Rational design of a calcium-binding protein

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.     

Fish and Plankton Interplay Determines Both Plankton Spatio-Temporal Pattern Formation and Fish School Walks: A Theoretical Study

The fascinating variety of spatio-temporal patterns in aquatic ecosystems and the understanding of the governing mechanisms of its generation and further dynamics requires ongoing experimental and theoretical studies. After introducing a certain hybrid mathematical model, this paper makes an attempt to demonstrate that the predation of a mobile planktivorous fish school on zooplankton can initiate both plankton pattern formation and fish school walks. Nonlinear interactions in the model of a fish-zooplankton-algae trophic chain prevent a simple intuitive understanding of the system dynamics. It is shown that the fish school predation and motion can give rise to plankton spiral waves. In the course of the spiral wave formation, the amplitudes of the spatially averaged plankton density oscillations are decreasing dramatically. Fish school walks are shown to resemble a fractional Brownian motions with a Hurst exponent depending on the fish predation rate.     

Oscillations vs. chaotic waves: Attractor selection in bistable stochastic reaction–diffusion systems

In bistable systems, the long-term behavior of solutions depends on the location of the initial conditions. In a deterministic setting, where the initial condition is kept fixed in one particular basin of attraction, repeated numerical simulations will always lead to the same long-term behavior. The other possible asymptotic solution type will never be observed. This clear distinction does not hold anymore if the system is forced by random fluctuations. In this case, both asymptotic solutions can be attained, and the relative frequency of different long-term behaviors observed in many repeated simulation runs will follow a certain probability distribution. We present a simple reaction–diffusion model of spatial predator–prey interaction, where depending on the initial spatial distribution of the two populations either spatially homogeneous or spatiotemporal irregular oscillations may be observed. We show by repeated stochastic simulations that, when starting in the basin of attraction of the spatiotemporal irregular solution, in the randomly forced system the probability to observe spatially homogeneous oscillations instead of spatiotemporally irregular oscillations follows a non-trivial bimodal distribution.