The effect of reactions on the formation and readout of the gradient of Bicoid

During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in {\it Drosophila melanogaster} embryos is well documented and studied. There are still controversies as to whether {\it SDD} models in which Bcd is {\it Synthesized} at one end, then {\it Diffuses} and is {\it Degraded} can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. In this work we analyze an {\it SDID} model that includes the {\it Interaction} of Bcd with binding sites. Using previously determined biophysical parameters we find that this model can explain the gradient formation within the experimentally observed time. Analyzing the differences between the free and bound Bcd distributions we observe that the latter spans over a longer lengthscale. We conclude that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the degree of cooperativity that explains the distribution of the protein Hunchback whose production is regulated by Bcd.


Similar Publications

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3. Read More


We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range $f \approx$ 20-80 THz, with a maximum transfer percentage close to 1. Read More


A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we formulated the physical model and developed a numerical fluid dynamics integrator. In this study, we incorporated the fluid dynamics integrator with the Amber simulation engine to conduct atomistic simulations of biomolecules. At this stage of the development, only nonelectrostatic interactions, i. Read More


We investigate the effective two- and three-body interactions mediated between non-active colloidal inclusions immersed in an active bath of chiral or non-chiral self-propelled particles (swimmers). We perform Brownian Dynamics simulations within a standard model comprising hard inclusions and swimmers in two spatial dimensions. In the absence of chirality, we corroborate previous findings by showing that strong, repulsive, two-body forces of medium range (up to surface separations of a few swimmer radii) emerge between colloidal inclusions in the active bath. Read More


We evaluate the practical performance of the zero-multiple summation method (ZMM), a method for approximately calculating electrostatic interactions in molecular dynamics simulations. The performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME). Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is found to be comparable to or better than that of the SPME. Read More


Quantitative nuclear magnetic resonance imaging (MRI) shifts more and more into the focus of clinical research. Especially determination of relaxation times without/and with contrast agents becomes the foundation of tissue characterization, e.g. Read More


Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft matter behaviour, active biological matter lives far from thermal equilibrium, and typically covers multiple length scales from the nanometre level of single molecules up several orders of magnitude to longer length scales in emergent structures of cells, tissues and organisms. Biological molecules are often characterized by an underlying instability, in that multiple metastable free energy states exist which are separated by energy levels of typically just a few multiples of the thermal energy scale of kBT, where kB is the Boltzmann constant and T the absolute temperature, implying complex, dynamic inter-conversion kinetics across this bumpy free energy landscape in the relatively hot, wet environment of real, living biological matter. Read More


DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with electromagnetic fields (beyond the usual dielectric response and damage by ionizing gamma radiations). Extensive investigations were carried out with both prokaryotic and eukaryotic purified DNA samples utilizing some of the most sensitive and precision instrumentation and methods available, while scanning the whole spectral region from 1Hz to 100KHz (in the low frequencies) and all the way to the high-frequency region of 100MHz (including investigations on the effects of 100MHz high-frequency fields as well as 2.4GHz microwave fields on the DNA). Read More


Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Read More


Active dynamic processes of cells are largely driven by the cytoskeleton, a complex and adaptable semiflexible polymer network, motorized by mechanoenzymes. Small dimensions, confined geome- tries and hierarchical structures make it challenging to probe dynamics and mechanical response of such networks. Embedded semiflexible probe polymers can serve as non-perturbing multi-scale probes to detect force distributions in active polymer networks. Read More