Physical properties of cytoplasm

Unraveling Ferroptosis Mechanisms: Tracking Cellular Viscosity with Small Molecular Fluorescent Probes

Ferroptosis is a recently identified form of regulated cell death characterized by iron accumulation and lipid peroxidation. Numerous functions for ferroptosis have been identified in physiological as well as pathological processes, most notably in the treatment of cancer. The intricate balance of redox homeostasis is profoundly altered during ferroptosis, leading to alteration in cellular microenvironment. One such microenvironment is viscosity among others such as pH, polarity, and temperature. Therefore, understanding the dynamics of ferroptosis associated viscosity levels within organelles is crucial. To date, there are a very few reviews that detects ferroptosis assessing reactive species. In this review, we have summarized organelle's specific fluorescent probes that detects dynamics of microviscosity during ferroptosis. Also, we offer the readers an insight of their design strategy, photophysics and associated bioimaging concluding with the future perspective and challenges in the related field.

Cytoplasm mechanics and cellular organization

As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.

FRET-based fluorescent probe with favorable water solubility for simultaneous detection of SO2 derivatives and viscosity

The intracellular viscosity is an important parameter of the microenvironment and SO₂ is a vital gas signal molecule. At present, some dual-response fluorescence probes for simultaneous measurements of viscosity and SO₂ derivatives (HSO₃^-/SO₃^2-) possessed poor water solubility. In this work, we developed a water-soluble fluorescence probe CIJ (0.0864 g/100 mL of water at 20 °C) for simultaneous measurements of viscosity and SO₂ derivatives. CIJ exhibited a sensitive fluorescence enhancement to environmental viscosity from 0.97 to 28.04 cP based on a twisted intramolecular charge transfer mechanism and was applied to effective measurement of viscosity in vitro and in vivo. CIJ could also respond to SO₂ derivatives with a low detection limit (44 nM) and a fast response time (5 min) based on the nucleophilic addition reaction. Furthermore, CIJ was applied to monitor SO₂ derivatives in ratiometric response manner in living cells.

The Diffusion Model of Intra-Golgi Transport Has Limited Power

The Golgi complex (GC) is the main station along the cell biosecretory pathway. Until now, mechanisms of intra-Golgi transport (IGT) have remained unclear. Herein, we confirm that the goodness-of-fit of the regression lines describing the exit of a cargo from the Golgi zone (GZ) corresponds to an exponential decay. When the GC was empty before the re-initiation of the intra-Golgi transport, this parameter of the curves describing the kinetics of different cargoes (which are deleted in Golgi vesicles) with different diffusional mobilities within the GZ as well as their exit from the GZ was maximal for the piecewise nonlinear regression, wherein the first segment was horizontal, while the second segment was similar to the exponential decay. The kinetic curve describing cargo exit from the GC per se resembled a linear decay. The Monte-Carlo simulation revealed that such curves reflect the role of microtubule growth in cells with a central GC or the random hovering of ministacks in cells lacking a microtubule. The synchronization of cargo exit from the GC already filled with a cargo using the wave synchronization protocol did not reveal the equilibration of cargo within a Golgi stack, which would be expected from the diffusion model (DM) of IGT. Moreover, not all cisternae are connected to each other in mini-stacks that are transporting membrane proteins. Finally, the kinetics of post-Golgi carriers and the important role of SNAREs for IGT at different level of IGT also argue against the DM of IGT.

A benzothiophene-quinoline-based targetable fluorescent chemosensor for detection of viscosity and mitochondrial imaging in live cells

Mitochondria are the sites of respiration in cells, and they participate in many indispensable biological processes. Because variations in mitochondrial viscosity can lead to dysfunctions of mitochondrial structure and function (and even induce malignant diseases), new sensors that can accurately monitor changes in mitochondrial viscosity are essential. To better investigate these changes, we report the development and evaluation of a novel benzothiophene-quinoline-based fluorescent chemosensor (BQL) that was designed especially for monitoring mitochondrial viscosity. BQL demonstrated a large Stokes shift (minimizing interference from autofluorescence) and a good response to viscosity (using the TICT principle). Moreover, BQL demonstrated little to no pH-dependency, polarity-dependency, or interference from other analytes. Thus, BQL has an excellent specificity for viscosity. BQL was used to monitor viscosity changes in mitochondria induced by ion carriers, and was used to report on viscosity in real time during mitophagy. To sum up, BQL provided a new approach for detecting viscosity in living cells and in vivo. BQL should prove to be an excellent tool for the analysis of viscosity changes in live cells.

A High Spatiotemporal Iontronic Single-Cell Viscometer

Ideal single-cell viscometer has remained unachieved, leaving a gap in current palette of single-cell nanotools. Information of single-cell viscosity could contribute to our knowledge of fundamental biological processes, e.g., mass diffusion, biochemical interaction, and cellular responses to many diseases and pathologies. Although advances have been made to this end, existing methods generally suffer from limitations, e.g., low spatiotemporal resolution. Here, we describe a high spatiotemporal iontronic single-cell viscometer that operates upon a patch clamp integrated with double-barreled nanopores separated by a septum of ca. 32 nm. The system enables reversible electroosmotic manipulation of the adjacent small fluid bridging two nanopores, the viscous alternation of which could be sensitively monitored by the ionic responses. In practical cellular studies, significantly, our findings reveal not only the less deviated medium viscosities than those of lysosomes and mitochondria but also the highest viscosities in the near-nuclear region than those of mitochondrion-dense and lysosome-dense regions. This work has provided an accessible single-cell viscometer and enriched the armory of single-cell nanotools.

