2TP4-06 Macroscopic Relationships between Protein Phosphorylation and Physical Interaction(The 47th Annual Meeting of the Biophysical Society of Japan)
2TP4-06 大規模データマイニングから明らかになったタンパク質リン酸化と複合体形成の関係(生命情報科学-機能ゲノミクス,第47回日本生物物理学会年会)

Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama
2009 Seibutsu Butsuri  
TheBiophysicalSociety of Japan General IncorporatedAssociation whieh containg highLi and lower ordeT oligorners (e g dimers and monomeis) The higher oTder ohgorners of each famity inctude at least one msernon or deletion region m their mterfaee areas The aveiage length of mseitJon/deletion iegion is 15 residual sites and the loop stmctures are frequentltr observed as compaied "ith "hele proLem A]though the amino amd composition ef the ingeihon rcgiong is smnlar "ith that of other mterface sites
more » ... ther mterface sites the delta ASA of them upon oligomelization is lcLrger than that of other mterfaLe sites We will dilso estimate the LontmbutTe"s of insLrtions md ammo aad gubstituticms to mleractions and discuss the ditterence between these two types 2TP403 ieE{FM7'n77.r)LigreLik re5XigS)S-/SONOiRE ffMifi]1mant Post doLking proLetss ter tlexible protem doLlang problems by usmgmteraLUonimgcrpmnts Nobu,uki ULhikoga (1) Takdtsugu 1]iruKawa (2) (fl)JBIC CERC C2) CBRO Protein flexibility is importdnt for formm.g piotem Lomplexes Protem protem mteraction netwoikts mclude hub piotems -hiLh Lan mteraLt with vamous pieteins Mdny hub pTote]ns arc obgunted ag mtnngiLill} disordcrLd piotLins ThLrciorL it ig ]rnporlant to analyze protein dockrng pToblems in ternis of protein withconformationalchnnges We htive beell studymg post pieLessmg methods ]n ngid body docking ioi searLhing nLar nftLive deco)s by using interaction tmgerprmtg <IFP) ot moleculai eornplex IFP is a sequence composed of frequencies of mteraLtion numbers between atoms belonging to aTnino acTd res]dues In geneTd] Lluster an ilysTs is ubeful mLthod ±ei discnTninanng near nati}e deco}s tiom otherg Althetigh RMgD is uguall) used in cluster analysis it depends on method of superposing structures ot decoys We compaied these 2 methods IrP and RMSD in dubtei analybis and vve Lould ebtain better clusters b) using IFP than RMSD Vdrious struLturLs of Lalmoduhn (CaM) obLamLd {iom gLruLLuieg analyLLd by using NMR wLre used for doLkmg analysig DaLaget cornpoged ol dLcoys gcncTated tiom varioug CaM structures were mvestagated by cluster anaTyss by usmg lbP We attempted doLking simutatiom wJth a post deLkmg anaJysis for CNG CaMKK and PMCA as pLptidL hgands ol CaM 2TP4 04 GPCR"asmsAfiXtGetzISbfil:afffiVOiaeatlth Relation between GPCR structure and G protein couplmg seleLtivity Mak]ko Suwa {1) Yukitcru Ono (2) Mmoru Sugihaia (1) ((i) National lnftuute of Ad)anccd Industriat S"ence avd leLhneivgy r2) 1oprmanon and WathematEcttt S"cnc[ laboratoc}lnc} The external 1igand stimulus to G protem coupled receptors (GPCRs) mduces the couplmg with G proteins (G . G-" G, GL. ij etc ) fo11owed b} different kinds of signal tranbduLtion Though many expemmental/ theoretical studies haLe been performed thL rnLLhanism oE Lhig coupling gclectivity ig noL )cL clucidatLd Recently ne" stnictures of CiPCRs -ere revealed i) and the (JPCR sequences bLcemc abundant by vRnuus genome proJects 1 n this situition it is possiblL to argue dbout funLttonaJly impurtdnt regiens by wnneLtmg Lompiehenbive scqucncL analysis