Refined NMR structure of α-sarcin by 15N-1H residual dipolar couplings

15N–1H residual dipolar couplings (RDC) have been used as additional restraints to refine the solution structure of the ribotoxin α-sarcin. The RDC values were obtained by partial alignment of α-sarcin in the binary mixture of n-dodecyl hexa(ethylene glycol)/hexanol. A total of 131 RDCs were measured and 106 were introduced in the final steps of the calculation protocol following the main calculation based on nuclear Overhauser enhancements and torsion angle restraints. A homogeneous family of 81 conformers was obtained. The resulting average pairwise root-mean-square deviation corresponding to the superposition of the 20 best structures is 0.69±0.12 Å for the backbone and 1.29±0.14 Å for all heavy atoms. The new structural features derived from the refined structure, compared with the non-refined structure of α-sarcin, consist of new hydrogen bonds and a better definition of the backbone conformation. In particular, the loop segment spanning Gly 60 to Lys 70 shows a single conformation, corresponding to the most populated family of conformers observed in the unrefined structure. The information derived from the analysis of the refined structure and the comparison with the homologous protein restrictocin could help in establishing further structure–function relationships concerning α-sarcin which can be reasonably extrapolated to other members of the ribotoxin family

Evolutionary Optimization with Dynamic Fidelity Computational Models

In this paper, we propose an evolutionary framework for model fidelity control that decides, at runtime, the appropriate fidelity level of the computational model, which is deemed to be computationally less expensive, to be used in place of the exact analysis code as the search progresses. Empirical study on an aerodynamic airfoil design problem based on a Memetic Algorithm with Dynamic Fidelity Model (MA-DFM) demonstrates that improved quality solution and efficiency are obtained over existing evolutionary schemes. © 2008 Springer-Verlag Berlin Heidelberg

Combined effects of marine heatwaves and reduced light on the physiology and growth of the surfgrass Phyllospadix torreyi from Baja California, Mexico

This study aimed to elucidate for the first time the combined effects of marine heatwaves (MHWs) and light limitation simulated in mesocosm on critical physiological descriptors of the surfgrass Phyllospadix torreyi, which constitutes highly productive meadows along the intertidal and subtidal rocky shores of the Pacific coast of North America. Our results revealed that short-term exposure (~7 days) to extreme thermal anomalies of + 9 ◦C had positive effects on the photosynthetic capacities of P. torreyi, as indicated by increments in maximum photosynthetic rates, photosynthetic efficiency (α), maximum electron transport rate, and effective quantum yield. Despite that its photosynthetic performance was enhanced, exposure to warming caused a decrease in its internal carbon reserves (i.e. energy status), likely as a consequence of carbon mobilization/utilization to activate heatstress responses. Plants exposed to light limitation generally exhibited an increase in α and/or a decrease in respiration, which ultimately allowed for a reduction in plant compensation irradiance. The combination of low light and seawater warming resulted in a decrease in non-structural carbohydrates content, daily net-productivity, and leaf growth rates. Gross photosynthetic rates at control saturating irradiance exhibited higher activation energy and, thus, greater responsiveness to seawater warming than plants kept under light limitation. While our results indicated that unusual warming events might favor the photosynthetic performance of P. torreyi, combining this condition with a drastic light reduction can lead to internal carbon depletion and potentially compromise plant survival in the long term.1,51