A novel water-soluble near-infrared fluorescent probe for monitoring mitochondrial viscosity

Mitochondria, the main source of energy of cells, play a significant role in aerobic respiration process. Some stimulants can result in changes of mitochondrial microenvironments such as viscosity, pH and polarity. Abnormal changes of mitochondrial viscosity have been shown to relate to pathological activities and diseases. Therefore, it is critical to focus our attention on mitochondrial viscosity under different conditions. A novel organic water-soluble molecule called JLQL that could monitor viscosity was conveniently synthesized in two steps. The near-infrared sensor with maximum emission wavelength of 734.6 nm and the Stokes shift of 134.6 nm consisted of a fluorophore and a mitochondrial-targeting moiety as an acceptor group; the two were connected by a double bond. The fluorescence intensity of the sensor increased 175 times with the enhancement of viscosity of a PBS-glycerol system. The interference of other microenvironments such as pH and polarity and other interference analytes could be reduced. JLQL could sensitively and selectively differentiate different levels of mitochondrial viscosity induced by monensin or nystatin. Furthermore, the probe may provide an attractive way to monitor real-time changes of viscosity during mitophagy. Possessing the above properties, JLQL can potentially be employed as a powerful tool for the observation of mitochondrial viscosity.

Fluid flow in the sarcomere

A highly organized and densely packed lattice of molecular machinery within the sarcomeres of muscle cells powers contraction. Although many of the proteins that drive contraction have been studied extensively, the mechanical impact of fluid shearing within the lattice of molecular machinery has received minimal attention. It was recently proposed that fluid flow augments substrate transport in the sarcomere, however, this analysis used analytical models of fluid flow in the molecular machinery that could not capture its full complexity. By building a finite element model of the sarcomere, we estimate the explicit flow field, and contrast it with analytical models. Our results demonstrate that viscous drag forces on sliding filaments are surprisingly small in contrast to the forces generated by single myosin molecular motors. This model also indicates that the energetic cost of fluid flow through viscous shearing with lattice proteins is likely minimal. The model also highlights a steep velocity gradient between sliding filaments and demonstrates that the maximal radial fluid velocity occurs near the tips of the filaments. To our knowledge, this is the first computational analysis of fluid flow within the highly structured sarcomere.

Cellular and Viral Determinants of HSV-1 Entry and Intracellular Transport towards Nucleus of Infected Cells

HSV-1 employs cellular motor proteins and modulates kinase pathways to facilitate intracellular virion capsid transport. Previously, we and others have shown that the Akt inhibitor miltefosine inhibited virus entry. Herein, we show that the protein kinase C inhibitors staurosporine (STS) and gouml inhibited HSV-1 entry into Vero cells, and that miltefosine prevents HSV-1 capsid transport toward the nucleus. We have reported that the HSV-1 UL37 tegument protein interacts with the dynein motor complex during virus entry and virion egress, while others have shown that the UL37/UL36 protein complex binds dynein and kinesin causing a saltatory movement of capsids in neuronal axons. Co-immoprecipitation experiments confirmed previous findings from our laboratory that the UL37 protein interacted with the dynein intermediate chain (DIC) at early times post infection. This UL37-DIC interaction was concurrent with DIC phosphorylation in infected, but not mock-infected cells. Miltefosine inhibited dynein phosphorylation when added before, but not after virus entry. Inhibition of motor accessory protein dynactins (DCTN2, DCTN3), the adaptor proteins EB1 and the Bicaudal D homolog 2 (BICD2) expression using lentiviruses expressing specific shRNAs, inhibited intracellular transport of virion capsids toward the nucleus of human neuroblastoma (SK-N-SH) cells. Co-immunoprecipitation experiments revealed that the major capsid protein Vp5 interacted with dynactins (DCTN1/p150 and DCTN4/p62) and the end-binding protein (EB1) at early times post infection. These results show that Akt and kinase C are involved in virus entry and intracellular transport of virion capsids, but not in dynein activation via phosphorylation. Importantly, both the UL37 and Vp5 viral proteins are involved in dynein-dependent transport of virion capsids to the nuclei of infected cells.Importance. Herpes simplex virus type-1 enter either via fusion at the plasma membranes or endocytosis depositing the virion capsids into the cytoplasm of infected cells. The viral capsids utilize the dynein motor complex to move toward the nuclei of infected cells using the microtubular network. This work shows that inhibitors of the Akt kinase and kinase C inhibit not only viral entry into cells but also virion capsid transport toward the nucleus. In addition, the work reveals that the virion protein ICP5 (VP5) interacts with the dynein cofactor dynactin, while the UL37 protein interacts with the dynein intermediate chain (DIC). Importantly, neither Akt nor Kinase C was found to be responsible for phosphorylation/activation of dynein indicating that other cellular or viral kinases may be involved.

A near-infrared fluorescent probe with large Stokes shift for visualizing and monitoring mitochondrial viscosity in live cells and inflammatory tissues

Mitochondria are cellular energy factory, having an essential role in cellular metabolism. Furthermore, abnormal changes in mitochondrial viscosity have been confirmed to be closely related to many diseases. Therefore, the development of probe that responsive to mitochondrial viscosity and its application in mitochondrial viscosity measurement is considered to be a new tool for understanding diseases. In this paper, a mitochondrial viscosity probe (DICB) with a large Stokes shift (214-253 nm) was designed and synthesized by modifying the structure of the carbazole fluorophore. The probe DICB has a favorable responsive to viscosity in the near-infrared (NIR) region (703 nm). In the water-glycerol system (0.893 cP -945 cP), the fluorescence intensity of DICB at 703 nm has a 74 times increase; in the range of 5.041 cP-856.0 cp, it has a well linear fitting relationship. Meantime, the probe has excellent sensitivity to viscosity. The probe (DICB) has been confirmed to be able to detect changes of mitochondrial viscosity in cell models induced by nystatin, carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and lipopolysaccharide (LPS); it has also been validated that DICB can be used in the process of autophagy to monitor mitochondrial viscosity. More importantly, DICB can be applied to the detection of abnormal mitochondrial viscosity in inflammatory tissues at the biological level. The outstanding characteristics of DICB for mitochondrial viscosity detection are not only of great importance to the development of viscosity probes, but also provides a universal strategy to study the relationship between inflammatory and mitochondrial viscosity.

