Role of cytochrome c oxidase nuclear-encoded subunits in health and disease.

Cytochrome c oxidase (COX), the terminal enzyme of mitochondrial electron transport chain, couples electron transport to oxygen with generation of proton gradient indispensable for the production of vast majority of ATP molecules in mammalian cells. The review summarizes current knowledge of COX structure and function of nuclear-encoded COX subunits, which may modulate enzyme activity according to various conditions. Moreover, some nuclear-encoded subunits posess tissue-specific and development-specific isoforms, possibly enabling fine-tuning of COX function in individual tissues. The importance of nuclear-encoded subunits is emphasized by recently discovered pathogenic mutations in patients with severe mitopathies. In addition, proteins substoichiometrically associated with COX were found to contribute to COX activity regulation and stabilization of the respiratory supercomplexes. Based on the summarized data, a model of three levels of quaternary COX structure is postulated. Individual structural levels correspond to subunits of the i) catalytic center, ii) nuclear-encoded stoichiometric subunits and iii) associated proteins, which may constitute several forms of COX with varying composition and differentially regulated function.

Kinetics of empty viral capsid assembly in a minimal model.

The efficient construction of a protective protein shell or capsid is one of the most crucial steps in the replication cycle of a virus. The formation of the simplest capsid typically proceeds by the spontaneous assembly of identical building blocks. This process can also be achieved in vitro even in the absence of genetic material, thus opening the door to the production of artificial viral cages for a myriad of applications. In this work, we analyze the efficiency and the kinetic peculiarities of this self-assembly process using Brownian Dynamics simulations. We use a minimal model that considers identical assembly units and is able to reproduce successfully the correct final architecture of spherical capsids. The selection of a specific size and structure is achieved by changing a single parameter that imposes an angular anisotropy on the interaction. We analyze how the geometrical constraints of the interaction affect the efficiency of the assembly. We find that the optimal conditions for an efficient assembly from a kinetic point of view strongly depart from the lowest capsid energy corresponding to the minimum of the potential energy landscape. Our work illustrates the important differences between the equilibrium and dynamic characteristics of viral self-assembly, and provides important insights on how to design specific interactions for a successful assembly of artificial viral cages.

Optimizing the performance of the entropic splitter for particle separation.

Recently, it has been shown that entropy can be used to sort Brownian particles according to their size. In particular, a combination of a static and a time-dependent force applied on differently sized particles which are confined in an asymmetric periodic structure can be used to separate them efficiently, by forcing them to move in opposite directions. In this paper, we investigate the optimization of the performance of the "entropic splitter." Specifically, the splitting mechanism and how it depends on the geometry of the channel, and the frequency and strength of the periodic forcing is analyzed. Using numerical simulations, we demonstrate that a very efficient and fast separation with a practically 100% purity can be achieved by a proper optimization of the control variables. The results of this work could be useful for a more efficient separation of dispersed phases such as DNA fragments or colloids dependent on their size.

Antioxidant and regulatory role of mitochondrial uncoupling protein UCP2 in pancreatic beta-cells.

Research on brown adipose tissue and its hallmark protein, mitochondrial uncoupling protein UCP1, has been conducted for half a century and has been traditionally studied in the Institute of Physiology (AS CR, Prague), likewise UCP2 residing in multiple tissues for the last two decades. Our group has significantly contributed to the elucidation of UCP uncoupling mechanism, fully dependent on free fatty acids (FFAs) within the inner mitochondrial membrane. Now we review UCP2 physiological roles emphasizing its roles in pancreatic beta-cells, such as antioxidant role, possible tuning of redox homeostasis (consequently UCP2 participation in redox regulations), and fine regulation of glucose-stimulated insulin secretion (GSIS). For example, NADPH has been firmly established as being a modulator of GSIS and since UCP2 may influence redox homeostasis, it likely affects NADPH levels. We also point out the role of phospholipase iPLA2 isoform gamma in providing FFAs for the UCP2 antioxidant function. Such initiation of mild uncoupling hypothetically precedes lipotoxicity in pancreatic beta-cells until it reaches the pathological threshold, after which the antioxidant role of UCP2 can be no more cell-protective, for example due to oxidative stress-accumulated mutations in mtDNA. These mechanisms, together with impaired autocrine insulin function belong to important causes of Type 2 diabetes etiology.

Imaging the proton concentration and mapping the spatial distribution of the electric field of catalytic micropumps.

