Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace Lorenza Bordoli Biozentrum of the University of Basel and Swiss Institute of Bioinformatics Lecture 2 May 2009 Lecture 2: Outline • Protein Families evolution • Recapitulation: sequence alignments – Pair wise and multiple sequence alignments – Databases search (BLAST, PSI-BLAST) – Patter, PSSMs, Profiles, HMMs – InterPro: Database of protein families and domains • Introduction to Homology modeling: – Target sequence feature annotation – Homology Modeling: Template identification Evolution of Protein Families Hemoglobin HemoglobinHemoglobin(Hb)(Hb) is is thethe heme-iron- heme-iron- containingcontaining oxygen- oxygen- transporttransport protein protein in in thethe red red blood blood cells cells of of vertebrates.vertebrates. Hb Hb transportstransports oxygen oxygen fromfrom the the lungs lungs or or gills gills toto the the rest rest of of the the bodybody where where it it releasesreleases the the oxygen oxygen forfor cell cell use. use. In In the the tetramerictetrameric form form of of hemoglobin,hemoglobin, the the Image source:Commons. Wikimedia bindingbinding of of oxygen oxygen is is a a cooperativecooperative process. process. Human hemoglobin; PDB:1GZX Myoglobin MyoglobinMyoglobin(Mb)(Mb) is is a a single-chainsingle-chain globular globular proteinprotein containing containing a a hemeheme prosthetic prosthetic groupgroup in in the the center. center. MbMb is is the the primary primary oxygen-carryingoxygen-carrying pigmentpigment of of muscle muscle tissues.tissues. Image source:Commons. Wikimedia Sperm Whale myoglobin; PDB:1MBO Evolution of the globin family: • Multiple alignment of amino acid sequences: sp|P01922|HBA_HUMAN 1 -V LS PA DK TN VK AA WG KV GA HA GE YG AE AL ER MF LS FP TT KT YF PH F- DL SH -- -- -G SA sp|P01958|HBA_HORSE 1 -V LS AA DK TN VK AA WS KV GG HA GE YG AE AL ER MF LG FP TT KT YF PH F- DL SH -- -- -G SA sp|P02023|HBB_HUMAN 1 VH LT PE EK SA VT AL WG KV -- NV DE VG GE AL GR LL VV YP WT QR FF ES FG DL ST PD AV MG NP sp|P02062|HBB_HORSE 1 VQ LS GE EK AA VL AL WD KV -- NE EE VG GE AL GR LL VV YP WT QR FF DS FG DL SN PG AV MG NP sp|P02185|MYG_PHYCA 1 -V LS EG EW QL VL HV WA KV EA DV AG HG QD IL IR LF KS HP ET LE KF DR FK HL KT EA EM KA SE sp|P01922|HBA_HUMAN 54 QV KG HG KK VA DA LT NA VA HV DD MP NA LS AL SD LH AH KL RV DP VN FK LL SH CL LV TL AA HL sp|P01958|HBA_HORSE 54 QV KA HG KK VG DA LT LA VG HL DD LP GA LS NL SD LH AH KL RV DP VN FK LL SH CL LS TL AV HL sp|P02023|HBB_HUMAN 59 KV KA HG KK VL GA FS DG LA HL DN LK GT FA TL SE LH CD KL HV DP EN FR LL GN VL VC VL AH HF sp|P02062|HBB_HORSE 59 KV KA HG KK VL HS FG EG VH HL DN LK GT FA AL SE LH CD KL HV DP EN FR LL GN VL VV VL AR HF sp|P02185|MYG_PHYCA 60 DL KK HG VT VL TA LG AI LK KK GH HE AE LK PL AQ SH AT KH KI PI KY LE FI SE AI IH VL HS RH sp|P01922|HBA_HUMAN 114 PA EF TP AV HA SL DK FL AS VS TV LT SK YR -- -- -- sp|P01958|HBA_HORSE 114 PN DF TP AV HA SL DK FL SS VS TV LT SK YR -- -- -- sp|P02023|HBB_HUMAN 119 GK EF TP PV QA AY QK VV AG VA NA LA HK YH -- -- -- sp|P02062|HBB_HORSE 119 GK DF TP EL QA SY QK VV AG VA NA LA HK YH -- -- -- sp|P02185|MYG_PHYCA 120 PG DF GA DA QG AM NK AL EL FR KD IA AK YK EL GY QG HBA|B_HUMAN: Hemoglobin alpha|betachain from Homo sapiens (Human) HBA|B_HUMAN: Hemoglobin alpha|betachain from Equus caballus (Horse) MYG_PHYCA: Myoglobin from Physeter catodon (Sperm whale) Evolution of the globin family: • Variability at different positions reflects functional and/or structural importance: Human hemoglobin β chain His 92 His 63 sp|P01922|HBA_HUMAN 1 - V L S P A D K T N V K A A W G K V G A H A G E Y G A E A L E R M F L S F P T T K T Y F P H F - D L S H - - - - - G S A sp|P01958|HBA_HORSE 1 - V L S A A D K T N V K A A W S K V G G H A G E Y G A E A L E R M F L G F P T T K T Y F P H F - D L S H - - - - - G S A sp|P02023|HBB_HUMAN 1 V H L T P E E K S A V T A L W G K V - - N V D E V G G E A L G R L L V V Y P W T Q R F F E S F G D L S T P D A V M G N P sp|P02062|HBB_HORSE 1 V Q L S G E E K A A V L A L W D K V - - N E E E V G G E A L G R L L V V Y P W T Q R F F D S F G D L S N P G A V M G N P sp|P02185|MYG_PHYCA 1 - V L S E G E W Q L V L H V W A K V E A D V A G H G Q D I L I R L F K S H P E T L E K F D R F K H L K T E A E M K A S E sp|P01922|HBA_HUMAN 54 Q V K G H G K K V A D A L T N A V A H V D D M P N A L S A L S D L H A H K L R V D P V N F K L L S H C L L V T L A A H L sp|P01958|HBA_HORSE 54 Q V K A H G K K V G D A L T L A V G H L D D L P G A L S N L S D L H A H K L R V D P V N F K L L S H C L L S T L A V H L sp|P02023|HBB_HUMAN 59 K V K A H G K K V L G A F S D G L A H L D N L K G T F A T L S E L H C D K L H V D P E N F R L L G N V L V C V L A H H F sp|P02062|HBB_HORSE 59 K V K A H G K K V L H S F G E G V H H L D N L K G T F A A L S E L H C D K L H V D P E N F R L L G N V L V V V L A R H F sp|P02185|MYG_PHYCA 60 D L K K H G V T V L T A L G A I L K K K G H H E A E L K P L A Q S H A T K H K I P I K Y L E F I S E A I I H V L H S R H sp|P01922|HBA_HUMAN 114 P A E F T P A V H A S L D K F L A S V S T V L T S K Y R - - - - - - sp|P01958|HBA_HORSE 114 P N D F T P A V H A S L D K F L S S V S T V L T S K Y R - - - - - - sp|P02023|HBB_HUMAN 119 G K E F T P P V Q A A Y Q K V V A G V A N A L A H K Y H - - - - - - sp|P02062|HBB_HORSE 119 G K D F T P E L Q A S Y Q K V V A G V A N A L A H K Y H - - - - - - sp|P02185|MYG_PHYCA 120 P G D F G A D A Q G A M N K A L E L F R K D I A A K Y K E L G Y Q G Evolution of the globin family: LeghemoglobinLeghemoglobinisis a a hemoproteinhemoprotein found found in in thethe nitrogen-fixing nitrogen-fixing rootroot nodules nodules of of leguminousleguminous plants. plants. LeghemoglobinLeghemoglobin has has a a highhigh affinity affinity for for oxygenoxygen - - high high enough enough toto allow allow nitrogenase nitrogenase to to functionfunction but but low low enoughenough so so that that it it can can provideprovide the the bacteria bacteria withwith oxygen oxygen for for respiration.respiration. Image source: A. Lesk Sperm Whale Myoglobin; PDB:1MBD Lupin leghemoglobin; PDB:2LH7 LeghemoglobinLeghemoglobinisis a a hemoproteinhemoprotein found found in in thethe nitrogen-fixing nitrogen-fixing rootroot nodules nodules of of leguminousleguminous plants.