Discriminating normal and inflammatory models by viscosity changes with a mitochondria-targetable fluorescent probe

Intracellular viscosity abnormalities can lead to diabetes, neurodegenerative diseases and cancer. In this work, we developed a mitochondria-targetable fluorescent probe (EIMV) for discriminating normal and inflammatory models by viscosity changes. It was found that EIMV showed excellent properties, including high photostability, low cytotoxicity, red emission and favorable biocompatibility. In view of these unique features, this probe could successfully identify normal and cancer cells via viscosity changes. Furthermore, the EIMV probe successfully identified zebrafish with different viscosities by the same method. Moreover, EIMV exhibited different fluorescence signals in normal and inflammatory mice due to changes in viscosity. Therefore, the probe provides a new method to study the relationship between diseases and viscosity in the fields of biology and medicine.

Models of Intracellular Transport: Pros and Cons

Intracellular transport is one of the most confusing issues in the field of cell biology. Many different models and their combinations have been proposed to explain the experimental data on intracellular transport. Here, we analyse the data related to the mechanisms of endoplasmic reticulum-to-Golgi and intra-Golgi transport from the point of view of the main models of intracellular transport; namely: the vesicular model, the diffusion model, the compartment maturation–progression model, and the kiss-and-run model. This review initially describes our current understanding of Golgi function, while highlighting the recent progress that has been made. It then continues to discuss the outstanding questions and potential avenues for future research with regard to the models of these transport steps. To compare the power of these models, we have applied the method proposed by K. Popper; namely, the formulation of prohibitive observations according to, and the consecutive evaluation of, previous data, on the basis on the new models. The levels to which the different models can explain the experimental observations are different, and to date, the most powerful has been the kiss-and-run model, whereas the least powerful has been the diffusion model.

A Mitochondrial-Targeting Near-Infrared Fluorescent Probe for Visualizing and Monitoring Viscosity in Live Cells and Tissues

The intracellular viscosity is closely related to many functional disorders and diseases. Especially, abnormal mitochondrial viscosity changes are one of the distinct indications in metabolite diffusion as well as mitochondrial metabolism. In this work, we report a novel fluorescent probe (NI-VIS), which uses quinoline as an acceptor group and employs a TICT mechanism (twisted intramolecular charge transfer) to detect viscosity. NI-VIS features a good mitochondrion targeting ability and near-infrared emission. NI-VIS possesses a highly sensitive response toward viscosity changes in aqueous environments. As the viscosity of a DPBS-glycerol system increased from 1.0 to 999 cP, NI-VIS exhibited a hundred-fold enhancement in fluorescence. We demonstrated that after the treatment with ionophores, NI-VIS could identify the variation of mitochondrial viscosity in HeLa cells. The probe also recognized the decrease of mitochondria viscosity during starvation-induced mitophagy. More importantly, NI-VIS was successfully applied to visualize the viscosity variation in cirrhotic liver tissues. Our trial with zebrafish suggested this probe could map the microviscosity in vivo. These findings reveal that NI-VIS can serve as a powerful tool to monitor viscosity of biological samples and shows broad potential applications in the biomedical field.

Role of Intracellular Transport in the Centriole-Dependent Formation of Golgi Ribbon

The intracellular transport is the most confusing issue in the field of cell biology. The Golgi complex (GC) is the central station along the secretory pathway. It contains Golgi glycosylation enzymes, which are responsible for protein and lipid glycosylation, and in many cells, it is organized into a ribbon. Position and structure of the GC depend on the position and function of the centriole. Here, we analyze published data related to the role of centriole and intracellular transport (ICT) for the formation of Golgi ribbon and specifically stress the importance of the delivery of membranes containing cargo and membrane proteins to the cell centre where centriole/centrosome is localized. Additionally, we re-examined the formation of Golgi ribbon from the point of view of different models of ICT.

Intracellular delivery of colloids: Past and future contributions from microinjection

The manipulation of single cells and whole tissues has been possible since the early 70's, when semi-automatic injectors were developed. Since then, microinjection has been used to introduce an ever-expanding range of colloids of up to 1000 nm in size into living cells. Besides injecting nucleic acids to study transfection mechanisms, numerous cellular pathways have been unraveled through the introduction of recombinant proteins and blocking antibodies. The injection of nanoparticles has also become popular in recent years to investigate toxicity mechanisms and intracellular transport, and to conceive semi-synthetic cells containing artificial organelles. This article reviews colloidal systems such as proteins, nucleic acids and nanoparticles that have been injected into cells for different research aims, and discusses the scientific advances achieved through them. The colloids' intracellular processing and ultimate fate are also examined from a drug delivery perspective with an emphasis on the differences observed for endocytosed versus microinjected material.

Simulating biological processes: stochastic physics from whole cells to colonies

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a 'minimal cell'. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

The chaperone dynein LL1 mediates cytoplasmic transport of empty and mature hepatitis B virus capsids

BACKGROUND & AIMS

Hepatitis B virus (HBV) has a DNA genome but replicates within the nucleus by reverse transcription of an RNA pregenome, which is converted to DNA in cytoplasmic capsids. Capsids in this compartment are correlated with inflammation and epitopes of the capsid protein core (Cp) are a major target for T cell-mediated immune responses. We investigated the mechanism of cytoplasmic capsid transport, which is important for infection but also for cytosolic capsid removal.