Catalytic engines can use hydrogen peroxide as a chemical fuel in order to drive motion at the microscale. The chemo-mechanical actuation is a complex mechanism based on the interrelation between catalytic reactions and electro-hydrodynamics phenomena. We studied catalytic micropumps using fluorescence confocal microscopy to image the concentration of protons in the liquid. In addition, we measured the motion of particles with different charges in order to map the spatial distributions of the electric field, the electrostatic potential and the fluid flow. The combination of these two techniques allows us to contrast the gradient of the concentration of protons against the spatial variation in the electric field. We present numerical simulations that reproduce the experimental results. Our work sheds light on the interrelation between the different processes at work in the chemomechanical actuation of catalytic pumps. Our experimental approach could be used to study other electrochemical systems with heterogeneous electrodes.

Effect of compressibility in bubble formation in closed systems.

We analyze the stability of small bubbles in a closed system with fixed volume, temperature, and number of molecules. We show that there exists a minimum stable size of a bubble. Thus there exists a range of densities where no stable bubbles are allowed and the system has a homogeneous density which is lower than the coexistence density of the liquid. This becomes possible due to the finite liquid compressibility. Capillary analysis within the developed "modified bubble" model illustrates that the existence of the minimum bubble size is associated to the compressibility and it is not possible when the liquid is strictly incompressible. This finding is expected to have very important implications in cavitation and boiling.

Entropic splitter for particle separation.

We present a particle separation mechanism which induces the motion of particles of different sizes in opposite directions. The mechanism is based on the combined action of a driving force and an entropic rectification of the Brownian fluctuations caused by the asymmetric form of the channel along which particles proceed. The entropic splitting effect shown could be controlled upon variation of the geometrical parameters of the channel and could be implemented in narrow channels and microfluidic devices.

Built-in mechanical stress in viral shells.

Mechanical properties of biological molecular aggregates are essential to their function. A remarkable example are double-stranded DNA viruses such as the φ29 bacteriophage, that not only has to withstand pressures of tens of atmospheres exerted by the confined DNA, but also uses this stored elastic energy during DNA translocation into the host. Here we show that empty prolated φ29 bacteriophage proheads exhibit an intriguing anisotropic stiffness which behaves counterintuitively different from standard continuum elasticity predictions. By using atomic force microscopy, we find that the φ29 shells are approximately two-times stiffer along the short than along the long axis. This result can be attributed to the existence of a residual stress, a hypothesis that we confirm by coarse-grained simulations. This built-in stress of the virus prohead could be a strategy to provide extra mechanical strength to withstand the DNA compaction during and after packing and a variety of extracellular conditions, such as osmotic shocks or dehydration.

Entropic stochastic resonance.

We present a novel scheme for the appearance of stochastic resonance when the dynamics of a Brownian particle takes place in a confined medium. The presence of uneven boundaries, giving rise to an entropic contribution to the potential, may upon application of a periodic driving force result in an increase of the spectral amplification at an optimum value of the ambient noise level. The entropic stochastic resonance, characteristic of small-scale systems, may constitute a useful mechanism for the manipulation and control of single molecules and nanodevices.

Entropic particle transport in periodic channels.

The dynamics of Brownian motion has widespread applications extending from transport in designed micro-channels up to its prominent role for inducing transport in molecular motors and Brownian motors. Here, Brownian transport is studied in micro-sized, two-dimensional periodic channels, exhibiting periodically varying cross-sections. The particles in addition are subjected to an external force acting alongside the direction of the longitudinal channel axis. For a fixed channel geometry, the dynamics of the two-dimensional problem is characterized by a single dimensionless parameter which is proportional to the ratio of the applied force and the temperature of the particle environment. In such structures entropic effects may play a dominant role. Under certain conditions the two-dimensional dynamics can be approximated by an effective one-dimensional motion of the particle in the longitudinal direction. The Langevin equation describing this reduced, one-dimensional process is of the type of the Fick-Jacobs equation. It contains an entropic potential determined by the varying extension of the eliminated channel direction, and a correction to the diffusion constant that introduces a space dependent diffusion. Different forms of this correction term have been suggested before, which we here compare for a particular class of models. We analyze the regime of validity of the Fick-Jacobs equation, both by means of analytical estimates and the comparisons with numerical results for the full two-dimensional stochastic dynamics. For the nonlinear mobility we find a temperature dependence which is opposite to that known for particle transport in periodic potentials. The influence of entropic effects is discussed for both, the nonlinear mobility and the effective diffusion constant.

Biased diffusion in confined media: test of the Fick-Jacobs approximation and validity criteria.

