Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells

Superstatistical modelling of protein diffusion dynamics in bacteria

A recent experiment (Sadoon AA, Wang Y. 2018 Phys. Rev. E98, 042411. (doi:10.1103/PhysRevE.98.042411)) has revealed that nucleoid-associated proteins (i.e. DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion constant but also the anomalous diffusion exponent fluctuates for the various proteins. The distribution of displacements of such proteins is observed to take a q-Gaussian form, which decays as a power law. Here, a statistical model is developed for the diffusive motion of the proteins within the bacterium, based on a superstatistics with two variables. This model hierarchically takes into account the joint fluctuations of both the anomalous diffusion exponents and the diffusion constants. A fractional Brownian motion is discussed as a possible local model. Good agreement with the experimental data is obtained.

Principles and Applications of Single Particle Tracking in Cell Research

It is a tough challenge for many decades to decipher the complex relationships between cell behaviors and cellular physical properties. Single particle tracking (SPT) with high spatial and temporal resolution has been applied extensively in cell research to understand physicochemical properties of cells and their bio-functions by tracking endogenous or exogenous probes. This review describes the fundamental principles of SPT as well as its applications in intracellular mechanics, membrane dynamics, organelles distribution, and processes of internalization and transport. Finally, challenges and future directions of SPT are also discussed.

Luminescent Quantum Dots Stabilized by N-Heterocyclic Carbene Polymer Ligands

We have tested the ability of N-heterocyclic carbene (NHC)-modified ligands to coordinate and stabilize luminescent CdSe-ZnS core-shell quantum dot (QD) dispersions in hydrophilic media. In particular, we probed the effects of ligand structure and coordination number on the coating affinity to the nanocrystals. We find that such NHC-based ligands rapidly coordinate onto the QDs (requiring ∼5-10 min of reaction time), which reflects the soft Lewis base nature of the NHC groups, with its two electrons sharing capacity. Removal of the hydrophobic cap and promotion of carbene-driven coordination on the nanocrystals have been verified by ¹H NMR spectroscopy, while ¹³C NMR was used to identify the formation of carbene-Zn complexes. The newly coated QD dispersions exhibit great long-term colloidal stability over a wide range of conditions. Additionally, we find that coordination onto the QD surfaces affects the optical and spectroscopic properties of the nanocrystals. These include a size-dependent red-shift of the absorption and fluorescence spectra and a pronounced increase in the measured fluorescence intensity when the samples are stored under white light exposure compared to those stored in the dark.

Size-Dependent Electroporation of Dye-Loaded Polymer Nanoparticles for Efficient and Safe Intracellular Delivery

Efficient and safe delivery of nanoparticles (NPs) into the cytosol of living cells constitutes a major methodological challenge in bio-nanotechnology. Electroporation allows direct transfer of NPs into the cytosol by forming transient pores in the cell membrane, but it is criticized for invasiveness, and the applicable particle sizes are not well defined. Here, in order to establish principles for efficient delivery of NPs into the cytosol with minimal cytotoxicity, the influence of the size of NPs on their electroporation and intracellular behavior is investigated. For this study, fluorescent dye-loaded polymer NPs with core sizes between 10 and 40 nm are prepared. Optimizing the electroporation protocol allows minimizing contributions of endocytosis and to study directly the effect of NP size on electroporation. NPs of <20 nm hydrodynamic size are efficiently delivered into the cytosol, whereas this is not the case for NPs of >30 nm. Moreover, only particles of core size <15 nm diffuse freely throughout the cytosol. While electroporation at excessive electric fields induces cytotoxicity, the use of small NPs <20 nm allows efficient delivery at mild electroporation conditions. These results give clear methodological and design guidelines for the safe delivery of NPs for intracellular applications.