METHODS

We used virion-derived capsids containing mature rcDNA (matC) and empty capsids (empC). RNA-containing capsids (rnaC) were used as a control. The investigations comprised pull-down assays for identification of cellular interaction partners, immune fluorescence microscopy for their colocalization and electron microscopy after microinjection to determine their biological significance.

RESULTS

matC and empC underwent active transport through the cytoplasm towards the nucleus, while rnaC was poorly transported. We identified the dynein light chain LL1 as a functional interaction partner linking capsids to the dynein motor complex and showed that there is no compensatory transport pathway. Using capsid and dynein LL1 mutants we characterized the required domains on the capsid and LL1.

CONCLUSIONS

This is the first investigation on the detailed molecular mechanism of how matC pass the cytoplasm upon infection and how empC can be actively removed from the cytoplasm into the nucleus. Considering that hepatocytes with cytoplasmic capsids are better recognized by the T cells, we hypothesize that targeting capsid DynLL1-interaction will not only block HBV infection but also stimulate elimination of infected cells.

LAY SUMMARY

In this study, we identified the molecular details of HBV translocation through the cytoplasm. Our evidence offers a new drug target which could not only inhibit infection but also stimulate immune clearance of HBV infected cells.

A near-infrared emission fluorescent probe with multi-rotatable moieties for highly sensitive detection of mitochondrial viscosity in an inflammatory cell model

We have designed a new near-infrared emission fluorescent probe with multi-rotatable moieties for the imaging of mitochondrial viscosity in an inflammatory cell model.

From mobility to crosstalk. A model of intracellular miRNAs motion may explain the RNAs interaction mechanism on the basis of target subcellular localization

MicroRNAs (miRNAs), 22 nucleotides long molecules with the function to reduce gene expression by inhibiting mRNA translation through partial complementary to one or more messenger RNA (mRNA) molecules. A single miRNA can reduce the expression levels of hundreds of genes and one mRNA can be a target for many miRNAs. Despite the study models used so far, miRNAs and mRNAs cannot be seen as acting in an isolated manner or even "in pairs". They most likely exert their complex actions through numerous overlapping interrelations. One of the models depicting interdependence of intracytoplasmic RNAs is the crosstalk model. It is based on a competition between several target mRNAs which are regulated by the same miRNA. In this paper, we will discuss the mobility mechanism of miRNAs, recently suggested by data from "single particle tracking" experiments. These data suggests that miRNA intracellular mobility may be of "intermittent active transport"(IAT) type. IAT is a mobility model composed by alternation of active transport (AT) and Brownian motion (BM). Based on a mathematical model, we concluded that, AT phase may explain the efficiency in reaching far targets and the BM phase may explain the competition. Furthermore, we suggest that the interaction between miRNAs and their targets depends on the concentration of the molecules, the affinity between the molecules and also on the intracellular localization of the molecules. Hence, the probability that a miRNA interacts with its target depends also on the distance to the target and the macromolecular crowding. Taken together, our data proposes an intracytoplasmic mobility mechanism for miRNA and shows that this model can partially explain the RNA crosstalk.

A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells

Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM).

Intracellular transport and egress of hepatitis B virus

Hepatitis B virus (HBV) replicates its genomic information in the nucleus via transcription and therefore has to deliver its partially double stranded DNA genome into the nucleus. Like other viruses with a nuclear replication phase, HBV genomes are transported inside the viral capsids first through the cytoplasm towards the nuclear envelope. Following the arrival at the nuclear pore, the capsids are transported through, using classical cellular nuclear import pathways. The arrest of nuclear import at the nucleoplasmic side of the nuclear pore is unique, however, and is where the capsids efficiently disassemble leading to genome release. In the latter phase of the infection, newly formed nucleocapsids in the cytosol have to move to budding sites at intracellular membranes carrying the three viral envelope proteins. Capsids containing single stranded nucleic acid are not enveloped, in contrast to empty and double stranded DNA containing capsids. A small linear domain in the large envelope protein and two areas on the capsid surface have been mapped, where point mutations strongly block nucleocapsid envelopment. It is possible that these domains are involved in the envelope--with capsid interactions driving the budding process. Like other enveloped viruses, HBV also uses the cellular endosomal sorting complexes required for transport (ESCRT) machinery for catalyzing budding through the membrane and away from the cytosol.

Early events in hepatitis B virus infection: From the cell surface to the nucleus

While most adults are able to clear acute hepatitis B virus (HBV) infection, chronic HBV infection is recalcitrant to current therapy because of the persistence of covalently closed circular DNA in the nucleus. Complete clearance of the virus in these patients is rare, and long-term therapy with interferon and/or nucleoside analogues may be required in an attempt to suppress viral replication and prevent progressive liver damage. The difficulty of establishing HBV infection in cell culture and experimental organisms has hindered efforts to elucidate details of the HBV life cycle, but it has also revealed the importance of the cellular microenvironment required for HBV binding and entry. Recent studies have demonstrated an essential role of sodium-taurocholate cotransporting polypeptide as a functional receptor in HBV infection, which has facilitated the development of novel infection systems and opened the way for more detailed understanding of the early steps of HBV infection as well as a potential new therapeutic target. However, many gaps remain in understanding of how HBV recognizes and attaches to hepatocytes prior to binding to sodium-taurocholate cotransporting polypeptide, as well as events that are triggered after binding, including entry into the cell, intracellular transport, and passage through the nuclear pore complex. This review summarizes current knowledge of the initial stages of HBV infection leading to the establishment of covalently closed circular DNA in the nucleus.

