Functional mechanisms of complex enzymes involved in RNA metabolism and methodology development for drug design
Figure 1: Overview of the structure of the complex between the Miwi-PAZ domain and the 3’-end 2’-O-methylated piRNA.
Figure 2: Schematic representation of the principle of the INPHARMA NOEs.
The Carlomagno group uses NMR spectroscopy in combination with biochemical and biophysical techniques to study the structure and dynamics of biomolecular complexes.
Previous and current research
Recent advances in the NMR methodology and instrumentation have overcome challenges relating to traditional size limitations and have made NMR a very powerful technique, in particular for the investigation of highly dynamic, partially inhomogeneous molecules and complexes.The laboratory focuses on studying: i) structure-activity and dynamics-activity relationships of RNP complexes and catalytic RNAs involved in RNA processing; and ii) the interaction of small drugs with cellular receptors.
Our work aims at describing the features of RNA-protein recognition in RNP complex enzymes and at characterising the structural basis for their function. Currently, we are investigating the nucleolar multimeric box C/D RNP complex responsible for the methylation of the 2’-O-position in rRNA. 2’-O-methylation is one of the most relevant modifications of newly transcribed RNA as it occurs around functional regions of the ribosome. This suggests that 2’-O-methylation may be necessary for proper folding and structural stabilisation of rRNA in vivo. In another project, we collaborate with the Pillai group to understand the structure, function and assembly control of RNP complexes involved in the regulation of gene expression through the piRNA pathway (figure 1).
Conformational switches occur in macromolecular receptors at all cellular levels in dependence of the presence of small organic molecules, which are able to trigger or inhibit specific cellular processes. In a second area of research, we develop both computational and experimental tools to access the structure of large receptors in complex with function regulators. In particular we focus on the development of methods that allow a ligand-based reconstruction of the receptor binding pocket (figure 2). The most prominent example of our activities in this field is INPHARMA, a novel approach to structure-based drug design that does not require high-resolution structural data on the receptordrug complex. We apply our methods to study the functional mechanisms of anti-cancer drug-leads, designed as inhibitors of kinases, proteasome and membrane receptors.
Future projects and goals
We use innovative NMR techniques to access the structure of large, dynamic multi-component complexes in combination with other structural biology techniques (SANS, X-ray and EM) and biochemical data. Our philosophy is to combine high-resolution structures of single-components of the complexes with both structural descriptors of the intermolecular interactions in solution and computational methods, in order to obtain an accurate picture of the molecular basis of cellular processes.