Mining the active proteome in plant science and biotechnology.

Protein activity is essential functional information, yet difficult to predict from transcript or protein data. Activity-based protein profiling (ABPP) displays active proteins in proteomes using small molecule probes that irreversibly label proteins in their active state. Here, we review proof-of-concept ABPP studies in plant science. These studies displayed activities of dozens of plant cysteine proteases, lipases, methylesterases and the proteasome. ABPP in plants revealed differential protein activities in development and immunity and uncovered striking selectivity of pathogen-derived inhibitors and unexpected targets of commercial inhibitors. The unique, high-content information of ABPP and the robustness and simplicity of the assays will make ABPP a powerful tool in future plant science and biotechnology

Large-Scale B3LYP Simulations of Ibuprofen Adsorbed in MCM-41 Mesoporous Silica as Drug Delivery System

The atomistic details of the interaction between ibuprofen (one of the most common nonsteroidal anti-inflammatory drugs) and a realistic model of MCM-41 (one of the most studied mesoporous silica materials for drug delivery) were elucidated by quantum mechanical modeling inclusive of London forces. Calculations are based on periodic density functional theory adopting all-electron Gaussian-type basis functions of polarized double-?? quality and the B3LYP hybrid functional. By docking the drug on different sites of the MCM-41 pore walls, we have sampled different local features of the potential energy surface of the drug???silica system, both for low and high loadings (one and seven drug molecules per unit cell, respectively). For all cases, ibuprofen adsorption in MCM-41 is exothermic (average ??H = ???99 kJ·mol???1) and exergonic (average ??G = ???33 kJ·mol???1), exclusively when London interactions are taken into account due to their dominant role in dictating all features of this system. The comparison between simulated IR and NMR spectra suggests that static disorder of the adsorbed ibuprofen due to surface sites heterogeneity can also be invoked together with the current interpretation based on a dynamic behavior of the adsorbed ibuprofen to interpret the spectral features. Analysis of H-bond patterns exhibited by the drug interacting with the MCM-41 surface silanol (SiOH) groups revealed the importance of cooperativity in the H-bond strength. The present work shows that large-scale all-electron full quantum mechanical simulations employing accurate hybrid functionals can soon become competitive over modeling studies based on molecular mechanics methods, both in terms of superior accuracy and absence of the problematic parametrization, due to organic/inorganic interface

Genetics of Whole Plant Morphology and Architecture

Plant architectural features directly impact plant fitness and adaptation, and traits related to plant morphology and development represent important targets for crop breeding. Decades of mutagenesis research have provided a wealth of mutant resources, making barley (Hordeum vulgare L.) an interesting model for genetic dissection of grass morphology and architecture. Recent advances in genomics have propelled the identification of barley genes controlling different aspects of shoot and root development. In addition to gene discovery, it is important to understand the interplay between different developmental processes in order to support breeding of improved ideotypes for sustainable barley production under different climatic conditions. The purpose of the present chapter is to: (i) provide an overview of the morphology and development of shoot and root structures in barley; (ii) discuss novel insights into the genetic, molecular and hormonal mechanisms regulating root and shoot development and architecture; and (iii) highlight the genetic and physiological interactions among organs and traits with special focus on correlations between leaf and tiller development, flowering and tillering, as well as row-type and tillering