Dynamic heterogeneity controls diffusion and viscosity near biological interfaces

At a nanometer scale, the behavior of biological fluids is largely governed by interfacial physical chemistry. This may manifest as slowed or anomalous diffusion. Here we describe how measures developed for studying glassy systems allow quantitative measurement of interfacial effects on water dynamics, showing that correlated motions of particles near a surface result in a viscosity greater than anticipated from individual particle motions. This effect arises as a fundamental consequence of spatial heterogeneity on nanometer length scales and applies to any fluid near any surface. Increased interfacial viscosity also causes the classic finding that large solutes such as proteins diffuse much more slowly than predicted in bulk water. This has previously been treated via an empirical correction to the solute size: the hydrodynamic radius. Using measurements of quantities from theories of glass dynamics, we can now calculate diffusion constants from molecular details alone, eliminating the empirical correction factor.

Aqueous Emulsion Droplets Stabilized by Lipid Vesicles as Microcompartments for Biomimetic Mineralization

Mineral deposition within living cells relies on control over the distribution and availability of precursors as well as the location and rates of nucleation and growth. This control is provided in large part by biomolecular chelators, which bind precursors and regulate their availability, and compartmentalization within specialized mineralizing vesicles. Biomimetic mineralization in self-assembled lipid vesicles is an attractive means of studying the mineralization process, but has proven challenging due to vesicle heterogeneity in lamellarity, contents, and size across a population, difficulties encapsulating high and uniform precursor concentrations, and the need to transport reagents across an intact lipid bilayer membrane. Here, we report the use of liposome-stabilized all-aqueous emulsion droplets as simple artificial mineralizing vesicles (AMVs). These biomimetic microreactors allow the entry of precursors while retaining a protein catalyst by equilibrium partitioning between internal and external polymer-rich phases. Small molecule chelators with intermediate binding affinity were employed to control Ca(2+) availability during CaCO3 mineralization, providing protection against liposome aggregation while allowing CaCO3 formation. Mineral deposition was limited to the AMV interior, due to localized production of CO3(2-) by compartmentalized urease. Particle formation was uniform across the entire population of AMVs, with multiple submicrometer amorphous CaCO3 particles produced in each one. The all-aqueous emulsion-based approach to biomimetic giant mineral deposition vesicles introduced here should be adaptable for enzyme-catalyzed synthesis of a wide variety of materials, by varying the metal ion, enzyme, and/or chelator.

Model cell membranes: discerning lipid and protein contributions in shaping the cell

The high complexity of biological membranes has motivated the development and application of a wide range of model membrane systems to study biochemical and biophysical aspects of membranes in situ under well defined conditions. The aim is to provide fundamental understanding of processes controlled by membrane structure, permeability and curvature as well as membrane proteins by using a wide range of biochemical, biophysical and microscopic techniques. This review gives an overview of some currently used model biomembrane systems. We will also discuss some key membrane protein properties that are relevant for protein-membrane interactions in terms of protein structure and how it is affected by membrane composition, phase behavior and curvature.

Regulation of cellular gas exchange, oxygen sensing, and metabolic control

Cells must continuously monitor and couple their metabolic requirements for ATP utilization with their ability to take up O2 for mitochondrial respiration. When O2 uptake and delivery move out of homeostasis, cells have elaborate and diverse sensing and response systems to compensate. In this review, we explore the biophysics of O2 and gas diffusion in the cell, how intracellular O2 is regulated, how intracellular O2 levels are sensed and how sensing systems impact mitochondrial respiration and shifts in metabolic pathways. Particular attention is paid to how O2 affects the redox state of the cell, as well as the NO, H2S, and CO concentrations. We also explore how these agents can affect various aspects of gas exchange and activate acute signaling pathways that promote survival. Two kinds of challenges to gas exchange are also discussed in detail: when insufficient O2 is available for respiration (hypoxia) and when metabolic requirements test the limits of gas exchange (exercising skeletal muscle). This review also focuses on responses to acute hypoxia in the context of the original "unifying theory of hypoxia tolerance" as expressed by Hochachka and colleagues. It includes discourse on the regulation of mitochondrial electron transport, metabolic suppression, shifts in metabolic pathways, and recruitment of cell survival pathways preventing collapse of membrane potential and nuclear apoptosis. Regarding exercise, the issues discussed relate to the O2 sensitivity of metabolic rate, O2 kinetics in exercise, and influences of available O2 on glycolysis and lactate production.

Models of the collective behavior of proteins in cells: tubulin, actin and motor proteins

One of the most important issues of molecular biophysics is the complex and multifunctional behavior of the cell's cytoskeleton. Interiors of living cells are structurally organized by the cytoskeleton networks of filamentous protein polymers: microtubules, actin and intermediate filaments with motor proteins providing force and directionality needed for transport processes. Microtubules (MT's) take active part in material transport within the cell, constitute the most rigid elements of the cell and hence found many uses in cell motility (e.g. flagella andcilia). At present there is, however, no quantitatively predictable explanation of how these important phenomena are orchestrated at a molecular level. Moreover, microtubules have been demonstrated to self-organize leading to pattern formation. We discuss here several models which attempt to shed light on the assembly of microtubules and their interactions with motor proteins. Subsequently, an overview of actin filaments and their properties isgiven with particular emphasis on actin assembly processes. The lengths of actin filaments have been reported that were formed by spontaneous polymerization of highly purified actin monomers after labeling with rhodamine-phalloidin. The length distributions are exponential with a mean of about 7 μm. This length is independent of the initial concentration of actin monomer, an observation inconsistent with a simple nucleation-elongation mechanism. However, with the addition of physically reasonable rates of filament annealing and fragmenting, a nucleation-elongation mechanism can reproduce the observed average length of filaments in two types of experiments: (1) filaments formed from a wide range of highly purified actin monomer concentrations, and (2) filaments formed from 24 mM actin over a range of CapZ concentrations. In the final part of the paper we briefly review the stochastic models used to describe the motion of motor proteins on protein filaments. The vast majority of these models are based on ratchet potentials with the presence of thermal noise and forcing due to ATP binding and a subsequent hydrolysis. Many outstanding questions remain to be quantitatively addressed on a molecular level in order to explain the structure-to-function relationship for the key elements of the cytoskeleton discussed in this review.