with nc-3D strucLure mformation HerL we mtcnd Lo LxtiaLt structural regions whicli partiupate in seleLting G protem type WL perloTmLd a gtiuctural classification of GPCRg by dTawing dendrograins using inner interaction ot the proteins which are estarnated by physico chLmicat paramLtLrs oi ammo aud iesidues on trarismembramc iesiells <TMII) Applymg this dassthLdtioll to ydrious Lembmataon patternb of TMHs of GPCRs whobe Loup]ing se]eLtivity has already know" we narrowed down the demains that participated in G piotein selectaon Furthermere we identified the posihon of thL important residues (funLtJonil residue ytes) by pr{)Lebsmg statibt-s such as the PeasDn s Lorrdation malysis about G piotun type and stiuLtuial posmon rLlntionship ThLsL i[ILntiiicd iunctional residuc sitcg rLalltr sappurted the expenmental resultg suggesting that our resultg are propeT The resu]ts ftrL thL quJte fruitful information for understandmg the G protein coupling mechamsm these TLgiong aie Tequired To veuiy the piedittions an NMR baged method whether the predicted gequences adopt llnstruclured stateb has been deietoped [RESULTS and DISCUSSIONI For Lvalutting the ph}sLcochemical properties ot IUPs b} NMR we designed a novel fusion pretein expregsion systLm demved from PH0471 a theimo gtablc mLmbrane an ¢ heied OB fold protein PH0471 is divided mto t"o regions four mernbrane hehces and an OB fetd domam thdit are Lonnected by a flex]ble lmker The NMR signals from thL OB Iold regien are detectable only when Lhe hnku is tetall} disordered Thus we subsntuted this lmker by candidate sequences of IUPs lo bL Lvalutted 53 candLdates were selLLted by a prediLtien methed peodle S and 40 from them -Lie subjected to PCR LIoning Irom human oi rnouse cDNAs We succeeded m constructmg 35 expression vectors Fmally we obtained ]SN labLllLd Lhimeia PH0471 protems with 25 putative IVPbllURs as the lmkers Fram the NMR gpLLtra we cldssified them into three Ldtegor]es very flexible fiexible and ILss flLxiblL The ]ess flexiblc oneg involvc either rnembraneabso"atmg or aggregationprone sequenceg The sygtematic characteriiaUon ot IUPs vvtll validate the predictions dnd provide a large amount of data thereby contrihuting tu impreve the prediLtaon method Refference1) Hlnsoll MA StLvLnbRC Structure 17 8 14 (2009) 2Tp4os NMRIcs6xtticZlts)xlxegsgl]omaeeemeJ,t A mLthud for systcmatiL assLssrnLnt of int"nbLLal]y unstruLtuied proteins and protein iegions by NMR Narsuko Goda (1) Kina Shimi7u O) Yohta Kuwahara (D Tamotsu Noguchi (3) Likahi" Ikcgdmi (4) Vetonor7 Ota {S) Hideka7u Hiroakt (1) (fJ) aradttate Schooi of Mtit"ne Kehe Untversitt f2) 2 JnsttttstL for Bumpt)rmattt s ResLaieh and De"top}ntnt Japan 5ciFnre antl 7ethnotog} Agencv (BJRD J57) B) S C omputanonat Biotosi Research Center (CBRO Nahonat Jn!tttute of Advanced lndustrlat Sctence and 7lecitnoJog} (4) lttstttute for ProtetnReseanck Osaka VntLersttv r5) S Graduate SchooJofhdi?rmatton S"cn"s Nago)a VmvLrsrA)[INTRODUCTIONI Inuinsicnlly unstrucLured protcms ind protem regionb <hereindftei IUPs) which ldck stdble 3D structures and have high fiexib]1]Ly m the polypeptide chains have been widely known and aLLuratL prLdiLtTens for 2Tp406 ± Mec7--v.r:z)iethliE,ng6hil:tsoke;iAOHV)inclt 2P 239 tdeatsfffntOmapt Macrogcopie Re]ationships between Protem Phosphorylation and Physicallnteraction (2) lnst Adi BioTa Keio UntT HI lnst AdL BtosLt Kao