graph - theoretic approach to understand protein functioning using contact network

8/14/2019 Graph - Theoretic Approach to Understand Protein Functioning using Contact Network

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Akmadk Aks}a}|}l eg _oalkol Lm|od}ae

4 s V p e i l o } P l v e p }

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|kmlps}dkm v

oek}do} kl}~

Akmadk Aks}a}|}l eg_l

@D_AO ]BLEPQ9

Kl}~eph9 D kl}~eph oeksas}s eggce~ eg akgepjd}aek# jd}}lp ep l`l `|ac} gep dkq sqs}lj oeksas}ak

D cdpnl k|j`lp eg b|nl kl}~epdvvpedob+ Gep lrdjvcl cdpnl àevpe}lak ak}lpdo}aeks# loecenaodc

]qvaodccq d npdvb oek}daks9 Kemls ep Lcljlk}s "oej Cakhs "ak}lpdo}aeks! plv

Gecce~akn as d sajvcl npdvb ~a}bsbe~akn ak}lpdo}aeks l}~llk }

Ak }bas vpeilo} ~l bdwl jdvvlmkl}~eph+ Ak odsl eg vpe}laks kem

k ' Plsldpob# Hechd}d _ljls

ao dvvpedob }e

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phVpeilo} Plvep}

_oalkol Lm|od}aek ' Plsldpob# Hecjls}lp AW# Dvpac 0661

Vpeilo} Mekl @q9Bdpsb V|p~d

Ml`dkidk @ds_|mbdksb| Vdkml

oejveklk}s%lcljlk}s ~baob ak}lpdo} ak epmlplpnq }e gepj d oejvesa}l ~becl "sqs}lj!+ D

n eg d cdpnl k|j`lp eg ak}lpdo}akn |ka}s+

s bdwl `llk jemlclm eg jdvvlm |sakn }bl npdcenaodc sqs}ljs akwecwakn jl}dècao vd}b~dqs#l}~ephs l}o+ bdwl llk jdvvlm "|kmlps}eem!

eklk}s! plvplslk}lm ds d me} dkmplslk}lm q d cakl+

D# @# O+ ds a}s kemls dkm }bl cakls ieakakn }bllj+

Gan|pl / 4

sejl "kakl! vpe}laks dkm s}|malm wdpae|s oejvls dpl }bl dcvbd odpèk d}ej eg dk djake doam

lp AW# Dvpac 0661

akn

d}d

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eklk}s eg ddkm sakol


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Akmadk Aks}a}|}l eg _oalkol Lm|od}aek ' Plsldpob# Hechd}d _ljls}lp AW# Dvpac 0661


djake doams bdwl ekcq ekl dcvbd odpèk "O!# ~l odk dcse sdq }bd} ak d vpe}lak kl}~eph dkeml plvplslk}s dk djake doam+ ]bl ak}lpdo}aeks `l}~llk }bl wdpae|s d}ejs ep jeclo|cls akd vpe}lak dpl plvplslk}lm `q cakhs ak d kl}~eph+ ]blsl ak}lpdo}aeks jdq `l oewdclk} ep kek*oewdclk}+ Nlklpdccq cekn*pdknl ak}lpdo}aeks dpl kek*oewdclk} ak kd}|pl+ ]blsl ak}lpdo}aeks akvpe}laks odk `l jdvvlm |sakn }bl mas}dkol jd}par+

Mas}dkol Jd}par9 A} as dk jd}par ~baob s}epls }bl mas}dkol `l}~llk }bl a}b dkm i}bkemls+ Gep lrdjvcl ag ~l }pq }e oeks}p|o} d mas}dkol jd}par gep }bl Gan|pl / 4 dèwl ~l nl}#d 7 7 jd}par ~besl gaps} lcljlk} "4# 4! ~e|cm `l 6 dkm }bl klr} lcljlk} ak }bl sdjl pe~a+l+ "4# 0! s}epakn }bl mas}dkol `l}~llk }bl keml D dkm @ ag ~l oeksamlp D ds keml k|j`lp 4dkm @ ds 0km keml+ Dk ajvep}dk} }bakn ~baob janb} `l oekg|sakn blpl as }bd}# }bl mas}dkoljd}par s}epls }bl maplo} mas}dkols ep masvcdoljlk}s l}~llk }bl kemls# applsvlo}awl eg }blapak}lpdo}aeks+ Ak odsl eg vpe}laks mas}dkol jd}par s}epls }bl mas}dkols `l}~llk ldob vdap egdcvbd odpèks "ep djake doams!+