Correlated continuous-time random walk in a velocity field: Anomalous bifractional crossover

The diffusion of space-time correlated continuous-time random walk moving in the velocity field, which includes the fluid flowing freely and the fluid flowing through porous media, is investigated in this paper. Results reveal that it presents anomalous diffusion merely caused by space-time correlation in the freely flowing fluid, and the bias from the velocity field only supplies a standard advection, which is verified by the corresponding generalized diffusion equation which includes a standard advection term. However, the diffusion in the fluid flowing through porous media, i.e., the mean squared displacement, can display a bifractional form of which one originates from space-time correlation and the other one originates from dispersive bias caused by sticking of the porous media. The fractional advection term emerging in the corresponding generalized diffusion equation confirms the results. Moreover, the coexistence of correlation and dispersive bias result in crossover phenomenon in-between the diffusive process at an intermediate timescale, but just as the definition of diffusion, the one owning the largest diffusion exponent always prevails at large timescales. However, since the two fractional diffusions originate from a different mechanism, even if it owns the smaller diffusion exponent, that one can dominate the diffusion if it fluctuates much stronger than the other one, which no longer obeys the previous conclusion.

High-Precision Protein-Tracking With Interferometric Scattering Microscopy

The mobility of proteins and lipids within the cell, sculpted oftentimes by the organization of the membrane, reveals a great wealth of information on the function and interaction of these molecules as well as the membrane itself. Single particle tracking has proven to be a vital tool to study the mobility of individual molecules and unravel details of their behavior. Interferometric scattering (iSCAT) microscopy is an emerging technique well-suited for visualizing the diffusion of gold nanoparticle-labeled membrane proteins to a spatial and temporal resolution beyond the means of traditional fluorescent labels. We discuss the applicability of interferometric single particle tracking (iSPT) microscopy to investigate the minutia in the motion of a protein through measurements visualizing the mobility of the epidermal growth factor receptor in various biological scenarios on the live cell.

Getting around the cell: physical transport in the intracellular world

Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.

Microtubules Enhance Mesoscale Effective Diffusivity in the Crowded Metaphase Cytoplasm

Mesoscale macromolecular complexes and organelles, tens to hundreds of nanometers in size, crowd the eukaryotic cytoplasm. It is therefore unclear how mesoscale particles remain sufficiently mobile to regulate dynamic processes such as cell division. Here, we study mobility across dividing cells that contain densely packed, dynamic microtubules, comprising the metaphase spindle. In dividing human cells, we tracked 40 nm genetically encoded multimeric nanoparticles (GEMs), whose sizes are commensurate with the inter-filament spacing in metaphase spindles. Unexpectedly, the effective diffusivity of GEMs was similar inside the dense metaphase spindle and the surrounding cytoplasm. Eliminating microtubules or perturbing their polymerization dynamics decreased diffusivity by ~30%, suggesting that microtubule polymerization enhances random displacements to amplify diffusive-like motion. Our results suggest that microtubules effectively fluidize the mitotic cytoplasm to equalize mesoscale mobility across a densely packed, dynamic, non-uniform environment, thus spatially maintaining a key biophysical parameter that impacts biochemistry, ranging from metabolism to the nucleation of cytoskeletal filaments.

Barriers and Strategies of Cationic Liposomes for Cancer Gene Therapy

Cationic liposomes (CLs) have been regarded as the most promising gene delivery vectors for decades with the advantages of excellent biodegradability, biocompatibility, and high nucleic acid encapsulation efficiency. However, the clinical use of CLs in cancer gene therapy is limited because of many uncertain factors in vivo. Extracellular barriers such as opsonization, rapid clearance by the reticuloendothelial system and poor tumor penetration, and intracellular barriers, including endosomal/lysosomal entrapped network and restricted diffusion to the nucleus, make CLs not the ideal vector for transferring extrinsic genes in the body. However, the obstacles in achieving productive therapeutic effects of nucleic acids can be addressed by tailoring the properties of CLs, which are influenced by lipid compositions and surface modification. This review focuses on the physiological barriers of CLs against cancer gene therapy and the effects of lipid compositions on governing transfection efficiency, and it briefly discusses the impacts of particle size, membrane charge density, and surface modification on the fate of CLs in vivo, which may provide guidance for their preclinical studies.