Two-photon fluorescence correlation spectroscopy as a tool for measuring molecular diffusion within human skin

There is a need for tools enabling quantitative imaging of biological tissue for pharmaceutical applications. In this study, two-photon fluorescence microscopy (TPM) has been combined with fluorescence correlation spectroscopy (FCS), demonstrating proof-of-principle providing quantitative data of fluorophore concentration and diffusion in human skin. Measurements were performed on excised skin exposed to either rhodamine B (RB) or rhodamine B isothiocyanate (RBITC), chosen based on their similarity in fluorescence yield and molecular weight, but difference in chemical reactivity. The measurements were performed at tissue depths in the range 0 and 20 μm, and the diffusion coefficients at skin depths 5 and 10 μm were found to be significantly different (P<0.05). Overall median values for the diffusion coefficients were found to be 4.0×10(-13) m(2)/s and 2.0×10(-13) m(2)/s for RB and RBITC, respectively. These values correspond to the diffusion of a hard sphere with a volume eight times larger for RBITC compared to RB. This indicates that the RBITC have bound to biomolecules in the skin, and the measured signal is obtained from the RBITC-biomolecule complexes, demonstrating the potential of the TPM-FCS method to track molecular interactions in an intricate biological matrix such as human skin.

The kiss-and-run model of intra-Golgi transport

The Golgi apparatus (GA) is the main station along the secretory pathway. Mechanisms of intra-Golgi transport remain unresolved. Three models compete with each other for the right to be defined as the paradigm. The vesicular model cannot explain the following: (1) lipid droplets and aggregates of procollagen that are larger than coatomer I (COPI)-dependent vesicles are transported across the GA; and (2) most anterograde cargoes are depleted in COPI vesicles. The compartment progression/maturation model has the following problems: (1) most Golgi-resident proteins are depleted in COPI vesicles; (2) there are no COPI vesicles for the recycling of the resident proteins in the trans-most-Golgi cisterna; and (3) different proteins have different rates of intra-Golgi transport. The diffusion model based on permanent inter-cisternal connections cannot explain the existence of lipid, ionic and protein gradients across the Golgi stacks. In contrast, the kiss-and-run model has the potential to explain most of the experimental observations. The kiss-and-run model can be symmetric when fusion and then fission occurs in the same place, and asymmetric when fusion takes place in one location, whereas fission takes place in another. The asymmetric kiss-and-run model resembles the carrier maturation mechanism, and it can be used to explain the transport of large cargo aggregates.

Hindered diffusion in polymeric solutions studied by fluorescence correlation spectroscopy

Diffusion of molecules in the crowded and charged interior of the cell has long been of interest for understanding cellular processes. Here, we introduce a model system of hindered diffusion that includes both crowding and binding. In particular, we obtained the diffusivity of the positively charged protein, ribonuclease A (RNase), in solutions of dextrans of various charges (binding) and concentrations (crowding), as well as combinations of both, in a buffer of physiological ionic strength. Using fluorescence correlation spectroscopy, we observed that the diffusivity of RNase was unaffected by the presence of positively charged or neutral dextrans in the dilute regime but was affected by crowding at higher polymer concentrations. Conversely, protein diffusivity was significantly reduced by negatively charged dextrans, even at 0.4 μM (0.02% w/v) dextran. The diffusivity of RNase decreased with increasing concentrations of negative dextran, and the amount of bound RNase increased until it reached a plateau of ∼80% bound RNase. High salt concentrations were used to establish the electrostatic nature of the binding. Binding of RNase to the negatively charged dextrans was further confirmed by ultrafiltration.

Miniseries: Illustrating the machinery of life: Eukaryotic cell panorama

Diverse biological data may be used to create illustrations of molecules in their cellular context. This report describes the scientific results that support an illustration of a eukaryotic cell, enlarged by one million times to show the distribution and arrangement of macromolecules. The panoramic cross section includes eight panels that extend from the nucleus to the cell surface, showing the process of protein synthesis and export. Results from biochemistry, electron microscopy, NMR spectroscopy and x-ray crystallography were used to create the image.

How to quantify protein diffusion in the bacterial membrane

Lateral diffusion of proteins in the plane of a biological membrane is important for many vital processes, including energy conversion, signaling, chemotaxis, cell division, protein insertion, and secretion. In bacteria, all these functions are located in a single membrane. Therefore, quantitative measurements of protein diffusion in bacterial membranes can provide insight into many important processes. Diffusion of membrane proteins in eukaryotes has been studied in detail using various experimental techniques, including fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), and particle tracking using single-molecule fluorescence (SMF) microscopy. In case of bacteria, such experiments are intrinsically difficult due to the small size of the cells. Here, we review these experimental approaches to quantify diffusion in general and their strengths and weaknesses when applied to bacteria. In addition, we propose a method to extract multiple diffusion coefficients from trajectories obtained from SMF data, using cumulative probability distributions (CPDs). We demonstrate the power of this approach by quantifying the heterogeneous diffusion of the bacterial membrane protein TatA, which forms a pore for the translocation of folded proteins. Using computer simulations, we study the effect of cell dimensions and membrane curvature on measured CPDs. We find that at least two mobile populations with distinct diffusion coefficients (of 7 and 169 nm(2) ms(-1) , respectively) are necessary to explain the experimental data. The approach described here should be widely applicable for the quantification of membrane-protein diffusion in living bacteria.

