffering together is not the sum of each single contribution. In the presence of Ca(2+) gradients and high affinity mobile buffers the effective diffusion coefficient of Ca(2+) can be reduced by up to 60% in highly crowded environments. This suggests that molecular crowding may significantly affect the shape of Ca(2+) microdomains and wave propagation in cell types with high excluded volume fractions.

Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion

The transduction of signals depends on the translocation of signaling molecules to specific targets. Undirected diffusion processes play a key role in the bridging of spaces between different cellular compartments. The diffusion of the molecules is, in turn, governed by the intracellular architecture. Molecular crowding and the cytoskeleton decrease macroscopic diffusion. This article shows the use of a stochastic simulation method to study the effects of the cytoskeleton structure on the mobility of macromolecules. Brownian dynamics and single particle tracking were used to simulate the diffusion process of individual molecules through a model cytoskeleton. The resulting average effective diffusion is in line with data obtained in the in vitro and in vivo experiments. It shows that the cytoskeleton structure strongly influences the diffusion of macromolecules. The simulation method used also allows the inclusion of reactions in order to model complete signaling pathways in their spatio-temporal dynamics, taking into account the effects of the cellular architecture.

Photobleaching measurements of diffusion in cell membranes and aqueous cell compartments

This commentary unit discusses in great detail the theoretical nature of fluorescence recovery after photobleaching (FRAP). This information is crucial to an understanding of how and why FRAP works in a cell system. Further, understanding how to interpret the data sets requires a sound knowledge of the processes involved. Of primary importance are the nature of membrane diffusion and the nature of the multiple compartments into which fluorescent dyes can enter. The unit provides a complete discussion of all aspects of FRAP from the perspective of cellular measurements.

Guiding protein aggregation with macromolecular crowding

Macromolecular crowding is expected to have a significant effect on protein aggregation. In the present study we analyzed the effect of macromolecular crowding on fibrillation of four proteins, bovine S-carboxymethyl-alpha-lactalbumin (a disordered form of the protein with reduced three out of four disulfide bridges), human insulin, bovine core histones, and human alpha-synuclein. These proteins are structurally different, varying from natively unfolded (alpha-synuclein and core histones) to folded proteins with rigid tertiary and quaternary structures (monomeric and hexameric forms of insulin). All these proteins are known to fibrillate in diluted solutions, however their aggregation mechanisms are very divers and some of them are able to form different aggregates in addition to fibrils. We studied how macromolecular crowding guides protein between different aggregation pathways by analyzing the effect of crowding agents on the aggregation patterns under the variety of conditions favoring different aggregated end products in diluted solutions.

Endocytosis of a single mesoporous silica nanoparticle into a human lung cancer cell observed by differential interference contrast microscopy

The unique structural features of mesoporous silica nanoparticles (MSN) have made them very useful in biological applications, such as gene therapy and drug delivery. Flow cytometry, confocal microscopy, and electron microscopy have been used for observing the endocytosis of MSN. However, flow cytometry cannot directly observe the process of endocytosis. Confocal microscopy requires fluorescence labeling of the cells. Electron microscopy can only utilize fixed cells. In the present work, we demonstrate for the first time that differential interference contrast (DIC) microscopy can be used to observe the entire endocytosis process of MSN into living human lung cancer cells (A549) without fluorescence staining. There are three physical observables that characterize the locations of MSN and the stages of the endocytosis process: motion, shape, and vertical position. When it was outside the cell, the MSN underwent significant Brownian motion in the cell growth medium. When it was trapped on the cell membrane, the motion of the MSN was greatly limited. After the MSN had entered the cell, it resumed motion at a much slower speed because the cytoplasm is more viscous than the cell growth medium and the cellular cytoskeleton networks act as obstacles. Moreover, there were shape changes around the MSN due to the formation of a vesicle after the MSN had been trapped on the cell membrane and prior to entry into the cell. Finally, by coupling a motorized vertical stage to the DIC microscope, we recorded the location of the MSN in three dimensions. Such accurate 3D particle tracking ability in living cells is essential for studies of selectively targeted drug delivery based on endocytosis.