Dmidolkoq ep Oekklo}awa}q Jd}par9 Dg}lp oeks}p|o}akn }bl mas}dkol jd}par ~l sodk }bpe|nb}bl ~becl jd}par dkm ceeh gep wdpae|s hakms eg ak}lpdo}aeks+ ]bl ak}lpdo}aeks mlvlkm |vek

}bl mas}dkol `l}~llk }bl }~e kemls+ _e# ag }bl mas}dkol `l}~llk }~e kemls as `l}~llk ddkm ` }blk ~l sdq }bd} }bl }~e kemls ak}lpdo} ep dpl oekklo}lm `q d cakh+ Ak }bas vpeilo} ~lbdwl oeksamlplm }bd} ag }bl mas}dkol `l}~llk }bl }~e djake doam npe|vs ep }bl }~e dcvbdodpèks as clss }bdk >+6 }blk }blq ak}lpdo} dkm ~l odcclm a} sbep}*pdknl ak}lpdo}aeks+_ajacdpcq ag }bl mas}dkol as `l}~llk 47+6 dkm 42+6 ~l odcclm a} ds cekn pdknl ak}lpdo}aeks+]blsl cekn*pdknl ' sbep}*pdknl ak}lpdo}aeks vcdq d wa}dc pecl ak vpe}lak gecmakn dkm a}sg|ko}aekakn+ Ak dk dmidolkoq jd}par ag }bl }~e kemls "cl} |s sdq a}b dkm i}b! dpl oekklo}lm }bd}as ag }blq ak}lpdo} }blk ~l v|} 4 e}blp~asl 6 d} }bl a#i}b vesa}aek ak }bl dmidolkoq jd}par+ Ag ~loeks}p|o} d dmidolkoq jd}par gep }bl gan|pl / 4 dèwl ~l nl}#

D @ O M L G

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Akgepjd}aek _e|pol9 ]e s}|mq ak}lpdo}aeks ~l kllm d ml}daclm akgepjd}aek dè|} }bls}p|o}|pl eg }bl vpe}lak+ ]bl jdak se|pol eg akgepjd}aek |slm ak }bas vpeilo} ~ds }bl vpe}lakmd}d `dkh gacl ep +vm` gacl+ ]bas +vm` gacl as ldsacq dwdacd`cl ewlp }bl ak}lpkl} "_ll plglplkols

gep jepl ml}dacs!+ ]bas gacl s}epls dcjes} dcc }bl akgepjd}aek dè|} d svloagao vpe}lak ak d }lr}gepjd}+ ]bas md}d as e`}daklm }bpe|nb R*pdq maggpdo}aek jl}bems dkm `q KJP eg wdpae|svpe}laks lr}pdo}lm }acc md}l+ Ak }bas vpeilo} ~bd} ~l kllm as i|s} d sjdcc vep}aek eg }bas gacl}bd} s}epls }bl oeepmakd}ls eg wdpae|s d}ejs ak }bl vpe}lak oepl s}p|o}|pl+Clkn}b eg d vpe}lak9 Clkn}b eg d vpe}lak as nawlk `q }bl k|j`lp eg djake doams a} oeksas}s eg+_ejl vpe}laks dcse oek}dak olp}dak ncqoec*cavams# ncqolpec jeal}als# l}o ~baob akopldsls a}sclkn}b+ Ak }bas vpeilo} ~l bdwl ke} oeksamlplm }blj+


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? s V p e i l o } P l v e p }

Mlnpll eg d keml "ha!9 A} as }bl k|j`lp eg kemls }e ~baob a}b keml as maplo}cq oekklo}lm+

Oc|s}lpakn oelggaoalk} "Oa!9 Oc|s}lp oelggaoalk} as }bl gpdo}aek eg jdraj|j vessa`cl cakhs }bd}}bl klanbè|pakn kemls eg d keml a bdwl djekn }blj+ ^l mawaml a} `q }bl }e}dc k|j`lp egkemls }e nl} }bl dwlpdnl oc|s}lp oelggaoalk} gep }bl kl}~eph+

Vd}b clkn}b "Cai!9 K|j`lp eg kemls }bd} j|s} `l }pdwlpslm gpej keml a }e keml i `q }blsbep}ls} vd}b+ @q sbep}ls} vd}b ~l jldk }bl clds} k|j`lp eg kemls dkm ke} }bl mas}dkol+^l oe|cmk} odco|cd}l }bl oc|s}lp oelggaoalk}s dkm }bl vd}b clkn}bs m|l }e }bl caja}lm }ajl+

]BL PANB] MAPLO]AEK "JL]BEMECENQ!