Elucidating the Origin of Heterogeneous Anomalous Diffusion in the Cytoplasm of Mammalian Cells

Diffusion of tracer particles in the cytoplasm of mammalian cells is often anomalous with a marked heterogeneity even within individual particle trajectories. Despite considerable efforts, the mechanisms behind these observations have remained largely elusive. To tackle this problem, we performed extensive single-particle tracking experiments on quantum dots in the cytoplasm of living mammalian cells at varying conditions. Analyses of the trajectories reveal a strong, microtubule-dependent subdiffusion with antipersistent increments and a substantial heterogeneity. Furthermore, particles stochastically switch between different mobility states, most likely due to transient associations with the cytoskeleton-shaken endoplasmic reticulum network. Comparison to simulations highlight that all experimental observations can be fully described by an intermittent fractional Brownian motion, alternating between two states of different mobility.

A mathematical finance approach to the stochastic and intermittent viscosity fluctuations in living cells

Here we report on the viscosity of eukaryotic living cells, as a function of time, and on the application of stochastic models to analyze its temporal fluctuations. The viscoelastic properties of NIH/3T3 fibroblast cells are investigated using an active microrheological technique, where the magnetic wires, embedded into cells, are being actuated remotely. The data reveal anomalous transient responses characterized by intermittent phases of slow and fast rotation, revealing significant fluctuations. The time dependent viscosity is analyzed from a time series perspective by computing the autocorrelation functions and the variograms, two functions used to describe stochastic processes in mathematical finance. The resulting analysis gives evidence of a sub-diffusive mean-reverting process characterized by an autoregressive coefficient lower than 1. It also shows the existence of specific cellular times in the ranges 1-10 s and 100-200 s, not previously disclosed. The shorter time is found to be related to the internal relaxation time of the cytoplasm. To our knowledge, this is the first time that similarities are established between the properties of time series describing the intracellular metabolism and the statistical results from a mathematical finance approach. The current approach could be exploited to reveal hidden features from biological complex systems or to determine new biomarkers of cellular metabolism.

Zwitterion and Oligo(ethylene glycol) Synergy Minimizes Nonspecific Binding of Compact Quantum Dots

Quantum dots (QDs) are a class of fluorescent nanocrystals in development as labels for molecular imaging in cells and tissues. Recently, coatings for quantum dots based on multidentate polymers have improved labeling performance in a range of bioanalytical applications, primarily due to reduced probe hydrodynamic size. Now, an ongoing challenge is to eliminate nonspecific binding between these small probes and cellular components that mask specifically labeled molecules. Here, we describe insights into controlling and minimizing intermolecular interactions governing nonspecific binding using multidentate polymers with tunable hydrophilic functional groups that are cationic, anionic, zwitterionic (ZW), or nonionic (oligoethylene glycol; OEG). By fixing surface-binding groups and polymer length, coated colloids have similar sizes but diverse physicochemical properties. We measure binding to globular proteins, fixed cells, and living cells and observe a substantial improvement in nonspecific binding resistance when surfaces are functionalized with a combination of ZW and OEG. The independent underlying effects of counterion adsorption and flexibility appear to synergistically resist adsorption when combined, particularly for fixed cells enriched in both charged and hydrophobic moieties. We further show that ZW-OEG QDs are stable under diverse conditions and can be self-assembled with antibodies to specifically label surface antigens on living cells and cytoplasmic proteins in fixed cells. This surface engineering strategy can be adopted across the diverse range of colloidal materials currently in use and in development for biomedical applications to optimize their molecular labeling specificity.

Impact of global structure on diffusive exploration of organelle networks

We investigate diffusive search on planar networks, motivated by tubular organelle networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network is used to characterize the typical search time as a function of network connectivity. We find that global structural properties — the total edge length and number of loops — are sufficient to largely determine network exploration times for a variety of both synthetic planar networks and organelle morphologies extracted from living cells. For synthetic networks on a lattice, we predict the search time dependence on these global structural parameters by connecting with percolation theory, providing a bridge from irregular real-world networks to a simpler physical model. The dependence of search time on global network structural properties suggests that network architecture can be designed for efficient search without controlling the precise arrangement of connections. Specifically, increasing the number of loops substantially decreases search times, pointing to a potential physical mechanism for regulating reaction rates within organelle network structures.

