Msa & Sequence Dendogram

8/6/2019 Msa & Sequence Dendogram

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bioCamPusLIomologYChaPter4/ wl ld l rrcr I/l,.l;tc'" L."'"f;'ffii;'*L'*'-'yt-:T ;t

i l l i-., 'tt 't ncction bctwcctt[ l1c f . r tutwt" , { . . . . - roc0s and their }u} f , t ronal importance' IL ' r r rv

ruv' r r " ' - -onservat ionn al i tel :c j l :"""" - - : -^. .*1^n1,*rnenrinrosubgroupsaccordingtop..,r,.rr!frJ"rr.ttning rheprotein equencs rf interesr,xposed

u'itir he3D structure fthe proteln

sequenceimilaritv tl!9rmorc' '11! litjY-:,:;;;; t i,-',r,r,e, enzymitl.aiiiviiv ancsiducsrliich'areroLeikelyobc "clEon'll9tt-'' - ' ,=^., *=ttt *=r..'or.'"n':1.^"""" *n'in,.gri$Jrhf, *t'ro. canbeappl-d o proteins ithknown

xperimentaltructures

s ri'ellas heoreticalmode'ls'seqtte'tceligrtntetftandseqtrcnce endrogrant

u\ ./ i 'rr i ir , t .[ t


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grv\Ju.r 'y*JHonrologrrff;?

conserveclcsiciucs nd class-.rpcific residues rc callcd lruce rcsirirres Figure l)' When the-- ---- "evolutiortaryracemethods apptiedo different equencedentity utoffs br thesame equencefanri ly, racc csidues t diff 'ercntunctionalesolution il l be dcntrfied.f a sequenccs notsinri laro anyorher equencesnd s a subgroupy tselfat selectec lc, thisseq.ence ill beignoredn theanalysis.t wil l be ncludedn theanalysisnti l hePlc is owenoughomaket amember f a subgroup.f theqrrery equenceith 3D-stn^lctures not in anysubgroup t theselectedutoff,no race esidue il l be eported'Clusteringesiducs:

To dcfine he unctionalnterflrc s,ace resiclrrcsre nappedo thestructuref oneoitheproteinsn .the equenceamilyandclusteredn 3D space. inceprotein tructuresremoreconservedhansequences,specially t activesites,race esidue lustersdentifiedromoneprorein rructureanbeapplied"b ll themembersn thesequenceamily'

d F r 9 +Ar Po L lrvz D2POL-B IV z ?ConronruoPOL_l{P}fVPOL-JSRVPOL-RSVPPOL 1_HUlt.LNConrentusPOL_HTL 1CPOL_HTLVzPOL-BLVAUCotrtenr\r3POL-B}f,Vl{POL-ULVTPPOL-GALVConren*ulTrace

I P HP AGL KXKKSVTVI- DVGDA t.Fr FTRO.VAEKRR ITVI DVGDAY TL PYPPC KE C E HLTAID I KD YTT D DAYTLPSPVIIPQGYLKI I IDLKDCF TLPTPS I IP DKSYI IV ID L KDC ' Y.I.PVL3.I,LP RGI.IPLI{VLDL KD': T FLPSPAIIIPKDI.TPL I I IDLKDCT'F_P P --DLl(DCr'-P P- DLSSLPTTTILQTIDLKD AF FP P-D LTS LP TIHLQTID LTD AT TP P-DLTA IPTHHI IC L DLKD.A'FPtr-Dr. _PT_X DL_DA3FPYNLL S TL KPD TYTVL DL,KD.N,T'PYNLLSCLPPS I'YTVLDLKD AF TPYI\ILL S5 L PP S tYg\/t, D L RD if' fPYITLL S.L-P-INT.VLD LKDNT'I

D DAYred - Consenred

-a_-.-- .--rad-

Figure . Identificationf trace esidues:onservedesidues ndclass pecificesidues,rontasequencelignment. segmentf DNA polymerasecquences sh;"'; l for oursubgroupsn thesequenbeairlty, Conservedesidues re definedas residues onserved crosshe sequencefamilyandclass pecific esiduesredefined s esicluesonsenred ithin hesubgrorlphatarc