Me~kcedm d vpe}lak md}d `dkh gacl gep }bl vpe}lak eg qe|p ak}lpls}+

Lr}pdo} }bl oeepmakd}ls eg }bl wdpae|s dcvbd odpèk d}ejs gpej }bl gacl+

Odco|cd}l }bl mas}dkol `l}~llk wdpae|s dcvbd odpèk d}ejs |sakn L|ocamadk mas}dkol

gepj|cd# : ( (

dkm oeks}p|o} }bl mas}dkol jd}par+

_odk }bas mas}dkol jd}par dkm oeks}p|o} gepj a} }bl dmidolkoq jd}par ek }bl `dsas eg d

mas}dkol }bplsbecm+ ^l dss|jlm a} }e `l >+6 +

Odco|cd}l wdpae|s kl}~eph vdpdjl}lps dkm vce} npdvbs ek }bl `dsas eg }bl dmidolkoq

jd}par }e s}|mq qe|p vpe}lak+

OEJV\]LP VPENPDJ_9

Vpenpdj / 49

Gecce~akn as }bl vpenpdj ~baob lr}pdo}s }bl plt|aplm akgepjd}aek "a+l+ }bl oeepmakd}ls eg }bldcvbd odpèk d}ek ak }bl djake doam! gpej d vm` gacl dkm ~pa}ls }blj ak dke}blp gaclkdjlm dg}lp }bl kdjl eg }bl vm` gacl gecce~lm `q d s|ggar UOD0+ ]bd} as ag }bl kdjl eg }blvm` gacl as 4YTO }blk }bl gacl ~a}b }bl oeepmakd}ls eg }bl dcvbd odpèk d}ejs ~acc `l4YTOUOD0+ ]bas as d }lr} gacl dkm odk `l evlklm ak ~epm vdm "ploejjlkmlm! ep ke}l vdm ak~akme~s+ Cak|r ep |kar |slps odk evlk }bas gacl |sakn dkq }lr} lma}ep cahl nlma}# kdke# waj#l}o+ ]bas gacl as opld}lm ak }bl sdjl maplo}epq ak ~baob }bl jdak vpenpdj gacl as s}eplm+ ]basvpenpdj dcse opld}ls dk ak}lpjlmad}l gacl ~a}b s|ggar UOD+ Vpenpdj dcse vce}s ep mpd~solp}dak s}p|o}|pls eg gan|pls dkm sdwls }blj ak ivln ep ivn gepjd}+ ]blsl vce}s dpl9

Vpe}lak dohèkl "s|ggar U4+ivn! Vpe}lak sbep} pdknl ak}lpdo}aeks "mas}dkol `l}~llk Os clss }bdk >+6 ! "s|ggar

U?+ivn! Vpe}lak ak}lpdo}aeks "mas}dkol `l}~llk Os ak pdknl 1+6 44+6 ! "s|ggar U=+ivn! Cekn pdknl vpe}lak ak}lpdo}aeks "mas}dkol ak pdknl 47+6 42+6 ! "s|ggar U+6 "s|ggar U0+ivn!


