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At least 433 records · Page 24Linked to original sources

Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes

Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of non-covalent interactions with ligands. Typically, force decreases the lifetimes of intact complexes (slip-bonds), making the discovery that these lifetimes can also be prolonged ("catch-bonds"), a surprise. We created a microscopic analytic theory by incorporating the structures of selectin and integrin receptors into a conceptual framework based on the theory of stochastic equations, which quantitatively explains a wide range of experimental data (including catch-bonds at low forces and slip-bonds at high forces). Catch-bonds arise due to force-induced remodeling of hydrogen bond networks, a finding that also accounts for unbinding in structurally unrelated integrin-fibronectin and actomyosin complexes. For the selectin family, remodeling of hydrogen bond networks drives an allosteric transition resulting in the formation of maximum number of hydrogen bonds determined only by the structure of the receptor and is independent of the ligand. A similar transition allows us to predict the increase in number of hydrogen bonds in a particular allosteric state of $α_5 β_1$ integrin-fibronectin complex, a conformation which is yet to be crystallized. We also make a testable prediction that a single point mutation (Tyr51Phe) in the ligand associated with selectin should dramatically alter the nature of the catch-bond compared to the wild type. Our work suggests that nature utilizes a ductile network of hydrogen bonds to engineer function over a broad range of forces.

q-bio.BM↗

Allocating dissipation across a molecular machine cycle to maximize flux

Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapid-turnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that---in contrast to previous findings---the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both `irreversible' and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that in evolved machines different transitions differ significantly in their dissipation.

cond-mat.stat-mech↗

Robust nonequilibrium pathways to microcompartment assembly

Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that posit microcompartments as stable equilibrium arrangements of the constituent proteins. Here we describe a different mechanism for microcompartment assembly, one that is fundamentally nonequilibrium and yet highly reliable. This pathway is revealed by simulations of a molecular model resolving the size and shape of a cargo droplet, and the extent and topography of an elastic shell. The resulting metastable microcompartment structures closely resemble those of carboxysomes, with a narrow size distribution and faceted shells. The essence of their assembly dynamics can be understood from a simpler mathematical model that combines elements of classical nucleation theory with continuum elasticity. These results highlight important control variables for achieving nanoscale encapsulation in general, and for modulating the size and shape of carboxysomes in particular.

cond-mat.soft↗

pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study

In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This protein structure presents a remarkable chain stiffness andis formed by two or more long helical peptides that are interacting like the strands of a rope. Chain length and rigidity are the key aspects needed to extend previous peptide interaction potentials to this particular case; however the original model is naturally recovered when the length or the ridigity of the simulated chain are reduced. We apply the model and discuss results for two cases: (a) the folding/unfolding transition of a generic coiled coil as a function of pH; (b) behavior of a specific sequence as a function of the acidity conditions. In this latter case results are compared with experimental data from the literature in order to comment about the consistency of our approach.

physics.bio-ph↗

Assessing the influence of the solar orbit on terrestrial biodiversity

The terrestrial fossil record shows a significant variation in the extinction and origination rates of species during the past half billion years. Numerous studies have claimed an association between this variation and the motion of the Sun around the Galaxy, invoking the modulation of cosmic rays, gamma rays and comet impact frequency as a cause of this biodiversity variation. However, some of these studies exhibit methodological problems, or were based on coarse assumptions (such as a strict periodicity of the solar orbit). Here we investigate this link in more detail, using a model of the Galaxy to reconstruct the solar orbit and thus a predictive model of the temporal variation of the extinction rate due to astronomical mechanisms. We compare these predictions as well as those of various reference models with paleontological data. Our approach involves Bayesian model comparison, which takes into account the uncertainties in the paleontological data as well as the distribution of solar orbits consistent with the uncertainties in the astronomical data. We find that various versions of the orbital model are not favored beyond simpler reference models. In particular, the distribution of mass extinction events can be explained just as well by a uniform random distribution as by any other model tested. Although our negative results on the orbital model are robust to changes in the Galaxy model, the Sun's coordinates and the errors in the data, we also find that it would be very difficult to positively identify the orbital model even if it were the true one. (In contrast, we do find evidence against simpler periodic models.) Thus while we cannot rule out there being some connection between solar motion and biodiversity variations on the Earth, we conclude that it is difficult to give convincing positive conclusions of such a connection using current data.

astro-ph.GA↗

Do Periodicities in Extinction -- with Possible Astronomical Connections -- Survive a Revision of the Geological Timescale?

