Martin, O. A. | bioRxiv Science

bioRxiv2018

Does protein A mirror image exist in solution? Outline of an experimental design aimed to detect it

There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on computational simulations indicating that the use of a mutant of protein A, namely 01 OH, could be used to detect the mirror image conformation in solution. Our results indicate that the native conformation of the protein A should have a pKa, for the 01 OH mutant, at r06.2, while the mirror image conformation should have a pKa close to {approx}7.3. Naturally, if all the population is in the native state for the 01 OH mutant, the pKa should be {approx}6.2, while, if all are in the mirror image state, it would be {approx}7.3, and, if it is a mixture, the pKa should be larger than 6.2, presumably in proportion to the mirror population. In addition, evidence is provided indicating the tautomeric distribution of H1O must also change between the native and mirror conformations. Although this may not be completely relevant for the purpose of determining whether the protein A mirror image exists in solution, it could provide valuable information to validate the pKa findings. We hope this proposal will foster experimental work on this problem either by direct application of our proposed experimental design or serving as inspiration and motivation for other experiments.

biophysics↗

bioRxiv2018

Nature representativeness in South American protected areas: Country contrasts and conservation priorities

BackgroundSouth America faces strong environmental transformations due to agriculture and infrastructure expansion and due to demographic growth, demanding immediate action to preserve natural assets by means of the deployment of protected areas. Currently, 7.1% of the (sub)continent is under strict conservation categories (I to IV, IUCN), but the spatial distribution of these 1.3 x 106 km2 is poorly understood. We evaluate protected area representativeness, map conservation priorities and assess demographic, productive or geopolitical causes of the existing protection spatial patterns using a random forest method.\n\nMethodsWe characterized representativeness by two dimensions: the extent and the equality of protection. The first refers to the fraction of a territory under protection, while the second refers to the spatial distribution of this protection along natural conditions. We characterized natural conditions by 113 biogeographical units (specifically, ecoregions) and a series of limited and significant climatic, topographic and edaphic traits. We analyzed representativeness every ten years since 1960 at national and continental levels. In the physical approach, histograms allowed us to map the degree of conservation priorities. Finally, we ranked the importance of different productive or geopolitical variables driving the observed distributions with a random forest technique.\n\nResultsRepresentativeness was variable across countries in spite of its priority in conservation agendas. Brazil, Peru and Argentina underrepresented a significant fraction of their natural diversity, while Bolivia and Venezuela protected their natural diversity equitably under extensive conservation networks. As protected networks increased their extent, so did their equality across countries and within them through time. Mapping revealed as top continental priorities southern temperate, subhumid and fertile lowland environments, and other country- specific needs (e.g., hot, humid plains of Venezuela). Protection extent was generally driven by a low population density and isolation, while other variables -like distance to frontiers, were relevant only locally (e.g., in Argentina).\n\nDiscussionOur description of the spatial distribution can help societies and governments to improve the allocation of conservation efforts, being top continental priorities the southern temperate, subhumid and fertile lowland environments. We identify the main limitations that future conservation efforts will face, as protection was generally driven by the opportunities provided by low population density and isolation. From a methodological perspective, the complementary physical approach reveals new properties of protection and provides tools to explore nature representativeness at different spatial, temporal and conceptual levels, complementing the traditional ones based on biodiversity or biogeographical attributes.

ecology↗