Fluorescence fluctuation spectroscopy: ushering in a new age of enlightenment for cellular dynamics

Originally developed for applications in physics and physical chemistry, fluorescence fluctuation spectroscopy is becoming widely used in cell biology. This review traces the development of the method and describes some of the more important applications. Specifically, the methods discussed include fluorescence correlation spectroscopy (FCS), scanning FCS, dual color cross-correlation FCS, the photon counting histogram and fluorescence intensity distribution analysis approaches, the raster scanning image correlation spectroscopy method, and the Number and Brightness technique. The physical principles underlying these approaches will be delineated, and each of the methods will be illustrated using examples from the literature.

An experimental and computational study of the effect of ActA polarity on the speed of Listeria monocytogenes actin-based motility

Listeria monocytogenes is a pathogenic bacterium that moves within infected cells and spreads directly between cells by harnessing the cell's dendritic actin machinery. This motility is dependent on expression of a single bacterial surface protein, ActA, a constitutively active Arp2,3 activator, and has been widely studied as a biochemical and biophysical model system for actin-based motility. Dendritic actin network dynamics are important for cell processes including eukaryotic cell motility, cytokinesis, and endocytosis. Here we experimentally altered the degree of ActA polarity on a population of bacteria and made use of an ActA-RFP fusion to determine the relationship between ActA distribution and speed of bacterial motion. We found a positive linear relationship for both ActA intensity and polarity with speed. We explored the underlying mechanisms of this dependence with two distinctly different quantitative models: a detailed agent-based model in which each actin filament and branched network is explicitly simulated, and a three-state continuum model that describes a simplified relationship between bacterial speed and barbed-end actin populations. In silico bacterial motility required a cooperative restraining mechanism to reconstitute our observed speed-polarity relationship, suggesting that kinetic friction between actin filaments and the bacterial surface, a restraining force previously neglected in motility models, is important in determining the effect of ActA polarity on bacterial motility. The continuum model was less restrictive, requiring only a filament number-dependent restraining mechanism to reproduce our experimental observations. However, seemingly rational assumptions in the continuum model, e.g. an average propulsive force per filament, were invalidated by further analysis with the agent-based model. We found that the average contribution to motility from side-interacting filaments was actually a function of the ActA distribution. This ActA-dependence would be difficult to intuit but emerges naturally from the nanoscale interactions in the agent-based representation.

Cells tightly regulate the branched actin networks involved in motility, division, and other important cellular functions through localized activation of the Arp2,3 protein, which nucleates new actin filaments off the sides of existing ones. The pathogenic bacterium, Listeria monocytogenes, expresses its own Arp2,3 activator, ActA, in a polarized fashion and can thus nucleate dynamic actin networks at its surface to generate forces to move through the cytoplasm. This bacterium has thus served as a simplified system for experimental and modeling studies of actin-based motility. We use this bacterial system to quantify the relationship between ActA polarity and bacterial speed of motion by experimentally manipulating this polarity and analyzing the resultant ActA distributions and bacterial trajectories. Like many cellular behaviors, L. monocytogenes motility emerges from a complex set of biochemical and force-based interactions. We therefore probe this polarity-speed relationship with a detailed agent-based simulation which encodes the predominant biochemical reactions and whose agents (actin filaments, ActA proteins, and the bacterium) exchange forces. We contrast conclusions from this agent-based model with those from a simpler mathematical model. From these studies we assert the importance of a heretofore neglected force in this system – friction between actin filaments and the bacterial surface.

Dynamic Organization of Aminoacyl-tRNA Synthetase Complexes in the Cytoplasm of Human Cells

The localization in space and in time of proteins within the cytoplasm of eukaryotic cells is a central question of the cellular compartmentalization of metabolic pathways. The assembly of proteins within stable or transient complexes plays an essential role in this process. Here, we examined the subcellular localization of the multi-aminoacyl-tRNA synthetase complex in human cells. The sequestration of its components within the cytoplasm rests on the presence of the eukaryotic-specific polypeptide extensions that characterize the human enzymes, as compared with their prokaryotic counterparts. The cellular mobility of several synthetases, assessed by measuring fluorescence recovery after photobleaching, suggested that they are not freely diffusible within the cytoplasm. Several of these enzymes, isolated by tandem affinity purification, were copurified with ribosomal proteins and actin. The capacity of aminoacyl-tRNA synthetases to interact with polyribosomes and with the actin cytoskeleton impacts their subcellular localization and mobility. Our observations have conceptual implications for understanding how translation machinery is organized in vivo.

Equilibrium characteristics of semiflexible polymer solutions near probe particles

We present a numerical analysis of the mean-field theory for the structure of semiflexible polymer solutions near spherical surfaces, and use the framework to study the depletion characteristics of semiflexible polymers near colloids and nanoparticles. Our results suggest that the depletion characteristics depend sensitively on the polymer concentrations, the persistence lengths, and the radius of the particles. Broadly, two categories of features are identified based on the relative ratios of the persistence lengths to the correlation length of the polymer solution. For the limit where the correlation length is larger than the persistence length, the correlation length proves to be the critical length scale governing both the depletion thickness and the curvature effects. In contrast, for the opposite limit, the depletion thickness and the curvature effects are dependent on a length scale determined by an interplay between the persistence length and the correlation length. This leads to nontrivial (numerical) scaling laws governing the concentration and radii dependence of the depletion thicknesses. Our study also highlights the manner by which the preceding features rationalize the parametric dependencies of insertion free energies of small probes in semiflexible polymer solutions.