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i b ioCamPus rllonrtll


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biocarnpus ilHonrotogr il


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bioCermpHonrology. Chapter

f ine the subs.toc.ording o one of the accessibieurface.t),pes.or hesclccted AS ypr:,f a residuc asanSAS argerhan heSAS-Cutofft vri l lbeincludedn thesubset.orexample,,,7[snfractional AS s chosen nd hecutoff s set o0'1,residues irha fractional AS argerhen .1will be ncludedn thesubser.hesubset

amesautomaticallyet o protein-name$SAS'$6 fF,OCUECK(Modelevaluation)l '1Introduction:1

For a homologynodel rom anysource,t isimportant o cJemolstratehat hegtructurfeaturesf themodelare easonablen terms f what s knowaLrotttrotein tructuresn generaThat is , rglearglers aveanalyzedhree-dimension.altructures f.prclteinsrom vrhichbasrpr-inciplesf protein tructurernd otdinghavebeen evelc,peil-{:'neralrograms re,-ryailabro as ist i n rh s analysis. f "*f9-::l:-t .?lfl:l:[.g'H1"gdt I'

,6The ritcri l oranalysisf con'ccttlesson nclude,;3"'r t i v.Lr,' , -.mainchainco,1!_9--q.na.rlonsn acceptableegions f theRamac!.11-9:?Lt-$ap,. ij, ,..PrtiinarePtide o1f1.,".' -i,; rside hain onformationsif'at orresponclo thosen the otalrreribrary

' : .hydrogen-bondingf polar tomsf they reburied, . ' . , ' -"i-*"

rproprenvironmentsor hydrophobic nd hydrophilic esidues,' , ,.er10adatom-atom ontacts:]-: ; '/-.'' ' 'r..'i'l ,rlreiholes nside he structur"//L*..-.

' t^ 'publicationncludepRbCHnCX.'and Q-Profiler.The airnof PRoCF{ECKs to assesso$normal, r converselyowunusuallth'geometryf the esidriesn a givenprotein tructuresas compare,Slvith stereochemir:alarameters erived fronr well-refined,high-resoluti'g-srrucrures.pOCIUCK is based n an analysis f (phi,psi) ngles,Pepjiile ond.planarity,on

. lgngths, ondangles, ydrogen-boncieometry,ndside-chainonformationsf knownproteistrucruressa function f ator"njc.resolution.hus, heexpectedalues f thesePerrametersrknorvnand can be comparedo a modeled_st,ructureaied on the atomic esolution f th,siructuresrom vhichhemodel vrsdevelopedU.\/ChecksPerfornred Y 'IIOCHECIi: vThecurrent hecks erformedyPROCFIECKna givenproteirr tructure reas ollows:

A. '


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bioCampusHomologYChapter4.Covaien gcotl'letY,#/-.Planar i ty".Dihedi'r l ngles.Chiral i tY.Non-bondednteractions.Main-chainYdrogenontls.Disulphideonds.StereochemicalParameters.ParameteromPadsons.Residue-bY-resiiuean lYs i

stereochemicalaramreters.rsedn thePROCHECI{ rograms:TABLEA.I: SIat'crscltattt icalttrarrlctcrsf Morriset al ' (1992)' lerivedrontproteitt tnrclures.

higlt- csctlutot t

St.ereochemical Parameter I "{ .ean value I Scandard deviat ionphi-psi in most far, 'ouredregions of Ramachandran PIot 'chi l , dihedrai angie:gauche minus

transgauce pLuschi2 dihedral angleFrol ine phi Eorsic. 'n angleHel ix Phi t ,orsion arrgleHeLix psi torsion angleci : i3 (S-S bridEe) :r iqht-hanoedlef c-han, lecDisulphide bond separat iol" lomega dihedral- angleMain-chain hydrogenbond energy (kcal. /ntoi 1Calpha chiral ieY: zeLa' 'v i r tual ' ' tors ion angle(Calpha*N-C-CbeLa

>90tC,A l r ianrocrqv= . I !r - .:Jr vvv1Q? A r lc.. lY'oo q,M. v-66. ? c legreesL7' l .4 ci .egrees-65.4 r iegrees-65.3 degrees-39.4 degreesO ( Q r loarooq.JV.v-85.8 degreesz.v/. ,1an f l donroo


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bioCarnpusHomology9jsgler-l"b**rd i,^,,*t l ,,-fu f uSh-AUuber, 99I),a. Botd lertgtlw

BondI sigrma

I x-pt oR label i inEr)

1 141

| 1 tr ,

1 t r,4n

r . +oo

A i1 A0.0160.02cv.v4Ln n1Rn n??v.vz t0.020U. UIYU. U. j -Ot t t t I t

^tra ncH2G* Ccalpha-Cbeta I cHfr-cH:e

N-CaIpha^?tl F n"tl FI F I F -( F I F.