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= s V p e i l o } P l v e p }

KE]L9 ]bl npllk oece|plm me}s ep cd|k ak }bl dmidolkoq jd}par madnpdj as }bl vep}aek ~baoboepplsvekms }e }besl Os `l}~llk ~baob }bl mas}dkol as npld}lp }bdk >+6 a+l+ }blq dpl ke}oeksamlplm }e `l ak}lpdo}akn ~a}b ldob e}blp "`akdpq lt|awdclk} 6!# ~blplds }bl plm vep}aekas ~blpl }bl Os ak}lpdo} ep dpl oekklo}lm "`akdpq lt|awdclk} 4!+

vpak} .Lrlo|}akn jdak+vq.gak:akv|}"Lk}lp }bl kdjl eg }bl VM@ gacl9 "!/gep gak ak X.4YTO.#.4L>7.#.4AO1.#.4P\.#.4NND.#.4GOM.#.0Y^?.Z9g4:evlkgak#.p.!g0:evlkgak(.UOD.#.~(.!ves:6gep a ak g4+pldmcakls!9

g4+sllhves#6!s0:g4+pldmcakl466!ag clks0!;4


5/13


< s V p e i l o } P l v e p }

ves:6cas:XZgep a ak pdknl4#}e}(4!9

cas+dvvlkmves!g?+sllhves#6!s}:g?+pldmcakl

g6+~pa}lss4(ss0!ag mas;47+6 dkm mas342+69

g=+~pa}lss4(ss0!ag mas;6+64 dkm mas3>+69

vpak};;gg0#a(4#y(4lcsl9

vpak};;gg6#a(4#y(4

y(:4

ag a(4$:}e}9g?+sllhcasXa(4Z#6!g0+~pa}lss4(g?+pldmcakl


6/13



nv:Nk|vce}!nv"sl} }lpj ivln"!nv"sl} e|} ."(gak("U4+ivn."!nv"svce} ."(gak("UOD0. ~ cv cs >"!nv"|ksl} e|}"!nv"sl} e|} ."(gak("U0+ivn."!nv"vce} .L. ~ v# .G. ~ m"!nv"|ksl} e|}"!nv"sl} e|} ."(gak("U?+ivn."!nv"svce} .D. ~ c# ."(gak("UOD0. ~ cv cs >"!nv"|ksl} e|}"!nv"sl} e|} ."(gak("U=+ivn."!nv"svce} .@. ~ c# ."(gak("UOD0. ~ cv cs >"!nv"|ksl} e|}"!nv"sl} e|} ."(gak("U"!nv"|ksl} e|}"!

vpak} .Lra}akn gpej }bl vpenpdj+++.

Vpenpdj / 09

Gecce~akn as d vq}bek vpenpdj ~baob ~pa}ls }bl dmidolkoq jd}par ak d gacl ek }bl `dsas eg }blmas}dkol `l}~llk }bl }~e dcvbd odpèks ak dk djake doam+ Blpl ~l bdwl oeksamlplm }~edcvbd Odpèks }e `l oekklo}lm ag }bl mas}dkol `l}~llk }bl }~e dcvbd odpèks as clss }bdk>+6 }blk }blq dpl oekklo}lm dkm }bl àkdpq lt|awdclk} eg }bas as oeksamlplm }e `l 4+ Ake}blp ~epms ag }bl mas}dkol `l}~llk a}b O dkm i}b O as clss }bdk >+6 }blk ak}lpvpl}lp v|}s4 ak }bl a}b pe~ dkm i}b oec|jk eg }bl dmidolkoq jd}par e}blp~asl a} v|}s 6 ak }bl a}b pe~ dkm

i

}b

oec|jk eg }bl jd}par+ ]bl e|}v|} gacl as ~a}b s|ggar UNpdvb+osw+

KE]L9 ]bas gacl }dhls d gacl kdjlm dg}lp }bl kdjl eg }bl vm` gacl ~a}b s|ggar UOD0 ds akv|}#se jdhl s|pl }bd} a} as vplslk} ak }bl sdjl maplo}epq ak }bl gecce~akn vpenpdj gacl as vplslk}+

/ Nlklpd}ls }bl e|}v|} gacl gep vce}akn }bl dmidolkoq ep }bl oekklo}awa}q jd}par ak osw gepjd}gep jd}bljd}aod ep jd}cd`+

gep gak ak X.4YTO.#.4L>7.#.4AO1.#.4P\.#.4NND.#.4GOM.#.0Y^?.Z9/gak:akv|}.Lk}lp }bl VM@ gaclkdjl9 .!

g?:evlkgak(.UOD0.#.p.!g0:evlkgak(.UNpdvb+osw.#.~.!