Statistical Tests for Force Inference in Heterogeneous Environments

We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious” force term when the diffusivity varies in space. We show how Bayesian inference can be leveraged to reliably infer forces by taking into account such spurious forces of unknown amplitude as well as experimental sources of error. The method is based on marginalizing the force posterior over all possible spurious force contributions. The approach is combined with a Bayes factor statistical test for the presence of forces. The performance of our method is investigated analytically, numerically and tested on experimental data sets. The main results are obtained in a closed form allowing for direct exploration of their properties and fast computation. The method is incorporated into TRamWAy, an open-source software platform for automated analysis of biomolecule trajectories.

Matrix mechanics and water permeation regulate extracellular vesicle transport

Cells release extracellular vesicles (EVs) to communicate over long distances, which requires EVs to traverse the extracellular matrix (ECM). However, given that the size of EVs is usually larger than the mesh size of the ECM, it is not clear how they can travel through the dense ECM. Here we show that, in contrast to synthetic nanoparticles, EVs readily transport through nanoporous ECM. Using engineered hydrogels, we demonstrate that the mechanical properties of the matrix regulate anomalous EV transport under confinement. Matrix stress relaxation allows EVs to overcome the confinement, and a higher crosslinking density facilitates a fluctuating transport motion through the polymer mesh, which leads to free diffusion and fast transport. Furthermore, water permeation through aquaporin-1 mediates the EV deformability, which further supports EV transport in hydrogels and a decellularized matrix. Our results provide evidence for the nature of EV transport within confined environments and demonstrate an unexpected dependence on matrix mechanics and water permeation.

Zwitterionic Stealth Dye-Loaded Polymer Nanoparticles for Intracellular Imaging

Intracellular applications of fluorescent nanoparticles (NPs) as probes and labels are currently limited by significant molecular crowding and the high level of complexity encountered inside living cells. The solution is to develop very small, bright, and noninteracting (stealth) NPs. Combining these properties requires implementing the stealth behavior through the thinnest possible hydrophilic shell. Here, we propose a one-step process for preparing ultrasmall and bright stealth NPs based on a zwitterionic (ZI) methacrylate-based copolymer. Dye-loaded polymer NPs are assembled through nanoprecipitation of the copolymer together with the salt of a rhodamine B derivative and a bulky hydrophobic counterion to achieve high particle brightness. We found that 10 mol % ZI groups in the polymer yield NPs of less than 15 nm that are stable in physiological salt conditions and practically resistant to protein adsorption, as suggested by fluorescence correlation spectroscopy. The combination of the very small size with the nonfouling nature of these particles enables spreading of ZI polymer NPs in the whole cytosol after their microinjection into living cells. In addition, single-particle tracking showed up to four times faster diffusion of ZI NPs in the cytosol compared to PEGylated NPs. The obtained dye-loaded ZI polymer NPs open the route to intracellular single-particle tracking and biosensing applications.

Diffusion and flow in complex liquids

Thermal motion of particles and molecules in liquids underlies many chemical and biological processes. Liquids, especially in biology, are complex due to structure at multiple relevant length scales. While diffusion in homogeneous simple liquids is well understood through the Stokes-Einstein relation, this equation fails completely in describing diffusion in complex media. Modeling, understanding, engineering and controlling processes at the nanoscale, most importantly inside living cells, requires a theoretical framework for the description of viscous response to allow predictions of diffusion rates in complex fluids. Here we use a general framework with the viscosity η(k) described by a function of wave vector in reciprocal space. We introduce a formulation that allows one to relate the rotational and translational diffusion coefficients and determine the viscosity η(k) directly from experiments. We apply our theory to provide a database for rotational diffusion coefficients of proteins/protein complexes in the bacterium E. coli. We also provide a database for the diffusion coefficient of proteins sliding along major grooves of DNA in E. coli. These parameters allow predictions of rate constants for association of proteins. In addition to constituting a theoretical framework for description of diffusion of probes and viscosity in complex fluids, the formulation that we propose should decrease substantially the cost of numerical simulations of transport in complex media by replacing the simulation of individual crowding particles with a continuous medium characterized by a wave-length dependent viscosity η(k).

