28 KB227 KB26 KB199820252011Janežič, DušankaKonc, JanezPenca, MatejTrykowska Konc, Joannaštevilka:3letnik:58str. 396-401ISSN:1318-0207COBISSID:4787738URN:URN:NBN:SI:doc-XPGGO1HBenSlovenian Chemical SocietySlovensko kemijsko društvoActa chimica slovenicabinding-sitesbiokemijadockingpredictionprobisprotein structureproteiniproteinsko sidranjestructural similaritystrukturaBinding-sites prediction assisting protein-protein docking|Most biological actions of proteins, including their ability to interact with one another, involve some specific parts of their three-dimensional structure,called binding sites. These have evolved for their ability to bind other molecules effectively and are often conserved in different proteins. Identifying protein-protein binding sites in a protein that is known to interact with other proteins can provide important clues to the function of the protein and can also be used in proteinprotein docking studies to reduce the search space explored by docking algorithms. We have developed an algorithm for structural similarity search in a database of non-redundant protein structures to find conserved binding regions on proteins involved in protein-protein interactions. We have used this algorithm to find conserved regions on a protein surface. The structurally conserved residues found were labeled as a protein-protein binding site, which allowed us to tune the AutoDock docking algorithm to predict the native protein complex structure from unbound protein structures. The conservation of protein structures that correctly predicted protein-protein binding site was used in AutoDock program to improve protein-protein docking. A web application based on our method is available at http://probis.cmm.ki.siBiološka funkcija proteinov, med drugim sposobnost tvorjenja medsebojnih interakcij, je odvisna predvsem od tridimenzionalne strukture njihovih vezavnih mest. Le-ta so se skozi evolucijo razvila tako, da učinkovito vežejo molekule, in so pogosto evolucijsko ohranjena. Identifikacija proteinskih vezavnih mest na proteinu za katerega vemo, da vstopa v interakcije z drugimi proteini, pomagajo predvsem pri odkrivanju njegove funkcije, lahko pa jih uporabimo tudi za izboljšanje proteinskega sidranja. Pri zadnjem pristopu poznavanje vezavnih mest zmanjša iskalni prostor algoritma za sidranje, s čimer se pospeši iskanje nativne konformacije proteinskega kompleksa. Razvili smo algoritem za iskanje lokalnih strukturnih podobnosti med proteinom in bazoneredundančnih proteinskih struktur, z namenom iskanja ohranjenih vezavnih mest na proteinih. Ta algoritem smo uporabili za odkrivanje ohranjenih mest na površini proteinskih struktur, ki smo jih označili kot proteinska vezavna mesta. Nato smo spremenili AutoDock program tako, da se pri sidranju osredotoča samo na napovedana proteinska vezavna mesta, s čimer smo pohitrili in izboljšali postopek proteinskega sidranja. Spletni program, ki to omogoča, je na voljo na http://probis.cmm.ki.siTEXTznanstveno časopisjejournalsSlovenian National E-content AggregatorNational and University Library of SloveniaSlovensko kemijsko društvo