Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.

Accessibility instruments for planning practice: bridging the gap between academic research and decision-making.

One of the core objectives of urban planning practice is to provide spatial equity in terms of opportunities and use of public space and facilities. Accessibility is the element that serves this purpose as a concept linking the reciprocal relationship between transport and land use, thus shaping individual potential mobility to reach the desired destinations. Accessibility concepts are increasingly acknowledged as fundamental to understand the functioning of cities and urban regions. Indeed, by introducing them in planning practice, better solutions can be achieved in terms of spatial equity. The COST Action TU1002 "Accessibility instruments for planning practice" was specifically designed to address the gap between scientific research in measuring and modelling accessibility, and the current use of indicators of accessibility in urban planning practice. This paper shows the full process of introducing an easily understandable measure of accessibility to planning practitioners in Madrid, which is one of the case studies of the above-mentioned COST action. Changes in accessibility after the opening of a new metro line using contour measures were analyzed and then presented to a selection of urban planners and practitioners in Madrid as part of a workshop to evaluate the usefulness of this tool for planning practice. Isochrone maps were confirmed as an effective tool, as their utility can be supplemented by other indicators, and being GIS-based, it can be easily computed (when compared with transport models) and integrated with other datasets.