We study biased, diffusive transport of Brownian particles through narrow, spatially periodic structures in which the motion is constrained in lateral directions. The problem is analyzed under the perspective of the Fick-Jacobs equation, which accounts for the effect of the lateral confinement by introducing an entropic barrier in a one-dimensional diffusion. The validity of this approximation, based on the assumption of an instantaneous equilibration of the particle distribution in the cross section of the structure, is analyzed by comparing the different time scales that characterize the problem. A validity criterion is established in terms of the shape of the structure and of the applied force. It is analytically corroborated and verified by numerical simulations that the critical value of the force up to which this description holds true scales as the square of the periodicity of the structure. The criterion can be visualized by means of a diagram representing the regions where the Fick-Jacobs description becomes inaccurate in terms of the scaled force versus the periodicity of the structure.

Entropic transport: kinetics, scaling, and control mechanisms.

We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle current and the diffusion coefficient in terms of the ratio between the work done to the particles and available thermal energy. This interesting property, genuine to the entropic nature of the barriers, can be utilized to effectively control transport through quasi-one-dimensional structures in which irregularities or tortuosity of the boundaries cause entropic effects. The accuracy of the kinetic description has been corroborated by simulations. Applications to different dynamic situations involving entropic barriers are outlined.

The mesoscopic dynamics of thermodynamic systems.

Concepts of everyday use such as energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and the general rules that the macroscopic properties of systems at equilibrium follow. Outside equilibrium and away from macroscopic regimes, most of those rules cannot be applied directly. Here we present recent developments that extend the applicability of thermodynamic concepts deep into mesoscopic and irreversible regimes. We show how the probabilistic interpretation of thermodynamics together with probability conservation laws can be used to obtain Fokker-Planck equations for the relevant degrees of freedom. This approach provides a systematic method to obtain the stochastic dynamics of a system directly from its equilibrium properties. A wide variety of situations can be studied in this way, including many that were thought to be out of reach of thermodynamic theories, such as nonlinear transport in the presence of potential barriers, activated processes, slow relaxation phenomena, and basic processes in biomolecules, such as translocation and stretching.

Fusion of the extended modified liquid drop model for nucleation and dynamical nucleation theory.

We present a new phenomenological approach to nucleation, based on the combination of the "extended modified liquid drop" model and dynamical nucleation theory. The new model proposes a new cluster definition, which properly includes the effect of fluctuations, and it is consistent both thermodynamically and kinetically. The model is able to predict successfully the free energy of formation of the critical nucleus, using only macroscopic thermodynamic properties. It also accounts for the spinodal and provides excellent agreement with the result of recent simulations.

Kinetic equations for diffusion in the presence of entropic barriers.

We use the mesoscopic nonequilibrium thermodynamics theory to derive the general kinetic equation of a system in the presence of potential barriers. The result is applied to a description of the evolution of systems whose dynamics is influenced by entropic barriers. We analyze in detail the case of diffusion in a domain of irregular geometry in which the presence of the boundaries induces an entropy barrier when approaching the exact dynamics by a coarsening of the description. The corresponding kinetic equation, named the Fick-Jacobs equation, is obtained, and its validity is generalized through the formulation of a scaling law for the diffusion coefficient which depends on the shape of the boundaries. The method we propose can be useful to analyze the dynamics of systems at the nanoscale where the presence of entropy barriers is a common feature.

Diffusion in stationary flow from mesoscopic nonequilibrium thermodynamics.

We analyze the diffusion of a Brownian particle in a fluid under stationary flow. By using the scheme of nonequilibrium thermodynamics in phase space, we obtain the Fokker-Planck equation that is compared with others derived from the kinetic theory and projector operator techniques. This equation exhibits violation of the fluctuation-dissipation theorem. By implementing the hydrodynamic regime described by the first moments of the nonequilibrium distribution, we find relaxation equations for the diffusion current and pressure tensor, allowing us to arrive at a complete description of the system in the inertial and diffusion regimes. The simplicity and generality of the method we propose makes it applicable to more complex situations, often encountered in problems of soft-condensed matter, in which not only one but more degrees of freedom are coupled to a nonequilibrium bath.

Controlling anomalous stresses in soft field-responsive systems

We report a phenomenon occurring in field-responsive suspensions: shear-induced anomalous stresses. Competition between a rotating field and a shear flow originates a multiplicity of anomalous stress behaviors in suspensions of bound dimers constituted by induced dipoles. The great variety of stress regimes includes nonmonotonic behaviors, multiresonances, negative viscosity effect, and blockades. The reversibility of the transitions between the different regimes and the self-similarity of the stresses make this phenomenon controllable and therefore applicable to modify macroscopic properties of soft condensed matter phases.