^ r r { 6 A??4 Fult* ! vrl-s

! NH1 -nrJ1Fl"^ '*r$rr1 -nH?n'*t l1* vaa& v^Yrt Fl\ -Lnr I

(except Pro)(Pro)(except GIy)(GlY)\ .frr cU( I1e,Thr,Val)( the resE)(except, Gly, Pro)(GlY)(Pro)

b. 8o.nd angrJos

AngIeValue I sigrmaI x-plon rabel l ing

C-N-Calpha

Calpha-C-N

Calpha-C-O

c-NH1-CHl-Ec-NHl- cHzG*n-r\ I -nlJ1 Ev var4 !alJl E'-n-I \ rH1

cHzG* C-NH1/^ IJ1 Ei-r i -NIlaIJI F-rr-ncH2c*c-o

Cbet.a-Calpha-C I CH3E-CHl-E-CAI' i F AY'A f lvta4! vaa4!,A""i F Ar?1 r

N*Ca1pha-C rr tta Ar" l n arNH1-CH2G"-CI\r-r\r{1 E -( -N-Calpha-cbet IwHr cnrE-cH3ENH1.-CHlE-CH]-BN-CH1E-CHzENH1-CHLE-CH2tso-c-NHL

(except Gly, Pro)(GlY)(Pro)/ ovr.orrF (] l rr Pr^ \\ s^us} / s vlJ t L .r\J I(GIY)/Drn\(except. GIy)(GlY)\. l - | j -cr l( I1e,Thr,Val)/ Fho roql- \\ e-.v ^ vvv,

(except, Gly, Pro)(GIY)(Pro)(Ala)( 1e, Thr, Val )(Pro)/ Flro roql- ' l\ v.^v - vv e,(except, Pr,c(Pro)

L2L.7L20 6L1,J . OLLO.Zrl_o.1*116.9Ltu .61)n q

I t tv I11fr 1

t ] - t .2LLz.51r-L.8110.4111_.1"0301IU. f ,L23.QLZZ.V

11

)1

112.L1.5) ' )

IY

z.o2.9z.>111111

1AL.a

q{{IEglAIaEBId.lire!i{c.dTfl.fldd-i|x-fl.{-l*t..!-I

{_l.Ir

Aa 1ALI


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'^ ;^,/^^*-, ,-ru\ -d i i iPu)Honrology'Chapter 1., 'The inprt to PRCCHECK s a single i ie,/ containing he coordinates f your protcrn

s::-ucture.his rnustbe i;r Brookhaveni le format. Thc olt tPuts omprise numberof ploi .s.roqerhervitha detai leciesidue-by.rcsidueist ing. heplotsareoutput n PostScr iplonnat.f) if ferent1;lots cttct 'ntc


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Dl0LanrpusHornologtChapter4rL"*th.t f f ipoinrson rhatgraph.The red numbersabove hedatapointsale the reside'numbers f theresiduesn questionie showinghoseesiduesying n unfavourableegions f theplot)'

. , ' iThemainoptionsor heplotare:-q,,oRant:ichandranlots orGly& Pro esiduesnly'. _,TSLcut-offvalue 9r theG-factor:efiningwhichpoints re o be abelled'.Theplotcanbe n colour rblack-and-white'

3rdplot: Clil-Cli2 PIot ,.r'The chil-chi2 plorsshow,rd{nit-.t i2 sideghfn torsion ngle ombinationsor nll

rcsiducypcs vSoscidccSainsre ongenou!f ',ohavg gth hcsc nglcs'rie'i[i,lirig"it; iactrptot ndicates ow favourable

each egionon theplot is ; thedarkerheshadehemore avourablehe egion. he dataon which heshadings based ascome romadata etof 163non-homologous,igh-resolutionrotein hains hosenromstructuresolved yX-raycrystallographyo a resolutionf 2.0Aor better ndanR-factor ogrEaterhanZATa

