arXiv subjects

Gergely J. Szollosi

Publications and source records attributed to Gergely J. Szollosi.

5 recordsLinked to original sources

arXiv2008

The relevance of neck linker docking in the motility of kinesin

Conventional kinesin is a motor protein, which is able to walk along a microtubule processively. The exact mechanism of the stepping motion and force generation of kinesin is still far from clear. In this paper we argue that neck linker docking is a crucial element of this mechanism, without which the experimentally observed dwell times of the steps could not be explained under a wide range of loading forces. We also show that the experimental data impose very strict constraints on the lengths of both the neck linker and its docking section, which are compatible with the known structure of kinesin.

physics.bio-ph↗

arXiv2008

The Effect of Recombination on the Neutral Evolution of Genetic Robustness

Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable, however, it has become apparent that the context dependent effect of mutations and the many-to-one nature inherent in these genotype-phenotype maps can have fundamental evolutionary consequences. It has previously been demonstrated that populations of genotypes evolving on the neutral networks corresponding to all genotypes with the same secondary structure only through neutral mutations can evolve mutational robustness [Nimwegen {\it et al.} Neutral evolution of mutational robustness, 1999 PNAS], by concentrating the population on regions of high neutrality. Introducing recombination we demonstrate, through numerically calculating the stationary distribution of an infinite population on ensembles of random neutral networks that mutational robustness is significantly enhanced and further that the magnitude of this enhancement is sensitive to details of the neutral network topology. Through the simulation of finite populations of genotypes evolving on random neutral networks and a scaled down microRNA neutral network, we show that even in finite populations recombination will still act to focus the population on regions of locally high neutrality.

q-bio.PE↗

arXiv2006

Reversible mesoscopic model of protein adsorption: From equilibrium to dynamics

We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a non-trivial (non- monotonic) dependence of the experimentally observable properties of the adsorbed layer (such as the surface density and surface coverage) on these parameters. We subsequently proceed to develop a dynamical model consistent with the equilibrium description, which qualitatively reproduces known experimental phenomena and offers a promising way of studying the exchange of the adsorbed proteins by the proteins of the solution.

cond-mat.soft↗

arXiv2006

Phase transition in the collective migration of tissue cells: experiment and model

We have recorded the swarming-like collective migration of a large number of keratocytes (tissue cells obtained from the scales of goldfish) using long-term videomicroscopy. By increasing the overall density of the migrating cells, we have been able to demonstrate experimentally a kinetic phase transition from a disordered into an ordered state. Near the critical density a complex picture emerges with interacting clusters of cells moving in groups. Motivated by these experiments we have constructed a flocking model that exhibits a continuous transition to the ordered phase, while assuming only short-range interactions and no explicit information about the knowledge of the directions of motion of neighbors. Placing cells in microfabricated arenas we found spectacular whirling behavior which we could also reproduce in simulations.

q-bio.CB↗

arXiv2006

The maintenance of sex in bacteria is ensured by its potential to reload genes

Why sex is maintained in nature is a fundamental question in biology. Natural genetic transformation (NGT) is a sexual process by which bacteria actively take up exogenous DNA and use it to replace homologous chromosomal sequences. As it has been demonstrated, the role of NGT in repairing deleterious mutations under constant selection is insufficient for its survival, and the lack of other viable explanations have left no alternative except that DNA uptake provides nucleotides for food. Here we develop a novel simulation approach for the long-term dynamics of genome organization (involving the loss and acquisition of genes) in a bacterial species consisting of a large number of spatially distinct populations subject to independently fluctuating ecological conditions. Our results show that in the presence of weak inter-population migration NGT is able to subsist as a mechanism to reload locally lost, intermittently selected genes from the collective gene pool of the species through DNA uptake from migrants. Reloading genes and combining them with those in locally adapted genomes allow individual cells to re-adapt faster to environmental changes. The machinery of transformation survives under a wide range of model parameters readily encompassing real-world biological conditions. These findings imply that the primary role of NGT is not to serve the cell with food, but to provide homologous sequences for restoring genes that have disappeared from or become degraded in the local population.

q-bio.PE↗