Resampling single-particle tracking data eliminates localization errors and reveals proper diffusion anomalies

Single-particle tracking (SPT) is a versatile tool for quantifying diffusional motion in complex soft-matter systems, e.g., in biological specimen. Evaluating SPT data often invokes the fitting of a trajectory's time-averaged mean-square displacement (TA-MSD) with a simple power law, 〈r^{2}(τ)〉_{t}∼τ^{α}, where the scaling exponent α can yield important insights into the nature of the transport process. Biological specimen, for example, frequently feature a diffusion anomaly, i.e., an exponent α<1 ("subdiffusion"). However, due to SPT-inherent static and dynamic localization errors, in combination with typically short trajectories, it is often a real challenge to determine the value of α reliably by simply fitting TA-MSDs. Here a straightforward resampling approach is presented and tested that eliminates both localization errors in the TA-MSD of trajectories originating from subdiffusive fractional Brownian motion processes. As a result, the mean anomaly exponent 〈α〉_{E} of an ensemble of trajectories is revealed in a robust fashion.

Diffusion-influenced reaction rates in the presence of pair interactions

The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi-analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

Atomistic molecular dynamics simulations of concentrated protein solutions in the presence of a phospholipid bilayer are presented to gain insights into the dynamics and interactions at the cytosol-membrane interface. The main finding is that proteins that are not known to specifically interact with membranes are preferentially excluded from the membrane, leaving a depletion zone near the membrane surface. As a consequence, effective protein concentrations increase, leading to increased protein contacts and clustering, whereas protein diffusion becomes faster near the membrane for proteins that do occasionally enter the depletion zone. Since protein-membrane contacts are infrequent and short-lived in this study, the structure of the lipid bilayer remains largely unaffected by the crowded protein solution, but when proteins do contact lipid head groups, small but statistically significant local membrane curvature is induced, on average.

Standard and fractional Ornstein-Uhlenbeck process on a growing domain

We study normal diffusive and subdiffusive processes in a harmonic potential (Ornstein-Uhlenbeck process) on a uniformly growing or contracting domain. Our starting point is a recently derived fractional Fokker-Planck equation, which covers both the case of Brownian diffusion and the case of a subdiffusive continuous-time random walk (CTRW). We find a high sensitivity of the random walk properties to the details of the domain growth rate, which gives rise to a variety of regimes with extremely different behaviors. At the origin of this rich phenomenology is the fact that the walkers still move while they wait to jump, since they are dragged by the deterministic drift arising from the domain growth. Thus, the increasingly long waiting times associated with the aging of the subdiffusive CTRW imply that, in the time interval between two consecutive jumps, the walkers might travel over much longer distances than in the normal diffusive case. This gives rise to seemingly counterintuitive effects. For example, on a static domain, both Brownian diffusion and subdiffusive CTRWs yield a stationary particle distribution with finite width when a harmonic potential is at play, thus indicating a confinement of the diffusing particle. However, for a sufficiently fast growing or contracting domain, this qualitative behavior breaks down, and differences between the Brownian case and the subdiffusive case are found. In the case of Brownian particles, a sufficiently fast exponential domain growth is needed to break the confinement induced by the harmonic force; in contrast, for subdiffusive particles such a breakdown may already take place for a sufficiently fast power-law domain growth. Our analytic and numerical results for both types of diffusion are fully confirmed by random walk simulations.

Nonuniform Crowding Enhances Transport

The cellular cytoplasm is crowded with macromolecules and other species that occupy up to 40% of the available volume. Previous studies have reported that for high crowder molecule concentrations, colloidal tracer particles have a dampened diffusion due to the higher solution viscosity. However, these studies employed uniform distributions of crowder molecules. We report a scenario, previously unexplored experimentally, of increased tracer transport driven by a nonuniform concentration of crowder macromolecules. In gradients of a polymeric crowder, tracer particles undergo transport several times higher than that of their bulk diffusion rate. The direction of the transport is toward regions of lower crowder concentration. Mechanistically, hard-sphere interactions and the resulting volume exclusion between the tracer and crowder increase the effective diffusion by inducing a convective motion of tracers, which we explain through modeling. Strikingly, soft deformable particles show even greater enhancement in transport in crowder gradients compared to similarly sized hard particles. Overall, this demonstration of enhanced transport in nonuniform distributions of crowders is anticipated to clarify aspects of multicomponent intracellular transport.