Statistical and sampling issues when using multiple particle tracking

Video microscopy can be used to simultaneously track several microparticles embedded in a complex material. The trajectories are used to extract a sample of displacements at random locations in the material. From this sample, averaged quantities characterizing the dynamics of the probes are calculated to evaluate structural and/or mechanical properties of the assessed material. However, the sampling of measured displacements in heterogeneous systems is singular because the volume of observation with video microscopy is finite. By carefully characterizing the sampling design in the experimental output of the multiple particle tracking technique, we derive estimators for the mean and variance of the probes' dynamics that are independent of the peculiar statistical characteristics. We expose stringent tests of these estimators using simulated and experimental complex systems with a known heterogeneous structure. Up to a certain fundamental limitation, which we characterize through a material degree of sampling by the embedded probe tracking, these estimators can be applied to quantify the heterogeneity of a material, providing an original and intelligible kind of information on complex fluid properties. More generally, we show that the precise assessment of the statistics in the multiple particle tracking output sample of observations is essential in order to provide accurate unbiased measurements.

Pre-steady-state decoding of the Bicoid morphogen gradient

Morphogen gradients are established by the localized production and subsequent diffusion of signaling molecules. It is generally assumed that cell fates are induced only after morphogen profiles have reached their steady state. Yet, patterning processes during early development occur rapidly, and tissue patterning may precede the convergence of the gradient to its steady state. Here we consider the implications of pre-steady-state decoding of the Bicoid morphogen gradient for patterning of the anterior–posterior axis of the Drosophila embryo. Quantitative analysis of the shift in the expression domains of several Bicoid targets (gap genes) upon alteration of bcd dosage, as well as a temporal analysis of a reporter for Bicoid activity, suggest that a transient decoding mechanism is employed in this setting. We show that decoding the pre-steady-state morphogen profile can reduce patterning errors caused by fluctuations in the rate of morphogen production. This can explain the surprisingly small shifts in gap and pair-rule gene expression domains observed in response to alterations in bcd dosage.

It was previously thought that cell fates were determined by morphogen gradients only after steady state was established. Here the authors show fate may precede gradient steady state.

Subdivision of naive fields of cells into separate cell populations, distinguished by the unique combinations of genes they express, constitutes a major aspect of organism development. Classically, this involves the generation of gradients of signaling molecules (morphogens), which induce distinct cell fates in a concentration-dependent manner. It has been generally assumed that morphogen gradients are interpreted only after they reach a spatially fixed, steady-state profile. Our study re-examines this assumption for the classical case of the Bicoid morphogen, a transcription factor that is distributed as a gradient in the early Drosophila embryo. We propose and present evidence for dynamic, pre-steady-state decoding of the Bicoid profile. We further show that such dynamic decoding can directly account for the surprisingly small shifts in the expression domains of target genes, observed in response to altered Bicoid dosage, without invoking additional mechanisms or contributing factors. Pre-steady-state decoding can thus provide a simple explanation for the relative robustness of this classical morphogen system, which has been a long-standing problem.

The ‘wet mind’: water and functional neuroimaging

Functional neuroimaging has emerged as an important approach to study the brain and the mind. Surprisingly, although they are based on radically different physical approaches both positron emission tomography (PET) and magnetic resonance imaging (MRI) make brain activation imaging possible through measurements involving water molecules. So far, PET and MRI functional imaging have relied on the principle that neuronal activation and blood flow are coupled through metabolism. However, a new paradigm has emerged to look at brain activity through the observation with MRI of the molecular diffusion of water. In contrast with the former approaches diffusion MRI has the potential to reveal changes in the intrinsic water physical properties during brain activation, which could be more intimately linked to the neuronal activation mechanisms and lead to an improved spatial and temporal resolution. However, this link has yet to be fully confirmed and understood. To shed light on the possible relationship between water and brain activation, this introductory paper reviews the most recent data on the physical properties of water and on the status of water in biological tissues, and evaluates their relevance to brain diffusion MRI. The biophysical mechanisms of brain activation are then reassessed to reveal their intimacy with the physical properties of water, which may come to be regarded as the 'molecule of the mind'.