A major revision of the geological timescale was published in 2012. We re-examine our past finding of a 27 Myr periodicity in marine extinction rates by re-assigning dates to the extinction data used previously. We find that the spectral power at this period is somewhat increased, and persists at a narrow bandwidth, which supports our previous contention that the Nemesis hypothesis is untenable as an explanation for the periodicity that was first noted by Raup and Sepkoski in the 1980s. We enumerate a number of problems in a recent study comparing extinction rates with time series models.

astro-ph.EP↗

First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor

A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But, whenever it commits an error by misincorporating an incorrect nucleotide, it can switch to an exonuclease mode. In the latter mode it excises the wrong nucleotide before switching back to its polymerase mode. We develop a stochastic kinetic model of DNA replication that mimics an {\it in-vitro} experiment where a single-stranded DNA, subjected to a mechanical tension $F$, is converted to a double-stranded DNA by a single DNAP. The $F$-dependence of the average rate of replication, which depends on the rates of both polymerase and exonuclease activities of the DNAP, is in good qualitative agreement with the corresponding experimental results. We introduce 9 novel distinct {\it conditional dwell times} of a DNAP. Using the methods of first-passage times, we also derive the exact analytical expressions for the probability distributions of these conditional dwell times. The predicted $F$-dependence of these distributions are, in principle, accessible to single-molecule experiments.

q-bio.SC↗

State diagram of a three-sphere microswimmer in a channel

Geometric confinements are frequently encountered in soft matter systems and in particular significantly alter the dynamics of swimming microorganisms in viscous media. Surface-related effects on the motility of microswimmers can lead to important consequences in a large number of biological systems, such as biofilm formation, bacterial adhesion and microbial activity. On the basis of low-Reynolds-number hydrodynamics, we explore the state diagram of a three-sphere microswimmer under channel confinement in a slit geometry and fully characterize the swimming behavior and trajectories for neutral swimmers, puller- and pusher-type swimmers. While pushers always end up trapped at the channel walls, neutral swimmers and pullers may further perform a gliding motion and maintain a stable navigation along the channel. We find that the resulting dynamical system exhibits a supercritical pitchfork bifurcation in which swimming in the mid-plane becomes unstable beyond a transition channel height while two new stable limit cycles or fixed points that are symmetrically disposed with respect to the channel mid-height emerge. Additionally, we show that an accurate description of the averaged swimming velocity and rotation rate in a channel can be captured analytically using the method of hydrodynamic images, provided that the swimmer size is much smaller than the channel height.

physics.flu-dyn↗

Equilibrium kinetics of self-assembling, semi-flexible polymers

Self-assembling, semi-flexible polymers are ubiquitous in biology and technology. However, there remain conflicting accounts of the equilibrium kinetics for such an important system. Here, by focusing on a dynamical description of a minimal model in an overdamped environment, I identify the correct kinetic scheme that describes the system at equilibrium in the limits of high bonding energy and dilute concentration.

cond-mat.soft↗

Morphological instabilities of stratified epithelia: a mechanical instability in tumour formation

Interfaces between stratified epithelia and their supporting stromas commonly exhibit irregular shapes. Undulations are particularly pronounced in dysplastic tissues and typically evolve into long, finger-like protrusions in carcinomas. In a previous work (Basan et al., Phys. Rev. Lett. 106, 158101 (2011)), we demonstrated that an instability arising from viscous shear stresses caused by the constant flow due to cell turnover in the epithelium could drive this phenomenon. While interfacial tension between the two tissues as well as mechanical resistance of the stroma tend to maintain a flat interface, an instability occurs for sufficiently large viscosity, cell-division rate and thickness of the dividing region in the epithelium. Here, extensions of this work are presented, where cell division in the epithelium is coupled to the local concentration of nutrients or growth factors diffusing from the stroma. This enhances the instability by a mechanism similar to that of the Mullins-Sekerka instability in single-diffusion processes of crystal growth. We furthermore present the instability for the generalized case of a viscoelastic stroma.

