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Register a new userA nonequilibrium strategy for fast target search on the genome
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Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on chromophoresis, the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colours (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled---a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform unidirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and dive deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for the location of DNA lesions.
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Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.
Filopodia are long, finger-like membrane tubes supported by cytoskeletal filaments. Their shape is determined by the stiffness of the actin filament bundles found inside them and by the interplay between the surface tension and bending rigidity of the membrane. Although one might expect the Euler buckling instability to limit the length of filopodia, we show through simple energetic considerations that this is in general not the case. By further analyzing the statics of filaments inside membrane tubes, and through computer simulations that capture membrane and filament fluctuations, we show under which conditions filopodia of arbitrary lengths are stable. We discuss several in vitro experiments where this kind of stability has already been observed. Furthermore, we predict that the filaments in long, stable filopodia adopt a helical shape.
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons against the concentration gradient across the membrane. ATPase is composed of two rotary motors, F0 and F1, which generate the opposing rotation and compete for control of their shared central gamma-shaft. Here we present a self-consistent physical model of the F1 motor as a simplified two-state Brownian ratchet based on the asymmetry of torsional elastic energy of the coiled-coil gamma-shaft. This stochastic model unifies the physical description of linear and rotary motors and explains the stepped unidirectional rotation of the $gamma$-shaft, in agreement with the `binding-change ideas of Boyer. Substituting the model parameters, all independently known from recent experiments, our model quantitatively reproduces the ATPase operation, e.g. the `no-load angular velocity is ca. 400~rad/s anticlockwise at 4 mM ATP, in close agreement with experiment. Increasing the pmf torque exerted by F0 can slow, stop and overcome the torque generated by F1, switching from ATP hydrolysis to synthesis at a very low value of `stall torque. We discuss the matters of the motor efficiency, which is very low if calculated from the useful mechanical work it produces - but is quite high when the `useful outcome is measured in the number of H+ pushed against the chemical gradient in the F1 ATP-driven operation.
Actin cytoskeletal protrusions in crawling cells, or lamellipodia, exhibit various morphological properties such as two characteristic peaks in the distribution of filament orientation with respect to the leading edge. To understand these properties, using the dendritic nucleation model as a basis for cytoskeletal restructuring, a kinetic-population model with orientational-dependent branching (birth) and capping (death) is constructed and analyzed. Optimizing for growth yields a relation between the branch angle and filament orientation that explains the two characteristic peaks. The model also exhibits a subdominant population that allows for more accurate modeling of recent measurements of filamentous actin density along the leading edge of lamellipodia in keratocytes. Finally, we explore the relationship between orientational and spatial organization of filamentous actin in lamellipodia and address recent observations of a prevalence of overlapping filaments to branched filaments---a finding that is claimed to be in contradiction with the dendritic nucleation model.
Generation of mechanical oscillation is ubiquitous to wide variety of intracellular processes. We show that catchbonding behaviour of motor proteins provides a generic mechanism of generating spontaneous oscillations in motor-cytoskeletal filament complexes. We obtain the phase diagram to characterize how this novel catch bond mediated mechanism can give rise to bistability and sustained limit cycle oscillations and results in very distinctive stability behaviour, including bistable and non-linearly stabilised in motor-microtubule complexes in biologically relevant regimes. Hitherto, it was thought that the primary functional role of the biological catchbond was to improve surface adhesion of bacteria and cell when subjected to external forces or flow field. Instead our theoretical study shows that the imprint of this catch bond mediated physical mechanism would have ramifications for whole gamut of intracellular processes ranging from oscillations in mitotic spindle oscillations to activity in muscle fibres.
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