Self-diffusion of a highly concentrated monoclonal antibody by fluorescence correlation spectroscopy: insight into protein-protein interactions and self-association

The dynamic behavior of monoclonal antibodies (mAbs) at high concentration provides insight into protein microstructure and protein-protein interactions (PPI) that influence solution viscosity and protein stability. At high concentration, interpretation of the collective-diffusion coefficient Dc, as determined by dynamic light scattering (DLS), is highly challenging given the complex hydrodynamics and PPI at close spacings. In contrast, self-diffusion of a tracer particle by Brownian motion is simpler to understand. Herein, we develop fluorescence correlation spectroscopy (FCS) for the measurement of the long-time self-diffusion of mAb2 over a wide range of concentrations and viscosities in multiple co-solute formulations with varying PPI. The normalized self-diffusion coefficient D0/Ds (equal to the microscopic relative viscosity ηeff/η0) was found to be smaller than η/η0. Smaller ratios of the microscopic to macroscopic viscosity (ηeff/η) are attributed to a combination of weaker PPI and less self-association. The interaction parameters extracted from fits of D0/Ds with a length scale dependent viscosity model agree with previous measurements of PPI by SLS and SAXS. Trends in the degree of self-association, estimated from ηeff/η with a microviscosity model, are consistent with oligomer sizes measured by SLS. Finally, measurements of collective diffusion and osmotic compressibility were combined with FCS data to demonstrate that the changes in self-diffusion between formulations are due primarily to changes in the protein-protein friction in these systems, and not to protein-solvent friction. Thus, FCS is a robust and accessible technique for measuring mAb self-diffusion, and, by extension, microviscosity, PPI and self-association that govern mAb solution dynamics.

Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function

In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.

Heterogeneities Shape Passive Intracellular Transport

A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion that controls cellular functionality. Here, we investigated two distinct fundamental features of the merely passive, non-biomotor-shuttled material transport within the cytoplasm of Dictyostelium discoideum cells: the anomalous non-linear scaling of the mean-squared displacement of a 150-nm-diameter particle and non-Gaussian distribution of increments. Relying on single-particle tracking data of 320,000 data points, we performed a systematic analysis of four possible origins for non-Gaussian transport: 1) sample-based variability, 2) rarely occurring strong motion events, 3) ergodicity breaking/aging, and 4) spatiotemporal heterogeneities of the intracellular medium. After excluding the first three reasons, we investigated the remaining hypothesis of a heterogeneous cytoplasm as cause for non-Gaussian transport. A, to our knowledge, novel fit model with randomly distributed diffusivities implementing medium heterogeneities suits the experimental data. Strikingly, the non-Gaussian feature is independent of the cytoskeleton condition and lag time. This reveals that efficiency and consistency of passive intracellular transport and the related anomalous scaling of the mean-squared displacement are regulated by cytoskeleton components, whereas cytoplasmic heterogeneities are responsible for the generic, non-Gaussian distribution of increments.

Novel Tools towards Magnetic Guidance of Neurite Growth: (I) Guidance of Magnetic Nanoparticles into Neurite Extensions of Induced Human Neurons and In Vitro Functionalization with RAS Regulating Proteins

Parkinson’s disease (PD) is a neurodegenerative disease associated with loss or dysfunction of dopaminergic neurons located in the substantia nigra (SN), and there is no cure available. An emerging new approach for treatment is to transplant human induced dopaminergic neurons directly into the denervated striatal brain target region. Unfortunately, neurons grafted into the substantia nigra are unable to grow axons into the striatum and thus do not allow recovery of the original connectivity. Towards overcoming this general limitation in guided neuronal regeneration, we develop here magnetic nanoparticles functionalized with proteins involved in the regulation of axonal growth. We show covalent binding of constitutive active human rat sarcoma (RAS) proteins or RAS guanine nucleotide exchange factor catalytic domain of son of sevenless (SOS) by fluorescence correlation spectroscopy and multiangle light scattering as well as the characterization of exchange factor activity. Human dopaminergic neurons were differentiated from neural precursor cells and characterized by electrophysiological and immune histochemical methods. Furthermore, we demonstrate magnetic translocation of cytoplasmic γ-Fe₂O₃@SiO₂ core-shell nanoparticles into the neurite extensions of induced human neurons. Altogether, we developed tools towards remote control of directed neurite growth in human dopaminergic neurons. These results may have relevance for future therapeutic approaches of cell replacement therapy in Parkinson’s disease.

