Abstract: The information carried by the aminoacidic sequence can be used by different bioinformatic methods, in order to predict the 3D structure of a protein or its domains. The tools for sequence alignment permit to individuate homologous regions among proteins, and this represent the basis for a homology modeling procedure. The algorithms of secondary structure prediction use chemical, physical and statistical parameters to recognize if a region of sequence could assume a specific secondary structure. Fold recognition servers can test if a protein sequence is compatible with one of the known folds in the PDB. If these different tools give rise to homogeneous responses, it is possible to predict with good reliability the fold of a protein or single domains of unknown structure. hSos1 is a multidomain protein involved in the activation of the Ras signaling by catalyzing guanine nucleotide exchange on Ras. The Ras-GEF domain of hSos1 (Sos-Cat) is flanked by amino- and carboxyl-terminal regions, which are able to inhibit hSos1 activity towards Ras. To investigate the structural determinants of this inhibition, it is necessary to know the structural features of the involved domains. The carboxyl terminus of hSos1 contains a proline rich domain with consensus sequences for binding to the SH3 domains, while the amino-terminal region of hSos1 includes three domains: Histone domain, Dbl Homology domain (DH) and Pleckstrin homology domain (PH). The Histone domain is involved in the inhibition of the Ras-GEF activity of hSos1. It can also bind the PH domain, while it cannot interact with the DH domain. The DH domain is implicated in the inhibition of the Ras-GEF activity of hSos1, possibly through direct interaction with Sos-Cat. The PH domain is able to interact with the DH domain; the crystal structure of the PH-DH complex is available. We have focused on the intra-molecular interactions that occur among these domains in the activation/inhibition of hSos1 by means of computational tools, like the low-resolution protein-protein docking. The essence of the procedure is the reduction of protein structures to digitized images on a three-dimensional grid. The structural elements smaller than the step of the grid (e.g., atom-size) are not present in the docking. This feature permits to reduce the negative effect of structural changes upon complex formation on docking calculation.

Abstract: Histone folds are structural elements that are able to form dimers by means of tight interactions between hydrophobic surfaces. Normally, a histone fold is composed by a long alpha-helix flanked by two or three shorter helices. In the nucleosome core particle, two pairs of H2a-H2b and H3-H4 histone heterodimers assemble together, giving rise to a disk-like octamer upon which DNA rolls up. The publication of the X-ray structure of the prokaryotic histone from Methanopyrus kandleri highlighted a novel protein fold, which is originated by the assembly of two consecutive histone folds included in the same peptide chain. More recently, the publication of the X-ray structure of the amino-terminal domain of hSos1 showed that also this protein module assumes a similar fold, dubbed the histone pseudodimer and here also referred to as “double histone fold”. In fact, the evolutionary relationship between the H2a histone and the domain spanning the protein sequence 96-190 of hSos1 had been already disclosed, due to high sequence similarity between the two domains. However, the first histone-like domain of hSos1, spanning the protein portion 6-95, does not show evident sequence similarity with histones (Sondermann et al, 2003). Moreover, it is unknown whether the double histone fold can be found in other protein families. In view of this, we initiated an in silico study aiming at the identification of other proteins characterized by a sequence that is compatible with the double histone fold.