The nu'rbcrs in brackets, ollowingeach esidr"leame, holv he otalnumber f drtapoints on rhxrgraph.The red nunrbersabove he datapointsare he reside'nurnbersf thercsicjuesn qucstiorric showing hose esiducsying in unfavourabicegions f the plot) '

ThemainoPtionsor thePlotare:-.Thecut-offvalue or theG-factor efiningwhiCh oins arc o b'e abelled'.The lotcanbe n colour r. lack-and-white',/lh plot/uait1 chainParanrcterr

The i^ gr"pt, on themain-chainarameterslo tshowhow hestructurerepresentedy'the solidsquare)ompares ith rvell-refinedtructurest a slm]iar esolution' he darkbandneachgraph epresentshe results rom the vell-refinecltructures;he central ine is a least-squaresit to themean rendas a function f resolution, hile he

viidthof thebandon eithersideof it correspondso a variation f onestandardeviation bcruthenrean.n some ases'hetrends dependentn he esolution,nd n other asest is not.

Note.Thisplot s intended sa roughguideonly and oonruckreiiance hould otbeplaced ngettingesultshatare be[terhan tructurest hesameesolutiot'l"'

429

-lilndIITilt |flfIrilt3.{II,{rd.J{.IJJJJJJJIIY


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bir-rCampusHomologyChaPter l--1-TM5 propert ies lot ted are: -. /-,./.a. Ranrachandraniot qualityLXtris ropcrtys measuredy the percentage f the

protein'sesidueshat are n ihe most favoured, r core, regionsof the Ramachandranplor. For a good mociei t ructure, btained t high resolut ion, ne would expect hispercentageo be over 907o. Horvever,as the resolutiongets poorer, so this f iguredecreasesas mrghtbe expected, 'heshadedegion eflects hisexpected ecreasev' ithrvorseninresol t iot i.

t/-.b. Pcpt idc borrt l plarrar i ty. . " fnisproperly s measured y calculat ing he standarddeviation of the proiein structure's-tmegaorsionangles.The smaller he value thet ighter hecluster insround he deaioi 180degreesr,vhichepresentsperfect ly lanarnantiJo hnrr,l \yvl /r ,u! vv" r , / .

.c. Bad non.bonCed nter;rct ions. 'This roperty s rneasured y the number of badcontacts per 100 resi. lucs.Bad contacts .rre elected rom the l ist of non-bondedinteract ionsoundby progrrr l Nl l . They arc dcf inecl s contactswhere he distance ic losest pproachs ess hanor equal o 2.6, \ .

.d. Calpha etrahedral .distort ion.fhis propen) 's measrlredy calculat inghe standard


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bioCanpusHomologyChapter ' ielch graph representshe results rom thesquares it to the mean rendas a functionsideof i t correspondso a variat ion f onetrend s dependentn the esolution.Note.This plot s inrended r 3j3qh guilg_ nly and oo much eilance houldnot beplaced rtgetting esults hat are"better hanstructures t thesame esolution".The 5_pr_op"qel lotge{aq.e;.

' :ai 'standard eviation f thechi-l gaucheminus orsion ngJ"es..b.Standard eviation f thechi-1 rans orsion ngles.-c.Standard cviation f thechi-l grucheplus orsion ngles..d.Pooled tandard eviation f all chi-l torsion ngles'.e .Standard eviationof thechi-2 trans orsionangles.

dn plot: RcsicftrcropertiesThe vlious graphsand cliagrams n this plot show hou' the protein'sgeometncal

. propert ies ary alonq ls sequnce.his givesa visualization fTfricir i-gions uppiot to i,oueconsistentlyooror unusual eometryperhaps ecauseheyarepoorlydefined) ndwhichhavemorenorrnalgeometry.

