In switching off the root effect in fish hemoglobins

tarix	24.06.2016
ölçüsü	0.56 Mb.

Supplementary material
AN ORDER-DISORDER TRANSITION PLAYS A ROLE

IN SWITCHING OFF THE ROOT EFFECT IN FISH HEMOGLOBINS

Vergara et al.
Table S1. Intra-layer packing contacts in the crystal of deoxyHb1Tn.
Table S2. Inter-layer packing contacts in the crystal of deoxyHb1Tn.
Fig. S1. Layers of tetramers forming the crystal packing of both DeoxyHb1Tn and DeoxyHbTb.
Fig. S2. Omit electron density maps of region 40-50 of the α chain of DeoxyHb1Tn countoured at 2.5  (A) and 2.0  (B).
Fig. S3. Aminoacid sequence of  and  chains of human and some fish Hbs. The secondary structure, the proximal and distal His, and Asp belonging to the triad at the ₁₂ interface are highlighted. Accession number SWISS-Prot Data Bank to the amino-acid sequence used in the figure are the following: Trematomus newnesi Hb1 (P45718, P45720) and HbC (P45718, P45721), Trematomus bernacchii Hb1 (P80043, P80044), Notothenia angustata Hb1 (P29624, P29628), Gobionotothen gibberifrons Hb1 (P83611, P83612), Gymnodraco acuticeps Hb (P29623, P29625), Cygnodraco mawsoni Hb1 (P23016, P23017), Artedidraco orianae Hb (P0C237, P0C239) Cottoperca gobio Hb1 (P84653, P84652), Thunnus thynnus Hb (P11748, P11749), Pseudaphritis urvillii Hb1 (P83623, P83624), Liparis tunicatus Hb (P85081, P85082) Chelidonichthys kumu Hb (P80270, P80271), Oncorhynchus mykiss Hb1 and Hb4 (P02019, P02142, P14527, P02141), Brycon cephalus Hb (UniProt ref. A1YZP4), Perca flavescens Hb (UniProt ref A8HTG8), Cyprinus carpio Hb (P02016, P02139) Leiostomus xanthurus Hb (P56250, P56251), Homo sapiens Hb (P01922, P02023).

Table S1. Intra-layer packing contacts in the crystal of deoxyHb1Tn.

Residue	Atom	Residue	atom
Ala8 α₁	O	Ser9 β₂	Oγ
Arg11 α₁	Cβ	Ser12 β₂	Oγ
Arg11 α₁	NH₂	His17 β₂	Nε₂
Asp75α₁	Oδ₂	Asp13 β₂	Oδ₁

Table S2. Inter-layer packing contacts in the crystal of deoxyHb1Tn.

deoxyHb1Tn
Residue	Atom	Residue	atom
Ala21 β₁	O	Tyr49 β₂	OH
Glu83 α₂	Cγ	Tyr49 β₂	Cδ₁
Glu83 α₂	Oε₁	Tyr49 β₂	Cδ₁
Glu83 α₂	O	Asn47 β₂	Oδ₁
Glu86 α₂	Cδ	Asn47 β₂	Cδ₁
Tyr90 α₂	Cδ₁	Ser56 β₂	O
Asp48 α₂	Cβ	Glu94 β₂	O
Pro47 α₂	O	Thr90 β₂	Cγ₂

deoxyHbTb
Residue	Atom	Residue	atom
Gln87 α₁	Oε₁	heme α₂	O2A
Glu83 α₁	Oε₂	His55 α₂	Nε₂
Pro47 α₁	Cβ	His69 α₂	Nε₂
Asn47 β₁	Oδ₁	Glu52 β₂	Oε₂
Tyr49 β₁	OH	Glu52 β₂	Oε₂
Gln87 α₁	Oε₁	heme α₂	O2A