Quantitative assessment of the spatial crowding heterogeneity in cellular fluids

Mammalian cells are crowded with macromolecules, supramolecular complexes, and organelles, all of which equip intracellular fluids, e.g., the cytoplasm, with a dynamic and spatially heterogeneous occupied volume fraction. Diffusion in such fluids has been reported to be heterogeneous, i.e., even individual single-particle trajectories feature spatiotemporally varying transport characteristics. Complementing diffusion-based experiments, we have used here an imaging approach to assess the spatial heterogeneity of the nucleoplasm and the cytoplasm in living interphase cells. As a result, we find that the cytoplasm is more crowded and more heterogeneous than the nucleoplasm on several length scales. This phenomenon even persists in dividing cells, where the mitotic spindle region and its periphery form a contiguous fluid but remain nucleoplasmlike and cytoplasmlike, respectively.

Anomalous transport in the soft-sphere Lorentz model

The sensitivity of anomalous transport in crowded media to the form of the inter-particle interactions is investigated through computer simulations. We extend the highly simplified Lorentz model towards realistic natural systems by modeling the interactions between the tracer and the obstacles with a smooth potential. We find that the anomalous transport at the critical point happens to be governed by the same universal exponent as for hard exclusion interactions, although the mechanism of how narrow channels are probed is rather different. The scaling behavior of simulations close to the critical point confirm this exponent. Our result indicates that the simple Lorentz model may be applicable to describing the fundamental properties of long-range transport in real crowded environments.

Brief update on endocytosis of nanomedicines

The complexity of nanoscale interactions between biomaterials and cells has limited the realization of the ultimate vision of nanotechnology in diagnostics and therapeutics. As such, significant effort has been devoted to advancing our understanding of the biophysical interactions of the myriad nanoparticles. Endocytosis of nanomedicine has drawn tremendous interest in the last decade. Here, we highlight the ever-present barriers to efficient intracellular delivery of nanoparticles as well as the current advances and strategies deployed to breach these barriers. We also introduce new barriers that have been largely overlooked such as the glycocalyx and macromolecular crowding. Additionally, we draw attention to the potential complications arising from the disruption of the newly discovered functions of the lysosomes. Novel strategies of exploiting the inherent intracellular defects in disease states to enhance delivery and the use of exosomes for bioanalytics and drug delivery are explored. Furthermore, we discuss the advances in imaging techniques like electron microscopy, super resolution fluorescence microscopy, and single particle tracking which have been instrumental in our growing understanding of intracellular pathways and nanoparticle trafficking. Finally, we advocate for the push towards more intravital analysis of nanoparticle transport phenomena using the multitude of techniques available to us. Unraveling the underlying mechanisms governing the cellular barriers to delivery and biological interactions of nanoparticles will guide the innovations capable of breaching these barriers.

All-in-One Synchronized DNA Nanodevices Facilitating Multiplexed Cell Imaging

Multifunctional DNA nanodevices perform ever more tasks with applications ranging from in vitro biomarker detection to in situ cell imaging. However, most developed ones consist of a series of split building blocks, which suffer from asynchronous behaviors in complicated cellular microenvironments (endocytosis pathway, diffusion-limited cytoplasm, etc.), causing the loss of stoichiometric information and additional postassembly processes. Herein, we constructed all-in-one DNA nanodevices to achieve synchronous multiplexed imaging. All DNA components, including two sets of probe modules (each containing target-specific walkers, i.e., hairpin tracks with chemically damaged bases), are modified on individual gold nanoparticles. This design not only enables their integrated internalization into cells, circumventing inhomogeneous distribution of different building blocks and increasing the local concentrations of the interacting modules, but also avoids the impact of stochastic diffusion in viscous cytoplasm. A couple of intracellular enzymes in situ actuate the synchronized motion of the modules, all on-particle, after specific recognition of intracellular targets (such as RNAs and proteins), thus facilitating synchronized, multiplexed cell imaging. Finally, the proposed all-in-one nanodevices were successfully applied to monitor intracellular microRNA-21 and telomerase expression levels. The flexible design can be extended to detect other cytoplasmic molecules and monitor related pathways by simply changing the sequences.