physics.bio-ph↗

Radical-pair model of magnetoreception with spin-orbit coupling

The mechanism used by migratory birds to orientate themselves using the geomagnetic field is still a mystery in many species. The radical pair mechanism, in which very weak magnetic fields can influence certain types of spin-dependent chemical reactions, leading to biologically observable signals, has recently imposed itself as one of the most promising candidates for certain species. This is thanks both to its extreme sensitivity and its capacity to reproduce results from behavioral studies. Still, in order to gain a directional sensitivity, an anisotropic mechanism is needed. Recent proposals have explored the possibility that such an anisotropy is due to the electron-nucleus hyperfine interaction. In this work we explore a different possibility, in which the anisotropy is due to spin-orbit coupling between the electron spin and its angular momentum. We will show how a spin-orbit-coupling-based magnetic compass can have performances comparable with the usually-studied nuclear-hyperfine based mechanism. Our results could thus help researchers actively looking for candidate biological molecules which may host magnetoreceptive functions, both to describe magnetoreception in birds as well as to develop artificial chemical compass systems.

physics.bio-ph↗

Exclusion processes on networks as models for cytoskeletal transport

We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks spontaneously develop density heterogeneities at various scales. These heterogeneities can be regulated through a variety of multi-scale factors, such as the interplay of exclusion interactions, the non-equilibrium nature of the transport process and the network topology. We show how an effective rate approach allows to develop an understanding of the stationary state of transport processes through complex networks from the phase diagram of one single segment. For exclusion processes we rationalize that the stationary state can be classified in three qualitatively different regimes: a homogeneous phase as well as inhomogeneous network and segment phases. In particular, we present here a study of the stationary state on networks of three paradigmatic models from non-equilibrium statistical physics: the totally asymmetric simple exclusion process, the partially asymmetric simple exclusion process and the totally asymmetric simple exclusion process with Langmuir kinetics. With these models we can interpolate between equilibrium (due to bi-directional motion along a network or infinite diffusion) and out-of-equilibrium active directed motion along a network. The study of these models sheds further light on the emergence of density heterogeneities in active phenomena.

cond-mat.stat-mech↗

Inverse counting statistics for stochastic and open quantum systems: the characteristic polynomial approach

We consider stochastic and open quantum systems with a finite number of states, where a stochastic transition between two specific states is monitored by a detector. The long-time counting statistics of the observed realizations of the transition, parametrized by cumulants, is the only available information about the system. We present an analytical method for reconstructing generators of the time evolution of the system compatible with the observations. The practicality of the reconstruction method is demonstrated by the examples of a laser-driven atom and the kinetics of enzyme-catalyzed reactions. Moreover, we propose cumulant-based criteria for testing the non-classicality and non-Markovianity of the time evolution, and lower bounds for the system dimension. Our analytical results rely on the close connection between the cumulants of the counting statistics and the characteristic polynomial of the generator, which takes the role of the cumulant generating function.

quant-ph↗

Modelling the effect of myosin X motors on filopodia growth

We present a numerical simulation study of the dynamics of filopodial growth in the presence of active transport by myosin X motors. We employ both a microscopic agent-based model, which captures the stochasticity of the growth process, and a continuum mean-field theory which neglects fluctuations. We show that in the absence of motors, filopodia growth is overestimated by the continuum mean-field theory. Thus fluctuations slow down the growth, especially when the protrusions are driven by a small number (10 or less) of F-actin fibres, and when the force opposing growth (coming from membrane elasticity) is large enough. We also show that, with typical parameter values for eukaryotic cells, motors are unlikely to provide an actin transport mechanism which enhances filopodial size significantly, unless the G-actin concentration within the filopodium greatly exceeds that of the cytosol bulk. We explain these observations in terms of order-of-magnitude estimates of diffusion-induced and advection-induced growth of a bundle of Brownian ratchets.

