The two-angle model and the phase diagram for Chromatin

We have studied the phase diagram for chromatin within the framework of the two-angle model. Rather than improving existing models with finer details our main focus of the work is getting mathematically rigorous results on the structure, especially on the excluded volume effects and the effects on the energy due to the long-range forces and their screening. Thus we present a phase diagram for the allowed conformations and the Coulomb energies

Transmissionselektronenmikroskopische Darstellung von Amelogenin im mineralisierenden Schmelz des Rattenfrontzahnes

Durch Immunohistochemie von zehn Rattenzähnen konnten signifikante Unterschiede in der Anzahl der Amelogenine in drei Phasen (sekretorische Phase, frühe Schmelzreifung, fortgeschrittene Schmelzreifung) der Amelogenese gefunden werden. In den Untersuchungen fanden sich Ansammlungen von Amelogeninen, die als Nanospheren bezeichnet wurden. Als Nanosphere wird eine Ansammlung von mindestens drei Amelogeninen im Abstand von 100nm definiert. 3 Zählungen über das TEM wurden durchgeführt: 1. Anzahl der Amelogenine pro µm2 am Tomeschen Fortsatz während der Entwicklung. 2. Anzahl der Nanospheren aus Amelogeninen pro µm2 am Tomeschen Fortsatz während der Entwicklung. 3. Anzahl der Amelogenine pro Nanosphere am Tomeschen Fortsatz während der Entwicklung

Approaching equilibrium and the distribution of clusters

We investigate the approach to stable and metastable equilibrium in Ising models using a cluster representation. The distribution of nucleation times is determined using the Metropolis algorithm and the corresponding $\phi^{4}$ model using Langevin dynamics. We find that the nucleation rate is suppressed at early times even after global variables such as the magnetization and energy have apparently reached their time independent values. The mean number of clusters whose size is comparable to the size of the nucleating droplet becomes time independent at about the same time that the nucleation rate reaches its constant value. We also find subtle structural differences between the nucleating droplets formed before and after apparent metastable equilibrium has been established.Comment: 22 pages, 16 figure

De novo design of a reversible phosphorylation-dependent switch for membrane targeting

Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a 'cargo' molecule reversibly to a permanent membrane 'anchor'; and (ii) creating a 'membrane-avidity switch' that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells. The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.The authors thank the Biochemistry Core Facility of the Max Planck Institute of Biochemistry for LC-MS and CD spectroscopy services, Stefan Pettera and Stephan Uebel for assistance with peptide synthesis and analytical HPLC, and Katharina Nakel for assistance with cloning

Dynamic and static properties of the invaded cluster algorithm

Simulations of the two-dimensional Ising and 3-state Potts models at their critical points are performed using the invaded cluster (IC) algorithm. It is argued that observables measured on a sub-lattice of size l should exhibit a crossover to Swendsen-Wang (SW) behavior for l sufficiently less than the lattice size L, and a scaling form is proposed to describe the crossover phenomenon. It is found that the energy autocorrelation time tau(l,L) for an l*l sub-lattice attains a maximum in the crossover region, and a dynamic exponent z for the IC algorithm is defined according to tau_max ~ L^z. Simulation results for the 3-state model yield z=.346(.002) which is smaller than values of the dynamic exponent found for the SW and Wolff algorithms and also less than the Li-Sokal bound. The results are less conclusive for the Ising model, but it appears that z<.21 and possibly that tau_max ~ log L so that z=0 -- similar to previous results for the SW and Wolff algorithms.Comment: 21 pages with 12 figure

The instability of Alexander-McTague crystals and its implication for nucleation

We show that the argument of Alexander and McTague, that the bcc crystalline structure is favored in those crystallization processes where the first order character is not too pronounced, is not correct. We find that any solution that satisfies the Alexander-McTague condition is not stable. We investigate the implication of this result for nucleation near the pseudo- spinodal in near-meanfield systems.Comment: 20 pages, 0 figures, submitted to Physical Review

Nucleation in Systems with Elastic Forces

Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with long-range elastic forces the description of the nucleation process can be quite subtle due to the presence of bulk/interface elastic compatibility constraints. We analyze the nucleation process in a simple 2d model with elastic forces and show that the nucleation process generates critical droplets with a different structure than the stable phase. This has implications for nucleation in many crystal-crystal transitions and the structure of the final state

Functional expression of electrogenic sodium bicarbonate cotransporter 1 (NBCe1) in mouse cortical astrocytes is dependent on S255-257 and regulated by mTOR

The electrogenic sodium bicarbonate cotransporter 1, NBCe1 (SLC4A4), is the major bicarbonate transporter expressed in astrocytes. It is highly sensitive for bicarbonate and the main regulator of intracellular, extracellular, and synaptic pH, thereby modulating neuronal excitability. However, despite these essential functions, the molecular mechanisms underlying NBCe1-mediated astrocytic response to extracellular pH changes are mostly unknown. Using primary mouse cortical astrocyte cultures, we investigated the effect of long-term extracellular metabolic alkalosis on regulation of NBCe1 and elucidated the underlying molecular mechanisms by immunoblotting, biotinylation of surface proteins, intracellular H+ recording using the H+ -sensitive dye 2',7'-bis-(carboxyethyl)-5-(and-6)-carboxyfluorescein, and phosphoproteomic analysis. The results showed significant downregulation of NBCe1 activity following metabolic alkalosis without influencing protein abundance or surface expression of NBCe1. During alkalosis, the rate of intracellular H+ changes upon challenging NBCe1 was decreased in wild-type astrocytes, but not in cortical astrocytes from NBCe1-deficient mice. Alkalosis-induced decrease of NBCe1 activity was rescued after activation of mTOR signaling. Moreover, mass spectrometry revealed constitutively phosphorylated S255-257 and mutational analysis uncovered these residues being crucial for NBCe1 transport activity. Our results demonstrate a novel mTOR-regulated mechanism by which NBCe1 functional expression is regulated. Such mechanism likely applies not only for NBCe1 in astrocytes, but in epithelial cells as well

Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment

We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous diffusion at intermediate times. The effective exponents for square distance versus time usually are below one at these intermediate times, but can be also larger than one for high barrier concentrations. Thus we observe sub- as well as super-diffusion in a crowded environment.Comment: 8 pages including 4 figure