Ligand-bound quantum dot probes for studying the molecular scale dynamics of receptor endocytic trafficking in live cells

Endocytic receptor trafficking is a complex, dynamic process underlying fundamental cell function. An integrated understanding of endocytosis at the level of single or small numbers of ligand bound-receptor complexes inside live cells is currently hampered by technical limitations. Here, we develop and test ligand nerve growth factor-bound quantum dot (NGF-QD) bioconjugates for imaging discrete receptor endocytic events inside live NGF-responsive PC12 cells. Using single particle tracking, QD hybrid gel coimmunoprecipitation, and immuno-colocalization, we illustrate and validate the use of QD-receptor complexes for imaging receptor trafficking at synchronized time points after QD-ligand-receptor binding and internalization (t = 15-150 min). The unique value of these probes is illustrated by new dynamic observations: (1) that endocytosis proceeds at strikingly regulated fashion, and (2) that diffusive and active forms of transport inside cells are rapid and efficient. QDs are powerful intracellular probes that can provide biologists with new capabilities and fresh insight for studying endocytic receptor signaling events, in real time, and at the resolution of single or small numbers of receptors in live cells.

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.

Dynamics of probe diffusion in rod solutions

Applications of probe diffusion in polymer matrices typically envision that for particles sizes (R) larger than the correlation length of the polymer solution (xi), the probe (at long times) diffuses as in a continuum polymer solution. We present simulation results for probe diffusion in rod solutions which challenge this conventional wisdom and indicate a new mechanism of a probe diffusion operative for R>xi. Our simulation results are rationalized by scaling arguments invoking a novel mechanism of the constraint release motion of the rods, and suggest that the dynamical characteristics of the polymer matrix also proves important in developing a complete description of the probe motion.

Mechanisms of intracellular fatty acid transport: role of cytoplasmic-binding proteins

Cytosolic binding proteins are ubiquitous, yet their functions have been poorly defined. Research in multiple labs has now clarified two major transport functions for fatty acid binding proteins (FABPs), one of the most commonly studied examples of this diverse class. Most cellular fatty acids are bound to membranes. Because fatty acids are almost insoluble in water, their movement across the water between cellular membranes is very slow without FABP. FABP increases this rate by increasing the solubility of fatty acids in water. Many forms of FABP can also increase this rate by catalyzing release of the fatty acids from membranes. The first function is most valuable over longer distances (e.g., >1 microm in rat liver cells), while the second is most valuable for shorter distances. Thus, FABPs serve complementary intracellular transport functions. These conclusions may apply to other cytosolic proteins that bind poorly-soluble molecules.

In vivo acetylation of CheY, a response regulator in chemotaxis of Escherichia coli

CheY, the excitatory response regulator in the chemotaxis system of Escherichia coli, can be modulated by two covalent modifications: phosphorylation and acetylation. Both modifications have been detected in vitro only. The role of CheY acetylation is still obscure, although it is known to be involved in chemotaxis and to occur in vitro by two mechanisms--acetyl-CoA synthetase-catalyzed transfer of acetyl groups from acetate to CheY and autocatalyzed transfer from AcCoA. Here, we succeeded in detecting CheY acetylation in vivo by three means--Western blotting with a specific anti-acetyl-lysine antibody, mass spectrometry, and radiolabeling with [(14)C]acetate in the presence of protein-synthesis inhibitor. Unexpectedly, the level and rate of CheY acetylation in vivo were much higher than that in vitro. Thus, before any treatment, 9-13% of the lysine residues were found acetylated, depending on the growth phase, meaning that, on average, essentially every CheY molecule was acetylated in vivo. This high level was mainly the outcome of autoacetylation. Addition of acetate caused an incremental increase in the acetylation level, in which acetyl-CoA synthetase was involved too. These findings may have far-reaching implications for the structure-function relationship of CheY.

A computational analysis of protein interactions in metabolic networks reveals novel enzyme pairs potentially involved in metabolic channeling

Protein-protein interactions are operative at almost every level of cell structure and function as, for example, formation of sub-cellular organelles, packaging of chromatin, muscle contraction, signal transduction, and regulation of gene expression. Public databases of reported protein-protein interactions comprise hundreds of thousands interactions, and this number is steadily growing. Elucidating the implications of protein-protein interactions for the regulation of the underlying cellular or extra-cellular reaction network remains a great challenge for computational biochemistry. In this work, we have undertaken a systematic and comprehensive computational analysis of reported enzyme-enzyme interactions in the metabolic networks of the model organisms Escherichia coli and Saccharomyces cerevisiae. We grouped all enzyme pairs according to the topological distance that the catalyzed reactions have in the metabolic network and performed a statistical analysis of reported enzyme-enzyme interactions within these groups. We found a higher frequency of reported enzyme-enzyme interactions within the group of enzymes catalyzing reactions that are adjacent in the network, i.e. sharing at least one metabolite. As some of these interacting enzymes have already been implicated in metabolic channeling our analysis may provide a useful screening for candidates of this phenomenon. To check for a possible regulatory role of interactions between enzymes catalyzing non-neighboring reactions, we determined potentially regulatory enzymes using connectivity in the network and absolute change of Gibbs free energy. Indeed a higher portion of reported interactions pertain to such potentially regulatory enzymes.