The properties lottedare:-.Grapls a-c: OptiorwlpropertiesThe first threegraphsat the op of thepage, an be selectedrom 14 possibies y theu-ser'The threedefaultgraphs,which areplottedwhenyou first run PROCHECK, are he ir'stthree f:-

l. Absolutedeviation rom rneanChi-1 value exc:I. lcl)2. Absolutedeviation rom meanof omega orsion3. C-alpha hiral i ty: bs.deviation f zeta orsion4. Absolutedeviation rom meanof H-bonci nergy5. GammaatornB-value6. AvcrlgeB-vllue of rt lain-chaintoms7. AveraseB-value f side-chain toms

well-ref ined tructures;he centralof resclution, hile thc width of thestandard eviation bout he mean.

l ine is a least-bandon either

ln all caseshe

flr|-l-lEEIi|;{;iEI.slr|{rii3lsld.dirxJr.{dil...r{.d.f,lfa..il..rilJIg

+J l


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bioCamPusHomologYChaPter& C- bI* fnEf r -p--sOs ribu o r9.G-frctororchil-ciri2 istribution10.Residuc-bY-residue-factorI l. Approx' ccessibil ityestimaterj1'Ooinunrbers)i2. Percentageesidue ain-chairriccessibil ity13.Stlrrcilrdeviationf main-chain-values14.Standar:deviationf side-chain-vaiues

For eachgraph, nusuar alues usualiyhose, ore han2.0standard eviations*'av

from he ,ic]cal,,tnean alue) reshown ighliglrted."Graplt d: Scc:rtrtda)) slr l lct l { ' 'c averctgc s! i r t tutct l

ccessibi l i ty

Thesecondaryrructure lotshows schematicepresentationf theKabsch sancier

( i983)secondirrystruCtu|assignments.Thekeyjustbelowthepictureshowslvhichsrructures rv'ic:h.Betastrirndsre akeno inclucle rl residues

ith a Kabsch sander

assignmentf E, heiicesorrespondsobothH andG assignments'hileeverythinglse

is takenobe andoni oil'Theshaci ingbehin


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fl{dTril;ldHEhl;dJ3l.fldJflgII.dx.fl.fl.d-{x.fl.dJIII=--t

bioCarnprusHomologyChapterlGCg ttt tht .o'tfile. Refer ro rhe final column of the .out file to seewhich is the parameterhat deviatesby heamount hown ere.

.Grapltg,WThe shaded quares ive a schematicepresentationf each esidue's -factor alues'(Note hat hechi-l G-factors reshown nly or thoseesiCueshatdo nothave ctri'2,andhence ochil ' 'chi2G-factor).Regionswith many dark squares onespond o regionswhere the properties re"ultusuul", sdefined y a low (or negative) -factor' hesemaycorrespondo highlymobileor poorlydefinedegions uchas oops, r mayneed urthernvestigation'

Themain ptionsor hePlotare:-.Which3 of 14plots o beprintedn the3 maingraphs t he opof thep.age'.Number f srandardeviationsor highlighting utliersdefaults2.0)..Theplot canbe n colour r black-and-white'

/h plot: Ma-in lnin bond engthdistibwtiortsT5e Sistogr.lnlsn thisplot. how hedistributionsf eachof !h ain-chain

bond engthsn thestructure. he solict ine in the centreof eachplcltcorrespondso the small'nroleculemeanvalue,while the dashed ineseithersideshow hesmall'molecule tandarddeviation,hedata oming romEngh& lluber(1991)'Highlighted ars on-espondo valuesmore han2.0 standardieviationsrom hemean,houghthevalue f 2.0canbechangecly editingheprocheck.prmile.

If anyof the histogram ars ie of f the graph, o the ef t or to the right,a largearrowindicateshenumber f these utliersas n theC'O plotabove).Significant utliers reshown ntheDistorted eometrylots.{h plot: rttain lwittbondangle aranieters

The histogrumsn rhisplot shorv hedistributions f eachof the differentmirin-chainbondanglesn thestructure.he solid ine n thecentre f eachpiot correspondso thesmall'moleculemeanvalue,while the dashed ineseithersideshow hesnial!-riolecule tancarcldeviation,hedata omingromEngh& Huber 1991)'

Highlighted arscorrespondo valuesmore han2.0 standarsleviationsromthemean'

433


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Homolog"vChaPter4f"'tlttt*ttt'P rn l [i e'