}e}:clkg?+pldmcakls!!g?+sllh6#6!ves4:6s}:..gep a ak pdknl4#}e}(4!9

g?+sllhves4#6!ss4:g?+pldmcakl


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> s V p e i l o } P l v e p }

g?+sllhves0#6!sg:X6Z)7ss0:g?+pldmcakl

s}:s}(s}p.4#.!lcsl9

s}:s}(s}p.6#.!s}:s}(.Sk.

g0+~pa}ls}!g0+ocesl!g?+ocesl!

Vpenpdj / ?9Gecce~akn as d vq}bek vpenpdj ~baob ~pa}ls }bl mas}dkol jd}par ak d gacl ~a}b s|ggarUMas}+osw+ Mas}dkol jd}par s}epls }bl mas}dkol l}~llk }bl a}b dkm }bl i}b dcvbd odp`ek d}ejak a}s a}b pe~ dkm i}b oec|jk+ ]bas vpenpdj dcse }dhls akv|} gpej d gacl ~a}b s|ggar UOD0# sejdhl s|pl a}s }blpl ak }bl sdjl maplo}epq+

gep gak ak X.4YTO.#.4L>7.#.4AO1.#.4P\.#.4NND.#.4GOM.#.0Y^?.Z9/gak:akv|}.Lk}lp }bl VM@ gaclkdjl9 .!

g?:evlkgak(.UOD0.#.p.!g0:evlkgak(.UMas}+osw.#.~.!

}e}:clkg?+pldmcakls!!g?+sllh6#6!ves4:6s}:..gep a ak pdknl4#}e}(4!9

g?+sllhves4#6!ss4:g?+pldmcakl


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g0+~pa}ls}!g0+ocesl!g?+ocesl!

Vpenpdj / =9

Gecce~akn as d vq}bek vpenpdj ~baob vce}s d npdvb `l}~llk }bl k|j`lp eg kemls ~a}b hcakhs ep mlnplls wlps|s k|j`lp eg cakhs eg d keml+ ]bl e|}v|} gacl nlklpd}lm as sdjl ds }blkdjl eg }bl vm` gacl ~a}b s|ggar Umln0+ivn+ ]bas vpenpdj }dhls }bl gacl opld}lm `q vpenpdj/ 0 "~baob opld}ls }bl dmidolkoq jd}par! ds akv|}+

gpej Nk|vce} ajvep} Nk|vce}gep gak ak X.4L>7.#.4AO1.#.4P\.Z9

g4:evlkgak(.UNpdvb+osw.#.p.!g0:evlkgak(.UOD0.#.p.!g0+sllh6#6!

clkn:clkg0+pldmcakls!!g4+sllh6#6!}e}:clkg4+pldmcakls!!ves:6hh:XZg?:evlkgak(.Umlnpll0+}r}.#.~.!gep a ak pdknl4#}e}(4!9

g4+sllhves#6!ss:g4+pldmcakl0)clkn!(46!ves:g4+}lcc!s}:ss+svca}.#.!s}+vev!gep h ak pdknlclks}!!9

s}XhZ:ak}s}XhZ!gep h ak pdknlclks}!!9

s}XhZ:ak}s}XhZ!hh+dvvlkms|js}!!

gep a ak hh9vpak};;g?#a#hh+oe|k}a!

g4+ocesl!g0+ocesl!g?+ocesl!

bv:Nk|vce}!bv"sl} }l ivln"!

bv"sl} e|} ."(gak("Umln0+ivn."!bv"vce} XZX69Z ."(gak("Umlnpll0+}r}. ~ bas}lvs"!bv"|ksl} e|}"!

Vpenpdj /


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Gecce~akn as d vq}bek vpenpdj }bd} vce}s }bl mlnpll eg d keml wlps|s }bl keml k|j`lp+ ]ble|}v|} gacl nlklpd}lm as kdjlm ds }bl kdjl eg }bl vm` gacl ~a}b dmma}aekdc s|ggar Umln+ivn+]bas dcse }dhls }bl gacl opld}lm `q vpenpdj / 0 "~baob opld}ls }bl dmidolkoq jd}par! ds akv|}+

gpej Nk|vce} ajvep} Nk|vce}

gep gak ak X.4L>7.#.4AO1.#.4P\.Z9g4:evlkgak(.UNpdvb+osw.#.p.!g0:evlkgak(.UOD0.#.p.!g0+sllh6#6!clkn:clkg0+pldmcakls!!g4+sllh6#6!}e}:clkg4+pldmcakls!!ves:6hh:XZg?:evlkgak(.Umlnpll+}r}.#.~.!gep a ak pdknl4#}e}(4!9

g4+sllhves#6!ss:g4+pldmcakl0)clkn!(46!