Non-Gaussian, non-ergodic, and non-Fickian diffusion of tracers in mucin hydrogels

Native mucus is polymer-based soft-matter material of paramount biological importance. How non-Gaussian and non-ergodic is the diffusive spreading of pathogens in mucus? We study the passive, thermally driven motion of micron-sized tracers in hydrogels of mucins, the main polymeric component of mucus. We report the results of the Bayesian analysis for ranking several diffusion models for a set of tracer trajectories [C. E. Wagner et al., Biomacromolecules, 2017, 18, 3654]. The models with "diffusing diffusivity", fractional and standard Brownian motion are used. The likelihood functions and evidences of each model are computed, ranking the significance of each model for individual traces. We find that viscoelastic anomalous diffusion is often most probable, followed by Brownian motion, while the model with a diffusing diffusion coefficient is only realised rarely. Our analysis also clarifies the distribution of time-averaged displacements, correlations of scaling exponents and diffusion coefficients, and the degree of non-Gaussianity of displacements at varying pH levels. Weak ergodicity breaking is also quantified. We conclude that-consistent with the original study-diffusion of tracers in the mucin gels is most non-Gaussian and non-ergodic at low pH that corresponds to the most heterogeneous networks. Using the Bayesian approach with the nested-sampling algorithm, together with the quantitative analysis of multiple statistical measures, we report new insights into possible physical mechanisms of diffusion in mucin gels.

Programming in situ accelerated DNA walkers in diffusion-limited microenvironments

Macromolecule diffusion in cellular microenvironments dictates the kinetics of biochemical processes, yet inevitably limiting the assembly and operation of biomimetic motors. Herein we program in situ accelerated DNA walkers in diffusion-limited microenvironments such as molecularly crowded solutions and cytoplasm. All DNA components, including single-foot walkers, chemically damaged tracks and calibration elements, are anchored on individual gold nanoparticles. Two endogenous enzymes participating in base repair pathways are used to actuate on-particle walking via a base excision/hydrolyzation coupled reaction. The walkers are in situ driven without requiring external drivers and accelerated several times. They also avoid low-efficiency diffusion/assembly procedures and respond to heterogeneous cellular milieus with calibration function. We further regulated the walking kinetics via DNA densities and sets of enzymes, and demonstrated cytoplasmic behaviors of three kinds of walkers. They were utilized to profile DNA repair pathways and monitor enzyme catalysis in living cells.

On-Demand Intracellular Delivery of Single Particles in Single Cells by 3D Hollow Nanoelectrodes

Delivery of molecules into intracellular compartments is one of the fundamental requirements in molecular biology. However, the possibility of delivering a precise number of nano-objects with single-particle resolution is still an open challenge. Here we present an electrophoretic platform based on 3D hollow nanoelectrodes to enable delivery of single nanoparticles into single selected cells and monitoring of the single-particle delivery by surface-enhanced Raman scattering (SERS). The gold-coated hollow nanoelectrode capable of confinement and enhancement of electromagnetic fields upon laser illumination can distinguish the SERS signals of a single nanoparticle flowing through the nanoelectrode. Tight wrapping of cell membranes around the nanoelectrodes allows effective membrane electroporation such that single gold nanorods are delivered on demand into a living cell by electrophoresis. The capability of the 3D hollow nanoelectrodes to porate cells and reveal single emitters from the background in continuous flow is promising for the analysis of both intracellular delivery and sampling.

Non-Gaussianity, population heterogeneity, and transient superdiffusion in the spreading dynamics of amoeboid cells

What is the underlying diffusion process governing the spreading dynamics and search strategies employed by amoeboid cells?