I fanyofthehistogrambarsl ieof f thegraph,tothelef tor tothgr ight,a largearTowL^rrC\i"oi.r,", ;.'";;, of theseutliersas n ttre A-c'o and B'cA'c plots bove)'Signifrcantutliersre hown n heDistortecleometq/lots'

plslqr$t: Fsr! plqt3t lqYp"sTheseistogramsho*1!9-*II9iSI nese [ l lSlUXr crrrrJin thestructure.Thedashedi inesindicatedi f ferent idealvaluesforaromattcnt.^6 ara n 011 anCn thg Structurg' I he oasnccl lrrsr I rrurv'

^' ' - ' ' ' . , .s"##e-His) and or plrrrar ncl-groupsArg'Asn'Asp'Cln' GIu) The "T:: "^lt:,are0'034and

;il;i;.,;, uu,,ii.r. aruesan earreredvecliringhe rocheck'prmile'Histogr ir r t rbir rsbcyondttredlsl iedl inesareslrorvnaslr iglr l ig lr ted'r r . .Wyrorr r igrr right ingout l iers|orr inggroupS(defaul t is0.03A).

.RMs risr*rrcc.*:ru' lurrur i tyfor ' igrrr ig' t ingurr icrsorothcr roupsdcfaults0'02i) '

'Theplotcanbe tt cololtror black-and-rvhite'1d^ Plot' Dis'Lo't'l'gn"' olots:

ThesePlotsshowsall distortedplanar roups.

The parametersefining ow distortedheseherearegivenn theprocheck'prmarameterile'

. For each nain-chainond engthandangleclehnedy theEngh&' Hubersmall-moleculeata)'the wo.

n-chainbondangles,and

properties eed o be beforebeing plotted

plotted, he plot shows the ideal value (asthe actualvalue,and he difference enveen

are plotted and the value

434

mai

For eachdistortecllanargroups'hreeofthogonal rojectionsslros,nist l reR}, lsc l is tanceoft l reatomsfromthebest. f i tp lane.


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bioCan'iPusI ' IonrologYChaJrterReferences:Blunclell ,T. L.; Sibtnda, B. I-. ; -\ ternberg,M, J. E"; Thorntt lr) ' , ' M' "Knowledge-b*sedpreciict ionf protein rructuresncl hedesign f novelmoleculcs"" tt ture'326'34' l i967)'

Blundel l ,T.L. ; Carney,D.; Gardner, . ; Hayes,F.; Flowl i l , B '; Hubbard'T' ; overington' ' , ;s ingh,D. A.; Sibanda, . L. ; Sutcl i f f ' , { . Knorvledge-basedrotein nocel l ing nddesign" ' t t r 'J . Bioclwn.,172,513 1988)'$pervne,W.J. ;North,A.C'T' ;Phi l l ips 'D'C' ;Brew'K' ;Vanaman'T'C' ;Hi l i 'R'L'"APossibicThree_ciimensionartructureof Bovine -Lactalbuminbased ()n trrai of Hen's Egg-whiteLysozyme," . Mol. Biol ' ,42,65 (i969) 'Dlyhoff, ivr. o.; Barker,w. c.l Hunr,J-.T. "Estabrishinglon,ologies n proteinsequences,"lvl t lnds n Etttyntology, 1,524(1983)'Andrej srl i tnd Tom L. Blundcll "comparativeprotcin modelingby satisfaction f spatiairestraints",MoI 8io1,234,779-815 1993)'AdobeSysterrrs lrrc.(1985).Postscr iptLanguageReferenceManuai.Addison-Wesley,ReadiA. Ai len F H, Bcl lardS, BriceM D, Cartwright A, DoublerJay' HiggsH' l lummelinkT'

l -{ummelink-PetersBG,Kennardc,Motherwel lDS,RocigersJR&watsonDG(1979) 'Hart igan, . A. (1975).Clustering lgorithms'New York: Wiley'Lichtarge, ' , Boume,H.R' andCohen'F'E" J' Mol' Biol" 257'342-158'(1996)'Licit targe, . Yantamoto, .R' andCoiren, 'E', ' Mol' Biol ' , 214,325.337' (L997),

rl i

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Msa & Sequence Dendogram