ves:g4+}lcc!s}:ss+svca}.#.!s}+vev!gep h ak pdknlclks}!!9

s}XhZ:ak}s}XhZ!gep h ak pdknlclks}!!9

s}XhZ:ak}s}XhZ!vpak};;g?#a#s|js}!hh+dvvlkms|js}!!

vpak};;g?#./ ]bl dwlpdnl mlnpll as9.#s|jhh!)4+6%clkn!g4+ocesl!g0+ocesl!g?+ocesl!bv:Nk|vce}!bv"sl} }l ivln"!bv"sl} e|} ."(gak("Umln+ivn."!bv"vce} XZX69Z ."(gak("Umlnpll+}r}. ~ bas}lvs"!bv"|ksl} e|}"!

Vpenpdj / 79

Gecce~akn as d vq}bek vpenpdj }bd} vpak}s }bl clkn}b eg d vpe}lak ek }bl sopllk gpej }bl

akgepjd}aek lr}pdo}lm gpej }bl vm` gacl+

gep gak ak X.4YTO.#.4L>7.#.4AO1.#.4P\.#.4NND.#.4GOM.#.0Y^?.Z9g0:evlkgak(.UOD0.#.p.!g0+sllh6#6!vpak} gak#clkg0+pldmcakls!!g0+ocesl!

PL_\C]_9 Gecce~akn dpl d gl~ vce}s oeks}p|o}lm |sakn NK\VCE]+


10/13



@doh`ekl eg d vpe}lak "0A>\+vm`!

Dmidolkoq Jd}par gep 0A>\+vm` "Mas}dkol 3 >+6 !

@an me}s oepplsvekm }e 4

dkm sjdcc me}s oepplsvekm

}e 6+


11/13



_bep}*pdknl Ak}lpdo}aek Kl}~eph "Mas}dkol 3 >+6 !

Ak}lpdo}aek Kl}~eph "Mas}dkol `l}~llk 1+6 44+6 !


12/13



Cekn*pdknl Ak}lpdo}aek Kl}~eph "Mas}dkol 47+6 42+6 !

OEKOC\_AEK_9

]b|s was|dcayd}aek eg vpe}lak kl}~ephs ds npdvbs cldms }e d ~dq e|} eg }bl oejvclr

vpe`clj eg vpe}lak gecmakn+

]bl lrvlpajlk}dc oepplcd}aek l}~llk vpe}lak gecmakn pd}ls dkm oepplcd}aek

oelggaoalk} O as d kek*}pawadc i|s}agaod}aek eg vpe}lak kl}~eph jemlccakn+

C|ohacq# a} slljs# }bl }lobkat|ls eg }evecenaodc kl}~ephs vplmao} }bl vpevlp}als eg

vpe}lak }e d oedpsl mlnpll eg dvvperajd}aek+

]bl }pa|jvb eg }bas dvvpedob as }bd} a} odk vesl }bas vpe`clj ds d sajvcagalm

oejv|}d}aekdc vpe`clj# |sakn }bl s}dkmdpm pls|c}s eg cakldp dcnl`pd+

DOKE^CLMNLJLK] ' PLGLPLKOL_9

^l }bdkh Mp+ _ejmd}}d _akbd gpej Olk}pl gep Olcc|cdp ' Jeclo|cdp @aecenq# Bqmlpd`dm gepblp npld} blcv dkm lggep}s sbl }eeh }e }pdwlc }e e|p Aks}a}|}l gep mlcawlpakn d gl~lr}pdepmakdpq clo}|pls ek sqs}lj `aecenq dkm vpe}lak oek}do} kl}~ephs+ ]blsl clo}|plsn|amlm |s d ce}+ ^l dcse }bdkh Mp+ Idqdspa _dpjd dkm Mp+ ]pdmav Ndkn|cq gep lkoe|pdnakn dkms|vvep}akn }bpe|nbe|} }bl m|pd}aek eg }bl oe|psl+


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4? s V p e i l o } P l v e p }

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graph - theoretic approach to understand protein functioning using contact network

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