A systematic investigation of the rate laws valid in intracellular environments

Recently there has been significant interest in deducing the form of the rate laws for chemical reactions occurring in the intracellular environment. This environment is typically characterized by low-dimensionality and a high macromolecular content; this leads to a spatial heterogeneity not typical of the well stirred in vitro environments. For this reason, the classical law of mass action has been presumed to be invalid for modeling intracellular reactions. Using lattice-gas automata models, it has recently been postulated [H. Berry, Monte Carlo simulations of enzyme reactions in two dimensions: Fractal kinetics and spatial segregation, Biophys. J. 83 (2002) 1891-1901; S. Schnell, T.E. Turner, Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws, Prog. Biophys. Mol. Biol. 85 (2004) 235-260] that the reaction kinetics is fractal-like. In this article we systematically investigate for the first time how the rate laws describing intracellular reactions vary as a function of: the geometry and size of the intracellular surface on which the reactions occur, the mobility of the macromolecules responsible for the crowding effects, the initial reactant concentrations and the probability of reaction between two reactant molecules. We also compare the rate laws valid in heterogeneous environments in which there is an underlying spatial lattice, for example crystalline alloys, with the rate laws valid in heterogeneous environments where there is no such natural lattice, for example in intracellular environments. Our simulations indicate that: (i) in intracellular environments both fractal kinetics and mass action can be valid, the major determinant being the probability of reaction, (ii) the geometry and size of the intracellular surface on which reactions are occurring does not significantly affect the rate law, (iii) there are considerable differences between the rate laws valid in heterogeneous non-living structures such as crystals and those valid in intracellular environments. Deviations from mass action are less pronounced in intracellular environments than in a crystalline material of similar heterogeneity.

Lipid membrane-induced optimization for ligand-receptor docking: recent tools and insights for the "membrane catalysis" model

Cells in living organisms are regulated by chemical and physical stimuli from their environment. Often, ligands interact with membrane receptors to trigger responses and Sargent and Schwyzer conceived a model to describe this process, "membrane catalysis". There is a notion that the physical organization of membranes can control the response of cells by speeding up reactions. We revisit the "membrane catalysis" model in the light of recent technical, methodological and theoretical advances and how they can be exploited to highlight the details of membrane mediated ligand-receptor interactions. We examine the possible effects that ligand concentration causes in the membrane catalysis and focus our attention in techniques used to determine the partition constant. The hypothetical diffusional advantage associated with membrane catalysis is discussed and the applicability of existing models is assessed. The role of in-depth location and orientation of ligands is explored emphasizing the contribution of new analysis methods and spectroscopic techniques. Results suggest that membranes can optimize the interaction between ligands and receptors through several different effects but the relative contribution of each must be carefully investigated. We certainly hope that the conjugation of the methodological and technical advances here reported will revive the interest in the membrane catalysis model.

Swelling of hepatocytes injured by oxidative stress suggests pathological changes related to macromolecular crowding

A fundamental property of living matter is the ability to establish and maintain order. Mild changes in cell volume have a role in metabolic control. Furthermore, cellular swelling is a way of living cells to react to a variety of stressors. Data from experimental pathology, biochemistry and biophysics and theoretical arguments from biology, biochemical evolution, cytology and biophysics are considered to attempt an integration of several current concepts on different subjects (intracellular compartmentation, cellular swelling, macromolecular crowding, perturbing and non-perturbing solutes). The purpose is to provide a framework for conceptualizing in modern terms the question whether cellular swelling induced by oxidative stress should be considered merely a cell adaptation balanced by antioxidant defenses and by other biochemical devices apt to preserve the intracellular environment and normal cell functioning, or whether swelling of high amplitude should be regarded as a true pathological change. The basic question dated 1982: "how crowded is the cytoplasm?" is a matter for discussion as far as swollen cells are concerned. This paper examines the liver for cellular swelling of high amplitude (about+30%) caused by iron or by thyroid hormone+iron (histological picture of "cloudy swelling") or the steatogenic poison CCl(4), also known as a source of oxyradicals, which causes an even more pronounced cellular swelling. In CCl(4)-toxic fatty liver the strong increase of tissue water is substantially masked by the parallel increase of tissue dry solids due to fat accumulation. This example of a "tissue dilution artefact" is discussed in connection with the increase of tissue water also in toxic fatty liver induced by white phosphorus and ethanol. In CCl(4)-toxic fatty liver the normal K(+)/Na(+) ratio (about 3) is substantially maintained, whereas the concentrations of the two cations ("perturbing osmolytes") in tissue water are noticeably decreased, a finding which was not further studied at the time the observations were made because biochemistry was not yet advanced enough to allow an explanation. Today, a logic hypothesis is that an increase of non-perturbing solutes such as taurine and betaine, maintains the physiological intracellular osmotic pressure and that the harmful effects of CCl(4) are limited because of the protective effects of these molecules and of molecular chaperones against damage by oxyradicals. However, as a consequence of cellular swelling, intracellular changes in ionic strength and macromolecular crowding should occur thus affecting enzyme activities. Models and techniques apt to investigate this problem experimentally are suggested.

Cytoplasmic-to-nuclear volume ratio affects AP-1 complex formation as an indicator of cell cycle responsiveness

Cytoplasmic volume undergoes a series of changes during mitosis in eukaryotes; in turn, signaling events such as osmotic stress can regulate the cytoplasmic volume in cells. In some organisms, increase in cytoplasmic-to-nuclear volume ratio was seen to affect the growth potential in cells, however, the mechanistics of such a regulation, if at all present, was unclear. In a computational model, we have constructed a growth factor-induced signaling pathway leading to AP-1 heterodimer formation through transcriptional regulation, and analyzed the effects of increasing the cytoplasmic-to-nuclear ratio on c-jun transcription and AP-1 complex. We have observed that larger cytoplasmic volumes caused both an increase in the final AP-1 product and a delay in the time of AP-1 accumulation.

Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws

We review recent evidence illustrating the fundamental difference between cytoplasmic and test tube biochemical kinetics and thermodynamics, and showing the breakdown of the law of mass action and power-law approximation in in vivo conditions. Simulations of biochemical reactions in non-homogeneous media show that as a result of anomalous diffusion and mixing of the biochemical species, reactions follow a fractal-like kinetics. Consequently, the conventional equations for biochemical pathways fail to describe the reactions in in vivo conditions. We present a modification to fractal-like kinetics following the Zipf-Mandelbrot distribution which will enable the modelling and analysis of biochemical reactions occurring in crowded intracellular environments.

Stochastic model of protein-protein interaction: why signaling proteins need to be colocalized

Colocalization of proteins that are part of the same signal transduction pathway via compartmentalization, scaffold, or anchor proteins is an essential aspect of the signal transduction system in eukaryotic cells. If interaction must occur via free diffusion, then the spatial separation between the sources of the two interacting proteins and their degradation rates become primary determinants of the time required for interaction. To understand the role of such colocalization, we create a mathematical model of the diffusion based protein-protein interaction process. We assume that mRNAs, which serve as the sources of these proteins, are located at different positions in the cytoplasm. For large cells such as Drosophila oocytes we show that if the source mRNAs were at random locations in the cell rather than colocalized, the average rate of interactions would be extremely small, which suggests that localization is needed to facilitate protein interactions and not just to prevent cross-talk between different signaling modules.

Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors

Extracellular signals received by membrane receptors are processed, encoded and transferred to the nucleus via phosphorylation and spatial relocation of protein members of multiple component pathways, such as mitogen activated protein kinase (MAPK) cascades. The receptor-induced membrane recruitment of the cytoplasmic protein SOS results in the activation of the Ras/MAPK cascade. It has been suggested that the membrane recruitment of signaling proteins causes an increase in the diffusion-limited rates. We have recently shown that this increase is too small to be responsible for enhanced signal transduction. Instead we demonstrate that the function of membrane localization is to increase the number (or average lifetime) of complexes between signaling partners. A hallmark of signaling pathways is the spatial separation of activation and deactivation mechanisms; e.g. a protein can be phosphorylated at the cell surface by a membrane-bound kinase and dephosphorylated in the cytosol by a cytosolic phosphatase. Given the measured values of protein diffusion coefficients and of phosphatase and kinase activities, the spatial separation is shown to result in precipitous phospho-protein gradients. When information transfer is hampered by slow protein diffusion and rapid dephosphorylation, phospho-protein trafficking within endocytic vesicles may be an efficient way to deliver messages to physiologically relevant locations. The proposed mechanism explains recent observations that various inhibitors of endocytosis can inhibit MAPK activation. Additional mechanisms facilitating the relay of signals from cell-surface receptors to the nucleus can involve the assembly of protein kinases on a scaffolding protein and active transport of signaling complexes by molecular motors. We also discuss long-range signaling within a cell, such as survival signaling in neurons. We hypothesize that ligand-independent waves of receptor activation or/and traveling waves of phosphorylated kinases emerge to spread the signals over long distances.

The molecular function of Ase1p: evidence for a MAP-dependent midzone-specific spindle matrix. Microtubule-associated proteins

The midzone is the domain of the mitotic spindle that maintains spindle bipolarity during anaphase and generates forces required for spindle elongation (anaphase B). Although there is a clear role for microtubule (MT) motor proteins at the spindle midzone, less is known about how microtubule-associated proteins (MAPs) contribute to midzone organization and function. Here, we report that budding yeast Ase1p is a member of a conserved family of midzone-specific MAPs. By size exclusion chromatography and velocity sedimentation, both Ase1p in extracts and purified Ase1p behaved as a homodimer. Ase1p bound and bundled MTs in vitro. By live cell microscopy, loss of Ase1p resulted in a specific defect: premature spindle disassembly in mid-anaphase. Furthermore, when overexpressed, Ase1p was sufficient to trigger spindle elongation in S phase-arrested cells. FRAP revealed that Ase1p has both a very slow rate of turnover within the midzone and limited lateral diffusion along spindle MTs. We propose that Ase1p functions as an MT cross-bridge that imparts matrix-like characteristics to the midzone. MT-dependent networks of spindle midzone MAPs may be one molecular basis for the postulated spindle matrix.

MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?

A hallmark of many signaling pathways is the spatial separation of activation and deactivation of signaling proteins. Quantitative analysis demonstrates that the spatial separation of a membrane-bound kinase and a cytosolic phosphatase potentially results in precipitous gradients of target phosphoproteins. Hypothetically, such gradients in the mitogen-activated protein kinase (MAPK) cascade would result in a strong attenuation of the phosphorylation signal towards the nucleus. When effective signal transduction is hampered by slow protein diffusion and rapid dephosphorylation, phosphoprotein trafficking within endocytic vesicles might be an efficient way to propagate the signals. Additional mechanisms facilitating information transfer could involve the assembly of MAP kinases on a scaffolding protein and active transport of signaling complexes by molecular motors. The proposed mechanism explains recent observations that MAPK activation can be strongly suppressed by various inhibitors of endocytosis.

Macromolecular crowding and its role as intracellular signalling of cell volume regulation

Macromolecular crowding has been proposed as a mechanism by means of which a cell can sense relatively small changes in volume or, more accurately, the concentration of intracellular solutes. According to the macromolecular theory, the kinetics and equilibria of enzymes can be greatly influenced by small changes in the concentration of ambient, inert macromolecules. A 10% change in the concentration of intracellular proteins can lead to changes of up to a factor of ten in the thermodynamic activity of putative molecular regulatory species, and consequently, the extent to which such regulator(s) may bind to and activate membrane-associated ion transporters. The aim of this review is to examine the concept of macromolecular crowding and how it profoundly affects macromolecular association in an intact cell with particular emphasis on its implication as a sensor and a mechanism through which cell volume is regulated.