Un" PRESTO JSDUncler thc recent adianccg in mAsg speLtrometry based technolog} ncarly half oi the eukaryotac proteome haive bLen suggLsted to have potentaal phosphosites However our understanding of protein phogphorylatlon is tstili hmited Here we demonstiated mdLrobcopic relationships betvveen protein phesphorylatJon and physiLal intLraetion by integrdtmg yeast phosphoproteomL and prote]n mteiactome data By usmg 1iquid chromatography ta]dem mass speetrornetry 6SIO phogphog]tes and 1 993 phosphoprotems were inMa]]y idLntitiLd and a large scale dataset ot yeagt phospheprutLome mdudmg t4 627 phosphogiteg and 3 433 phobphoprotemb were prepared with a combmation of the UniProt data Then wL mappcd thL un]fied phosphoproteome data on lhe yLast binaiy protein mteracuon net"ork Statistical data mining anatyses showed that phogphoproteing haie signif!Lantiy more mteraeting partneig than do non phosphoprotems For LxampTe thL ratL ef phosphopretems having ever 10 inteTaLting piotem partners was -・2 fold more than that ot non phosphoprotem Moreover by comparTng wTth randomly re"ired piotem mtuaLtion net"erks we showed that Le phosphorylataan of mteractmg protcing is mere Lommon than expected Indecd seNeral possible kmases yieldmg co phosphorylation ot protemts in the sdme piotcin Lomplex weie illummated by further tn sihLo analysLs These resultb vvill proude new msights inLo thL undLrsta"ding of large scale mtertwimng bct"cen protem phosphor} tauon aiid protein complLx [oitrintio" 2TP5 Ol TEM lt SEM l:S6Stz/sceKdeatsOesfimaut 2p o1 s Structure analysis of membranc pietem Lompiexes usgng TEM and SltM Ch]kara Sato Cl) Kazuhiro Miu (1) Teshilllko Ogura O) Yuuguke Maruyama (D Hidctohhi NishtvamT {2} Mitsuo Sugi (2) (tJ) National Jnsntul( of Advan"d Indt"tnai SaLnLw and T"hnotogy rAIST) r2) jFOr} Membrane proteins and their complexes are eggential for Larioub kmds of physiological functiong in ollr body Ho-evei they are freq"ent]y difhcult to make crystal We determmed thc 3D structure of d membrane bound prote]n RECK usmg Smgle PdrtiLle Analysis {SPA) irom FM image Some Matnx n]Ltal]opr{)teinatses {MMPs) are up regulated in cancLr Lellb tmd their expression is often associated "ith poor prognosLs The membrane anchaed piotease iegulator RECK plays important roles in mamma]]an deielopmetit and turner guppression RECK was reLonstructed using SPA in Lollaboiation "ith Dr Makoto Neda (Kyoto UniD AIthough gmall gtable protein complexcg can be reconstructed usmg SPA unsttble complexes are hardly vhuah7ed after the protem punficataon step An Atmespheric Seanning EleLtron MTcioscope <AgEM) is develDped to obtserve aqueous samplLs and cells m solunon at atmosphenc pressureg Conventional eleLtron microscopes view samplets m vaLuLim and are unable to image weL sarnplLs or sampies in solution FoT ths new micrescopt a gpLcHl dish with a windovv made ol Lhin film (ASEM Dish) was deNeloped to hold saxnples ThL prLgsure resistant film of thL vvindovv dlowb an e]eLtron beam te be projected from underneath the sample The top of the digh is open and Lan Lontam aqueouts sample of gevLia] ml 2TP5 02 Folding simulations of chigno]in by self learning mukiscale 2P O02 method We}Ifel Ll (1) ShoJi Taktldd {1) ((i) Kvoto U, Iapall Suence and 7lechnoiog) lvc ) wr"n DepaJtmenr ofBtophJsiLs r?) CREST -s,-)o-NII-Electronic
doi:10.2142/biophys.49.s50_4 fatcat:yl5kognzara4xdmd6nhtt3cgve