Guido Uguzzoni edited untitled.tex  almost 9 years ago

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\textit{Oh, \section{Introduction}  The tertiary structures of a protein impose hard constraints on the amino acid sequences.  that can produce by evolutions to form function and structure related protein families.   This constraints can be detected using methods that quantify direct correlations between positions in  an empty article!} alignment of the sequences of families proteins.  Most of the proteins evolved to perform interactions with other proteins ranging from quaternary assembly to functional docking, for example in signals transduction or enzymatic interactions.  In this work we are interested in detect quaternary assembly co-evolutionary signals between different chains.  One problem that we face is that the co- occurrence of different signals, presumably that have different magnitude: intra-chains structure constraint signal can shade the inter-chains structure signals that we search.  \section{Database}  In order to perform a large-scale analysis of structural co-evolutionary signals in homo-oligomers, we collect a DataBase of alignments of protein families (from Pfam 27.0) and related PDB structures to test the co-evolutionary signals extract with DCA method.  The selection of the protein domain families are based on two main criteria :  \begin{itemize}  \item there are a relevant statistical sample of protein in the family: the number of effective belonging sequences (similarity <0.8) more than 500.   \item there is at least a experimental solved structure by X-ray diffraction of a biological assembly of homo-oligomers with a good resolution (< 3 \AN)   \end{itemize}  The quaternary structure signals are likely to depends on the chains domains architecture.   In order to be sure to include all the different biological assembly that are at the time at disposal we compare the DCA co-evolutionary signal with different PDB structures informations.  On this """ some remarks are necessary.  We collect all PDB with a biological assembly that contains homo-oligomers of the pfam domains selected.  We create a map between the alignment positions and the 3D inter-residues real positions for each pfam - PDB.  To do so we extract the real positions between residues:  within the domains on the differents chains, i.e. the \textit{intra-chains distances},   between different chains (pairing of the domains with the homo-oligomers), i.e. the \textit{inter-chains distances}.  \section{Preliminary Results}  You can get started by \textbf{double clicking} this text block and begin editing. You can also click the \textbf{Insert} button below to add new block elements. Or you can \textbf{drag and drop an image} right onto this text. Happy writing!