physics.bio-ph↗

A non-linear irreversible thermodynamic perspective on organic pigment proliferation and biological evolution

The most important thermodynamic work performed by life today is the dissipation of the solar photon flux into heat through organic pigments in water. From this thermodynamic perspective, biological evolution is thus just the dispersal of organic pigments and water throughout Earth's surface, while adjusting the gases of Earth's atmosphere to allow the most intense part of the solar spectrum to penetrate the atmosphere and reach the surface to be intercepted by these pigments. The covalent bonding of atoms in organic pigments provides excited levels compatible with the energies of these photons. Internal conversion through vibrational relaxation to the ground state of these excited molecules when in water leads to rapid dissipation of the solar photons into heat, and this is the major source of entropy production on Earth. A non-linear irreversible thermodynamic analysis shows that the proliferation of organic pigments on Earth is a direct consequence of the pigments catalytic properties in dissipating the solar photon flux. A small part of the energy of the photon goes into the production of more organic pigments and supporting biomass, while most of the energy is dissipated and channeled into the hydrological cycle through the latent heat of vaporization of surface water. By dissipating the surface to atmosphere temperature gradient, the hydrological cycle further increases the entropy production of Earth. This thermodynamic perspective of solar photon dissipation by life has implications to the possibility of finding extra-terrestrial life in our solar system and the Universe.

nlin.AO↗

Molecular Dynamics Studies on 3D Structures of the Hydrophobic Region PrP(109-136)

Prion diseases caused by the conversion from a soluble normal cellular prion protein into insoluble abnormally folded infectious prions, are invariably fatal and highly infectious degenerative diseases that affect a wide variety of mammalian species. The palindrome and the Glycine-rich conserved segment in the hydrophobic region 109-136 control the conversion from normal prion protein to form into diseased prions. This paper gives detailed reviews on the 109-136 region and presents the studies of its 3D structures and structural dynamics.

q-bio.BM↗

Non-specific binding of Na$^+$ and Mg$^{2+}$ to RNA determined by force spectroscopy methods

RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters for secondary structure prediction have only been derived at 1M [Na$^+$]. Here, by mechanically unfolding and folding a 20 bp RNA hairpin using optical tweezers, we study the RNA thermodynamics and kinetics at different monovalent and mixed monovalent/Mg$^{2+}$ salt conditions. We measure the unfolding and folding rupture forces and apply Kramers theory to extract accurate information about the hairpin free energy landscape under tension at a wide range of ionic conditions. We obtain non-specific corrections for the free energy of formation of the RNA hairpin and measure how the distance of the transition state to the folded state changes with force and ionic strength. We experimentally validate the Tightly Bound Ion model and obtain values for the persistence length of ssRNA. Finally, we test the approximate rule by which the non-specific binding affinity of divalent cations at a given concentration is equivalent to that of monovalent cations taken at 100 fold that concentration for small molecular constructs.

q-bio.BM↗

Stability and Restoration phenomena in Competitive Systems

A conservation law and stability, recovering phenomena and characteristic patterns of a nonlinear dynamical system have been studied and applied to biological and ecological systems. In our previous study, we proposed a system of symmetric 2n-dimensional conserved nonlinear differential equations with external perturbations. In this paper, competitive systems described by 2-dimensional nonlinear dynamical (ND) model with external perturbations are applied to population cycles and recovering phenomena of systems from microbes to mammals. The famous 10-year cycle of population density of Canadian lynx and snowshoe hare is numerically analyzed. We find that a nonlinear dynamical system with a conservation law is stable and generates a characteristic rhythm (cycle) of population density, which we call the {\it standard rhythm} of a nonlinear dynamical system. The stability and restoration phenomena are strongly related to a conservation law and balance of a system. The {\it standard rhythm} of population density is a manifestation of the survival of the fittest to the balance of a nonlinear dynamical system.

physics.bio-ph↗