We have shown the power of network modelling for the task of unraveling properties of complex biological systems. First, we built a highly reliable manual model of signalling in Arabidopsis, which we then extended into an Arabidopsis comprehensive knowledge network, presenting a most complete compendium of known knowledge at the time. Knowledge within the network was translated to crop species, potato. The data generated in the project has been fed into the model. By application of graph theory approaches on the networks (shortest paths; modules) we identified a novel connection between two important pathways immune signaling pathways (ethylene and salicylic acid). Functional confirmation of the connection affirmed our belief in the strength of network modelling for analyses of complex systems. The findings were published in one of the most renowned journals in the field, Plant Physiology.
Physical and functional interactions between molecules in living systems are central to all biological processes. Identification of protein complexes therefore is becoming increasingly important to gain a molecular understanding of cells and organisms. Several powerful methodologies and techniques have been developed to study molecular interactions and thus help elucidate their nature and role in biology as well as potential ways how to interfere with them. All different techniques used in these studies have their strengths and weaknesses and since they are mostly employed in in vitro conditions, a single approach can hardly accurately reproduce interactions that happen under physiological conditions. However, complementary usage of as many as possible available techniques can lead to relatively realistic picture of the biological process. Here we describe several proteomic, biophysical and structural tools that help us understand the nature and mechanism of these interactions
Using cryo-electron microscopy, we determined the near-atomic structure of PVY’s flexuous virions, revealing a novel lumenal interplay between extended C-terminal regions of the coat protein units and viral RNA. RNA - coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein’s N- and C-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, high modularity of PVY virus-like particles suggests a new molecular scaffold for nanobiotechnological applications.