Annual Report of Activities CNC 2011 - Center for Neuroscience and ...

42mutations in several protein domains. IV. Ibercivis -­‐ A volunteer computing platform for the Iberian Peninsula Throughout 2011 efforts were made in increasing the general public awareness about the project and the integration of new Portuguese research teams. Main achievements: The main results achieved by the Structural and Computational Biology group are presented below: I. Characterization of the molecular mechanisms of amyloid formation by the protein transthyretin (TTR) Ia. Refolding kinetics of TTR Our results demonstrate that the in vitro refolding mechanisms of WT-­‐ and V30M-­‐TTR are similar, involving a dimeric intermediate. However, there are large differences in the refolding rate constants for the two variants, specially at nearly native conditions. Interestingly, tetramer formation occurs at a much slower rate in the amyloidogenic variant V30M-­‐TTR than in WT-­‐TTR, resulting in higher susceptibility for aggregation and amyloid formation instead of spontaneous refolding. Ib. Kinetics of the Early Stages of TTR Oligomerization The initial steps of TTR oligomerization can be described by a three-­‐state process. Our results suggest that prior to fibril formation, there is the accumulation of an oligomeric intermediate state. After the initial conformational changes, TTR aggregation proceeds via a nucleation-­and-­‐growth mechanism. II. Rational design of inhibitors of amyloid formation IIa. Characterization of Structural and Energetic Properties of known TTR binders. From ITC experiments it was possible to characterize the binding properties (association constants and cooperativity effects) and the thermodynamic profiles of the binding between WT-­‐TTR and four diferent carefully selected ligands. The average total interaction energy computed at structural level follows the same trend of the ΔG values determined by ITC. The computational study also suggests that the trend in ΔG values could be primarily determined by shape complementarity (translated into vdW interactions). IIb. Relational Learning Approach to Structure-­‐Activity Relationships in Drug Design Toxicity Studies. iLogCHEM, an interactive tool for chemo-­‐informatics based on ILP, was developed. This system is designed to allow search and manipulation of drug patterns. The input is given as a standard formatted description of the molecules. The output is provided visually, or as text files in standard chemical file formats. III. Structural modelling of viral proteins and rational design of new anti-­‐viral agents IIIa. Modeling of the Toll-­‐like receptor 3 and a putative Toll-­‐like receptor 3 antagonist encoded by the African swine fever virus (ASFV). Using homology modeling and other structure prediction simulation protocols, we proposed (a) a model for the so far experimentally unsolved TLR3-­‐TIR structure, assembled within the context of the overall TLR3-­‐dsRNA recognition complex, and (b) a structural model for the intracellular extension of the pI329L viral protein that reinforces the idea that the viral protein is a TLR3 antagonist. The proposed computational models are consistent with the available experimental data. IIIb. Identification and characterization of conserved features among different strains/serotypes of selected influenza A proteins. ClustalW2 was employed to analyse the sequence alignments of sets of selected viral proteins. The set of clusters obtained identifies conserved sequence regions. These results are currently being interpreted in conjunction with additional relevant epidemiologic information on the disease. IV. Ibercivis -­‐ A volunteer computing platform for the Iberian Peninsula In July 2011, a new Portuguese project, named Soluvel, joined Ibercivis and started benefiting from the computational power made available by thousands of volunteer citizens all over the world.