2P433 Modeling the emergence of cliques in the protein interaction networks(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
Takeshi Hase, Yoshihito Niimura, Soichi Ogishima, Tuguchika Kaminuma, Hiroshi Tanaka
2006
Seibutsu Butsuri
Inf6rmatics Society The iimeytttien of cxperimental technigues rnade it possible to consrmct protein intcraction nerworks (PINs> at the whole gcnome level. P[Ns are churacterincd by the high c]uster coefficient, In other words, PINs have u lot uf fully coimccted subnetworks, so called cliqucs. A step of evolutionury modcl presented so far is as follows: A randomly selected node is daplicated. A ILnk cennccting to the duplicated node is removed with H constant probabiliry, and a ncw link is
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... hed bctwecn the dup]ieated node and the eriginal nodc {eross-interaction). This mudcl can crcate cliqlles rll, However, it rcycalcd that this medel cannot explain the ernergence of cliqucs cerrectly, because doub]e of the number of cross-inteructions in the PINs arc required to predLee eliqucs in number similar to lhose observed in the PINs [1]. Here we present a new mechanism in which a dupticated nude cennects to n(ules two steps apart in thc PINs (second-neighbor cormccLiun). We incoTperated this mechanism into the conventiunal model. We estuiiated the number ot' secend-neighbor connections from local structures in the PINs. In the yeast PIN CMIPS [2]), vv'e found 346 second-neighbor connections and 74 crossinteractions. Nu[nericul unalysis showed rhat our modcl requiTed 334 secendneighber connections and 74 cross-interacliens to produce the high eluster coefficient of the yeast PfN, Our medel could reficct the actual mechumisTn in feming cliques in the PINs, Referenecs[11 I. Ispolatov et al. New J. Phys, 7 C2UOS)L21 U. GuldeneT et al. Nuc. Acid Res. 33, 364 (2{X)5) 2P434Emergence of protein-protein interfaces: lnsight from amino acid substitutions. 0HafumiNishi',MetonoriOta2 ' Grad. Sch. of Biosci. & Biotech.. Tbkyo Inst. of Tech., 2GSIC, Tokyo Inst, or Tech, Protein-pTotein interactions are csscntial for ma]iy bielogical processes. Arl of proteins that arc bound with other ones have p:etein-pretein interfaces, which shuuld be somcwhat differemt frem the rest part of protein surfaces. Yet, our llnderstundings ofprotein-protein interflates arc jnadcquate to detect their locations acuurateLy. Here we Eocused en thc variation of the oligemeric states ebserved within each of homologous families to investigate the cmergence of the pTeteinprotein intcrfaces. We cottected and analyscd S2 SCOP famities each of that contains proteins whieh are different in oligomeric states with at Eeast one of thc other members in the sarne family. From the structural alignments, we counted thc amino acid substitutions occuri'jng at the surface-illterface celumn {rhe residues at the site are involved in t]le interfaces in some pruteins and expesed to wuLers in the othcrs) as well as at the surfaec-surfacc ones. Finally, we devised an amine acid substitution scoring matrix to delect thc emergeuee of Lhe tnterfaces, Le., rclcvant substitutiens to the svrface-interface column. The jackknife cross-yalidation test was applied to assess the efficiency of the substitution maLrix nnd the results were compared with that of amimc} acid cemposition seore. BotJi two eollld clcarly distinguish the surfaue-interfacc columns from the surface-surface ones with different effieiencies on thc samples. The accuracy of the discrimination was improved by taking into accounr ot' the acce$sible suTface area of thc resjdues. 2P435Exp]oring the minimal pathivay maps C) M]sukc Axuma, Motoneri Ota TokyolnstituteofTechnology Recently, more than 350 microbjal and 30 eukaryotic genomcs have been cempletely sequenced, But ir js not yet ctear what kinds oi gencs are sufficient te ergatti7e thc smallest living thing, To detect thcsc genes set, i.e.. the minimal gcnome, a commen gelle set has bccn cetpputationaJly seught using the exhaustivc homolegy scarch. Hcre, we tried to detect minimat pathway maps instcad of the minimal gcnemc. The pathway inaps are functional medulcs of proteiri interactioii networks. reprcscntcd by KEGG dutabase, Using thc 30 microbiul genomes ati the rcpresentatives of 20S ones, we finally obtained a set of essential mups (we rcgard it aH [he minimal pathway map) that consists of 25 pfimary-essential maps { 1EMs>, 7 secondury-u$scntial maps (2EMs) und 2 tcrtiary-essential maps (3EMs). 1EMs are dcfincd as the maps that contain many omholegous gencs. 2EMs and 3EMs are required for IEMs and 2EMs heing runctional, rcspcctiyely. providing the inputcompounds into them {the detai1 wM be shown in the postcT). Analyzing these maps, it -・as detected that IEMs mainly ennslst ef those that concerning gcnctic preccsscs {ribesomal preteins, DNA. RNA metabolism ete.) on thc otheT hand, 2EMs and 3EMs are mainly consist of mups cunccrning energy rnetabolism, This clearly indicates the 1 EMs twe responsible t'or thc reprnduction of the urganism and they are Likely to be commen in many baclerial genemes. Tu sustain this system the energy metabolism is required, but this system is uncornmon probably dcpcnding untheirliving-clrcumstances. 2P436Feature finding of cis reg"latory elements by mutual entropy measurement The mechanism ot' gepe regutaLion bas not been studicd yet, and it is one ef thc eurrent tepics should he clarified in molecular biology. Transcription t'actors regulate gene expressions by binding to cis-elements on genomcs, Seme of binding sites uf transeription factors were investlgated by using thc pro ± 11img and the regular cxpression in databases and some reports. To understand thc relationship between cis-elements umd transcription factors, the computationai prediction mcthod is efficient. However, it is difficult to characterjze and to cempare with cis-elcments for transcription t'actors comprehensively becuusc sequence pattems of ciselements for a transcription imtor are not unified but diverse. In this study. we upplied mlltual entropy meusurcment fot tlle characterizat3on of cis-elements ior traiiscripton fuctoTs.Sequence data of cis-clcmcnts used in this study was rctrieved froin JASRdLR database and TRANSFAC database. These data eensist of cis-elemenTs for appreximatcly SSO transcription facturs derived from multicellular eukaryotes. We calculated so-czlled entropy cvolutional rates on the consellsus s¢ quences of their cis-e]emcnts for a transcription factor and u distribution of elltrepy evolutienal rates to be comparod, By cornpartng the ptttterns or the mutual elltropy values, we found somc dormain str-ctures clustered by cach domain, It seems thut structures of DNA binding domains havc good prospect for being charactcrizcdbyentropyevotutionalratesfromthecis-elements.
doi:10.2142/biophys.46.s404_1
fatcat:gjm5gksjwndqtmz6bf2fvtszgi