Figure S1

Figure S2

Figure S3
ALPHA CHAIN
1 10 20 30 40 48

| | | | | |

Trematomus newnesi Hb1 -SLSDKDKAAVRALWSKIGKSSDAIGNDALSR-MIVVYPQTKIYFSHW-PD

Trematomus newnesi HbC -SLSDKDKAAVRALWSKIGKSSDAIGNDALSR-MIVVYPQTKIYFSHW-PD

Trematomus bernacchii Hb1 -SLSDKDKAAVRALWSKIGKSADAIGNDALSR-MIVVYPQTKTYFSHW-PD

Notothenia angustata Hb1 -SLSDKDKAAVRALWSKIGKSADAIGNDALSR-MIVVYPQTKTYFSHW-PD

Gobionotothen gibberif. Hb1 -SLSVKDKAAVRALWSKISKSSDAIGNDALSR-MIVVYPQTKTYFSHW-PD

Gymnodraco acuticeps Hb -SLSDKDKAAVRALWSTISKSSDAIGNDALSR-MIVVYPQTKIYFSHW-PE

Cygnodraco mawsoni Hb1 -SLSDKDKAAVKALWTTISKSSDAIGNDALSR-MIVVYPQTKTYFSHW-PD

Artedidraco orianae Hb -SLSDKDKAAVKALWSKIAKSADVIGNDAVSR-MIVVYPQTKTYFAHW-PD

Cottoperca gobio Hb1 -SLTEKDKAAVRALWGKISKSADAIGADALSR-MLFVYPQTKTYFTHW-PD

Thunnus thynnus Hb TTLSDKDKSTVKALWGKISKSADAIGADALGR-MLAVYPQTKTYFSHW-PD

Pseudaphritis urvillii Hb1 -SLTDKDKATVKALWGKISKSADAVGADAVGR-MIVVYPQTKTYFSHW-PD

Liparis tunicatus Hb -SLSTKDKETVKDLWGHISASADAIGADALGR-LLVVYPQTKIYFLHW-PD

Chelidonichthys kumu Hb -SLSDKDKNTVRALWAKISKSADVIGAEALAR-MLTVYPQTKTYFTHW-TD

Trematomus newnesi Hb2 -SLSTKDKETVKAFWSKVSGKTEDIGNDALSR-MLVVYPQTKIYFSHW-KE

Oncorhynchus mykiss Hb4 -SLSAKDKANVKAIWGKILPKSDEIGEQALSR-MLVVYPQTKAYFSHW-AS

Brycon cephalus Hb -SLSDKDKDSIKAFWAKISPKAEDIGADALAR-MLTVYPQTKTYFSHW-KD

Perca flavescens Hb -SLSSKDKDAVKALWGKIADKAEEIGADALGR-MLAVYPQTKTYFSHW-KD

Oncorhynchus mykiss Hb1 -SLTAKDKSVVKAFWGKISGKADVVGAEALGR-MLTAYPQTKTYFSHW-AD

Cyprinus carpio Hb -SLSAKDKAAVKDLWAKISGKADDIGQDALSRGMLVVYPQTKTYFSHW-KD

Leiostomus xanthurus(spot)Hb –SLSATDKARVKALWDKIEGKSAELGAEALGR-MLVSFPQTKIYFSEWGQD

Homo sapiens Hb -VLSPADKTNVKAAWGKVGAHAGEYGAEALER-MFLSFPTTKTYFPHF--D

Secondary structure HHHHHHHHHHHHHH HHHHHHHHHHHHHHHH

50 60 70 80 90 98

| | | | | |

Trematomus newnesi Hb1 VTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSN

Trematomus newnesi HbC VTPGSPNIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPSN

Trematomus bernacchii Hb1 VTPGSPHIKAHGKKVMGGIALAVSKIDDLKTGLMELSEQHAYKLRVDPAN

Notothenia angustata Hb1 VTPGSAHIKAHGKKVMGGIALAVSKIDDLKAGLSDLSEQHAYKLRVDPAN

Gobionotothen gibberif. Hb1 VTPGSAHIKAHGKKVMGGIALAVSKIDDLNAGLLELSEQHAYKLRVDPAN

Gymnodraco acuticeps Hb VIPGSIHIKEHGKKVMGGIELAVSKIDDLKTGLFELSEQHAFKLRVDPGN

Cygnodraco mawsoni Hb1 VTPGSTHIRDHGKKVMGGISLAVSKIDDLKTGLFELSEQHAFKLRVDPAN

Artedidraco orianae Hb LTPGSTNIKAHGKKVMGGIALAVSKIDDLKAGLSDLSEQHAFKLRVDPAN

Cottoperca gobio Hb1 LSPGSVHVKKHGKNVMGGIALAVSKIDDLTNGLMELSEQHAYQLRVDPAN

Thunnus thynnus Hb MSPGSGPVKAHGKKVMGGVALAVTKIDDLTTGLGDLSELHAFKMRVDPSN

Pseudaphritis urvillii Hb1 LAPNSPHVKTHGKTVMTGIALAVSKIDDLTNGLLELSEEHAYKMRVDPAN

Liparis tunicatus Hb LSPNSPSVKNHGKNIMSGIALAVTKIDDLKSGLNALSEQHAFQLRVDPAN

Chelidonichthys kumu Hb LSPSSTSVKNHGKNIMVGVSLAVSKMDDLTAGLLELSEKHAFQLRVDPAN

Trematomus newnesi Hb2 LTPGSAPVRKHGMTVMKGVGDAVSKIEDLTAGLTELSELHAFTLRVDPGN

Oncorhynchus mykiss Hb4 VAPGSAPVKKHGITIMNQIDDCVGHMDDLFGFLTKLSELHATKLRVDPTN

Brycon cephalus Hb LSPGSAPVKKHGKTVMGSVAEAVSKIDDLTNGLLTLSELHAFQLRVDPAN

Perca flavescens Hb LSPGSAPVNKHGKTIMGGLVDAVASIDDLNAGLLALSELHAFTLRVDPAN

Oncorhynchus mykiss Hb1 LSPGSGPVKKHGGIIMGAIGKAVGLMDDLVGGMSALSDLHAFKLRVDPGN

Cyprinus carpio Hb LSPGSAPVRKHGKTVMSGVADAVSKIDDLTSGLLNLSELHAFQLRIDPAN

Leiostomus xanthurus(spot)Hb LGPQTPQVRNHGAVIMAAVGKAVKSIDNLVGGLSQLSELHAFKLRVDPAN

Homo sapiens Hb LSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVN

Secondary structure HHHHHHHHHHHHHHHHHHH HHHHTHHHHHHHH HH

100 110 120 130 140

| | | | |

Trematomus newnesi Hb1 FKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR

Trematomus newnesi HbC FKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR

Trematomus bernacchii Hb1 FKILNHCILVVISTMFPKEFTPEAHVSLDKFLSGVALALAERYR

Notothenia angustata Hb1 FKILNHCILVVISTMFPKDFTPEAHVSLDKFLSGVALALAERYR

Gobionotothen gibberif. Hb1 FKILNHCILVVISTMFPKDFTPEAHVSLDKFLSGVALALAERYR

Gymnodraco acuticeps Hb FKILNHCILVVIATMFPKEFTPEAHVSLDKFLSGVALALAERYR

Cygnodraco mawsoni Hb1 FKILNHCILVVIATMFPKEFTPEAHVSLDKFLSGVALALAERYR

Artedidraco orianae Hb FKILNHCIMVVISSMFPKDFTPEAHISLDKFLSAVALALAEKYR

Cottoperca gobio Hb1 FKILSHCILVVVSIMYPKDFTPEAHVSLDKFLSGVSLALAERYR

Thunnus thynnus Hb FKILSHCILVVVAKMFPKEFTPDAHVSLDKFLASVALALAERYR

Pseudaphritis urvillii Hb1 FKILSHCMLVVIATMFPKEFTPEAHVCLDKFLCAVSLALSERYR

Liparis tunicatus Hb FKLLSHCILVVLAIRFPHEFTPEAHVAMDKFFCGVSLALAEKYR

Chelidonichthys kumu Hb FKLLSHCLLVVISIMFPKEFGPEVHVSVDKFFANLALALSERYR

Trematomus newnesi Hb2 FKILSHNILVVFAIMFPNDFTPQVHVSMDKFLAALSRALSEKYR

Oncorhynchus mykiss Hb4 FKILAHNLIVVIAAYFPAEFTPEIHLSVDKFLQQLALALAEKYR

Brycon Cephalus Hb FKILSHNLLVVLAQQFPNDFTPEVHVSMDKFLSLLSWSLSEKYR

Perca flavescens Hb FKILSHCILVQLAVKFPKDFTPEVHLSYDKFFSAVARALAEKYR

Oncorhynchus mykiss Hb1 FKILSHNILVTLAIHFPSDFTPEVHIAVDKFLAAVSAALADKYR

Cyprinus carpio Hb FRILSHNILVVLATMFPDDFTPEAHVAMDKFLSALALALSEKYR

Leiostomus xanthurus(spot)Hb FKILAHNIILVISMYFPGDFTPEVHLSVDKFLACLALALSEKYR

Homo sapiens Hb FKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Secondary structure HHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHH

BETA CHAIN

1 10 20 30 40 49

| | | | | |

Trematomus newnesi Hb1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLY

Trematomus newnesi HbC VEWTDFERATIKDIFSKLEYDVVGPATLARCLVVYPWTQRYFGKFGNLY

Trematomus bernacchii Hb1 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLY

Notothenia angustata Hb1 VKWSDSERAIITDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLY

Gobionotothen gibberif. Hb1 VEWTDKERAIITDIFSHMDYDDIGPKALSRCLIVYPWTQRHFSGFGNLY

Gymnodraco acuticeps Hb VNWTLTEKATITDIFSHLDYDDIGPKALSRCLIVYPWTQRYFSGFGNLY

Cygnodraco mawsoni Hb1 VKWSKTELTIINDIFSHLDYDDIGPKALSRCLIVYPWTQRHFSGFGNLY

Artedidraco orianae Hb VQWSDSERTIINGIFSQLDYDDLGPKAFSRCLIVYPWTQRYFSSFGNLD

Cottoperca gobio Hb1 VEWTDFERATIKDVFSKIEYEVVGPAALARCLVVYPWTQRYFGNFGNLY

Thunnus thynnus Hb VEWTQQERSIIAGIFANLNYEDIGPKALARCLIVYPWTQRYFGAYGDLS

Pseudaphritis urvillii Hb1 VVWTNEERSIISSIFSNLDYDDIGPKALCRCLIVYPWTQRHFTTFGNLY

Liparis tunicatus Hb VHWTDFERSTIKDIFAKIDYDCVGPAAFARCLIVYPWTQRYFGNFGNLF

Chelidonichthys kumu Hb VEWTDFERATIQDIFSKMDYETVGPATLTRTVIVYPWTLRYFAKFGNIC

Trematomus newnesi Hb2 VEWTDKERSIISDIFSHMDYDDIGPKALSRCLVVYPWTQRYFSGFGNLY

Oncorhynchus mykiss Hb4 VDWTDAERSAIVGLWGKISVDEIGPQALARLLIVSPWTQRHFSTFGNLS

Brycon cephalus Hb VEWSTAERSAIAGLWGKISVDEIGPQALSRLLIVYPWTQRHFAAFGNLS

Perca flavescens Hb VVWTDFERATIADIFSKLDYEAVGGATLARCLIVYPWTQRYFGNFGNLY

Oncorhynchus mykiss Hb1 VEWTDAEKSTISAVWGKVNIDEIGPLALARVLIVYPWTQRYFGSFGNVS

Cyprinus carpio Hb VEWTDAERSAIIALWGKLNPDELGPEALARCLIVYPWTQRFFASYGNLS

Leiostomus xanthurus(spot)Hb VDWTDAERAAIKALWGKIDVGEIGPQALSRLLIVYPWTQRHFKGFGNIS

Homo sapiens Hb VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLS

Secondary structure HHHHHHHHHHHHH HHHHHHHHHHHHHHH

50 60 70 80 90 99

| | | | | |

Trematomus Newnesi Hb1 NAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVD

Trematomus Newnesi HbC NAAAIAQNAMVSKHGTTILNGLDRAVKNMDDITNTYAELSVLHSEKLHVD

Trematomus bernacchii Hb1 NAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYADLSTLHSEKLHVD

Notothenia angustata Hb1 NAEAILGNANVAAHGIKVLHGLDRGVKNMDNIAATYAELSILHSEKLHVD

Gobionotothen gibberifronsHb1 NAEAIIGNANVAAHGIKVLHGLDRGVKNMDNIAATYAELSTLHSEKLHVD

Gymnodraco acuticeps Hb NAAAIIGNAKVAEHGIKVLHGLDLGLKKMDNIEAAYADLSSLHSEKLHVD

Cygnodraco mawsoni Hb1 NAEAIIGNANVAAHGIKVLHGLDRGLKNMDNIVDAYAELSTLHSEKLHVD

Artedidraco orianae Hb NAEAIMGNANVAAHGIKVLHGLDRGVKNMDDIMGVYAELSSLHSEKLHVD

Cottoperca gobio Hb1 NAAAITGNPKVAKHGITILHGLDKAVKNMDDIRNTYAELSVLHSEKLHVD

Thunnus thynnus Hb TPDAIKGNAKIAAHGVKVLHGLDRAVKNMDNINEAYSELSVLHSDKLHVD

Pseudaphritis urvillii Hb1 TPEAIMTNSKVAEHGVKVLHGLDRAVKNMDNIKATYYDLSILHSEKLHVD

Liparis tunicatus Hb NAAAIIGNPNVAKHGITIMHGLERGVKNLDHLTETYEELSVLHSEKLHVD

Chelidonichthys kumu Hb STAAILGNKEIAKHGTTILHGLDRGVKNMDDIKNTYAELSKLHSEKLHVD

Trematomus Newnesi Hb2 NAEGIMSNANVAAHGIKVLHGLDRGMKNMDNIADAYTDLSTLHSEKLHVD

Oncorhynchus mykiss Hb4 TPAAIMGNPAVAKHGKTVMHGLDRAVQNLDDIKNTYVTLSVMHSEKLFVD

Brycon Cephalus Hb SPAAINGNPKVAHHGKVVMGGLERAIKNMDNIKAAYSSLSVMHSEKLHVD

Perca flavescens Hb NAAAIMGNPMIAKHGTTILHGLDRAVKNMDNIKATYAELSVLHSEKLHVD

Oncorhynchus mykiss Hb1 TPAAIMGNPKVAAHGKVVCGALDKAVKNMGNILATYKSLSETHANKLFVD

Cyprinus carpio Hb SPAAIMGNPKVAAHGRTVEGGLMRAIKDMDNIKATYAPLSVMHSEKLHVD

Leiostomus Xanthurus(spot)Hb TNAAILGNAKVAEHGKTVMGGLDRAVQNMDNIKNVYKQLSIKHSEKIHVD

Homo sapiens Hb TPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVD

Secondary structure HHHHHH HHHHHHHHHHHHHHHHHH HHHHHHHHHHHH

100 110 120 130 140 146

| | | | | |

Trematomus Newnesi Hb1 PDNFKLLSDCITIVLAAKMGHA-FTAETQGAFQKFLAAVVSALGKQYH

Trematomus Newnesi HbC PDNFKLLADCLTIVVAARFGSA-FTGEVQAAFQKFMAVVVSSLGKQYR

Trematomus bernacchii Hb1 PDNFKLLSDCITIVLAAKMGHA-FTAETQGAFQKFLAVVVSALGKQYH

Notothenia angustata Hb1 PDNFKLLSDCITIVVAAKMGQA-FTPETQAAVQKFLAVVVSALGKQYH

Gobionotothen gibberifrons Hb1 PDNFKLLSDCITIVVAAKLGHA-FTAETQGALQKFLAVVVSALGKQYH

Gymnodraco acuticeps Hb PDNFKLLSDCITIVLAAKLGSA-FTAETQATFQKFLGAVMSALGKQYH

Cygnodraco mawsoni Hb1 PDNFKLLSDCITIVLAAKLGKA-FTAETQAAFQKFMAVVVSALGKQYH

Artedidraco orianae Hb PDNFKLLSDCITIVVAAKLGNA-FTPETQAAFQKFLGAVVMFLGKQYH

Cottoperca gobio Hb1 PDNFKLLADCLTIVVAAQMGKA-FTGEIQAAFQKFLAVVVSSLGRQYH

Thunnus thynnus Hb PDNFRILGDCLTVVIAANLGDA-FTVETQCAFQKFLAVVVFALGRKYH

Pseudaphritis urvillii Hb1 PDNFKLLSDCLTIVVAAKMGSG-FTPETQAAFQKFLAVVVSALGKQYH

Liparis tunicatus Hb PDNFKLISDCLTIVVASRLGKA-FTGEVQAALQKFLAVVVFSLGKQYH

Chelidonichthys kumu Hb PDNFRLLSDCLTIVVAAKMGKD-FTGEVQAAFQKFLSVVVNSLGRQYH

Trematomus Newnesi Hb2 PDNFKLLSDCITIVLAAKMGHA-FTAETQGAFQKFLAAVVSALGKQYH

Oncorhynchus mykiss Hb4 PDNFRLLADCITVCVAAKLGPAVFSADTQEAFQKFLAVVVSALGRQYH

Brycon Cephalus Hb PDNFRLLADCITVCVAMKFGPSAFTPDVQEAWQKFLAVVVAALSR-YH

Perch Hb PDNFKLLSDCLTIVVAAQLGKA-FSGEVQAAFQKFLSVVVSALGKQYH

Oncorhynchus mykiss Hb1 PDNFRVLADVLTIVIAAKFGAS-FTPEIQATWQKFMKVVVAAMGSRYF

Cyprinus carpio Hb PDNFRLLADCITVCAAMKFGPSGFSPNVQEAWQKFLSVVVNALKRGYN

Leiostomus Xanthurus (spot) Hb PDNFRLLGEIITMCVGAKFGPSAFTPEIHEAWQKFLAVVVSALGRQYH

Homo sapiens Hb PENFRLLGNVLVCVLAHHFGKE-FTPPVQAAYQKVVAGVANALAHKYH

Secondary structure HHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHH