Dcartmel Week 14

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Purpose

The purpose of the assignment this week is to investigate our particular research question. For this project we will further investigate the structure-function relationship between SARS-CoV-2 and ACE2 in terms of possible weaker interactions between the proteins. We will compare the amino acid sequences of the different strains of the SARS virus and determine if variances in amino acid sequence has any effects on the overall function of the SARS viruses.

Combined methods/results

Multiple Sequence Alignment

  • Sequences of different spike proteins were aligned using www.phylogeny.fr
    • Used "One Click" option and uploaded the FASTSA sequences for all S proteins
    • Exported sequence in clustal format
AAP50485.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAP30713.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAP13441.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAP41037.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAU04664.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAV49730.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAV97995.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
AAV98000.1      MFI--------FLLFLTLTS-------GSDLDRCTTFDDVQ--APNYTQHTSSMRGVYYP
n6VXX_1|Ch      MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTN--SFTRGVYYP
QHR63300.2      MFV--------FLVLLPLVS-----------SQCVNLTTRTQLPPAYTN--SSTRGVYYP
sp|P0DTC2|      MFV--------FLVLLPLVS-----------SQCVNLTTRTQLPPAYTN--SFTRGVYYP
QHD43416.1      MFV--------FLVLLPLVS-----------SQCVNLTTRTQLPPAYTN--SFTRGVYYP
                * :        :* ::.* *            .*..:      .* **:  *  ******
AAP50485.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FGNPVIPFKDGIYFAATEKSN
AAP30713.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FGNPVIPFKDGIYFAATEKSN
AAP13441.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FGNPVIPFKDGIYFAATEKSN
AAP41037.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FGNPVIPFKDGIYFAATEKSN
AAU04664.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FDNPVIPFKDGIYFAATEKSN
AAV49730.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FDNPVIPFKDGIYFAATEKSN
AAV97995.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FDNPVIPFKDGIYFAATEKSN
AAV98000.1      DEIFRSDTLYLTQDLFLPFYSNVTGFHTINHT-------FDNPVIPFKDGIYFAATEKSN
n6VXX_1|Ch      DKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSN
QHR63300.2      DKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSN
sp|P0DTC2|      DKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSN
QHD43416.1      DKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSN
                *::***..*: ********:**** **:*: :       *.***:**:**:***:*****
AAP50485.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHT----MI
AAP30713.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHT----MI
AAP13441.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHT----MI
AAP41037.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHT----MI
AAU04664.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFVVSKPMGTRTHT----MI
AAV49730.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFVVSKPMGTRTHT----MI
AAV97995.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFVVSKPMGTQTHT----MI
AAV98000.1      VVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFVVSKPMGTQTHT----MI
n6VXX_1|Ch      IIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRV
QHR63300.2      IIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRV
sp|P0DTC2|      IIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRV
QHD43416.1      IIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRV
                ::***:**:*::.*:**::*:**:*****..*:*::*::**: *    ...:.      :
AAP50485.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAP30713.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAP13441.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAP41037.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAU04664.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAV49730.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAV97995.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
AAV98000.1      FDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSG
n6VXX_1|Ch      YSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQG
QHR63300.2      YSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPPG
sp|P0DTC2|      YSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQG
QHD43416.1      YSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQG
                :..* ******:*:.* :*:. *.****:******** **:: :*. : **::***** *
AAP50485.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDI--WGTSAAAYFVGYLKPTTFMLKY
AAP30713.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDI--WGTSAAAYFVGYLKPTTFMLKY
AAP13441.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDI--WGTSAAAYFVGYLKPTTFMLKY
AAP41037.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDI--WGTSAAAYFVGYLKPTTFMLKY
AAU04664.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDT--WGTSAAAYFVGYLKPTTFMLKY
AAV49730.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDT--WGTSAAAYFVGYLKPTTFMLKY
AAV97995.1      FNTLKPIFKLPLGINITNFRAIL----TAFSPAQDT--WGTSAAAYFVGYLKPTTFMLKY
AAV98000.1      FNTLKPIFKLPLGIKITNFRAIL----TAFSPAQGT--WGTSAAAYFVGYLKPTTFMLKY
n6VXX_1|Ch      FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKY
QHR63300.2      FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKY
sp|P0DTC2|      FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKY
QHD43416.1      FSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKY
                *.:*:*:..**:**:**.*.::*    : ::*.:.   * :.****:****:* **:***
AAP50485.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAP30713.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAP13441.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG 
AAP41037.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAU04664.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAV49730.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAV97995.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
AAV98000.1      DENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFG
n6VXX_1|Ch      NENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFG
QHR63300.2      NENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTDSIVRFPNITNLCPFG
sp|P0DTC2|      NENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFG
QHD43416.1      NENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFG
                :***********: :**:* **::*** ::*********** *: .:*************
AAP50485.1      EVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADS
AAP30713.1      EVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADS
AAP13441.1      EVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADS
AAP41037.1      EVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADS
AAU04664.1      EVFNATKFPSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADS
AAV49730.1      EVFNATKFPSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADS
AAV97995.1      EVFNATKFPSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADS
AAV98000.1      EVFNATKFPSVYAWERKRISNCVADYSVLYNSTSFSTFKCYGVSATKLNDLCFSNVYADS
n6VXX_1|Ch      EVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADS
QHR63300.2      EVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADS
sp|P0DTC2|      EVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADS
QHD43416.1      EVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADS
                ****** *.*****:**.**************: **********.********:******
AAP50485.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAP30713.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAP13441.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAP41037.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAU04664.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAV49730.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
AAV97995.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKFRYLRHG
AAV98000.1      FVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHG
n6VXX_1|Ch      FVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKS
QHR63300.2      FVITGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSKHIDAKEGGNFNYLYRLFRKA
sp|P0DTC2|      FVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKS
QHD43416.1      FVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKS
                **: **:********** ************ ***:***:.::*:.  **:** :* :*:.
AAP50485.1      KLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLN
AAP30713.1      KLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLN
AAP13441.1      KLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLN
AAP41037.1      KLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLN
AAU04664.1      KLRPFERDISNVPFSPDGKPCT-PPAPNCYWPLRGYGFYTTSGIGYQPYRVVVLSFELLN
AAV49730.1      KLRPFERDISNVPFSPDGKPCT-PPAPNCYWPLRGYGFYTTSGIGYQPYRVVVLSFELLN
AAV97995.1      KLRPFERDISNVPFSPDGKPCT-PPAPNCYWPLRGYGFYTTSGIGYQPYRVVVLSFELLN
AAV98000.1      KLRPFERDISNVPFSPDGKPCT-PPAPNCYWPLRGYGFYTTSGIGYQPYRVVVLSFELLN
n6VXX_1|Ch      NLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLH
QHR63300.2      NLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFYPTDGVGHQPYRVVVLSFELLN
sp|P0DTC2|      NLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLH
QHD43416.1      NLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLH
                :*.*******.  :.....**.   . ***:**  *** .* *:*:*************:
AAP50485.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAP30713.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAP13441.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAP41037.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAU04664.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAV49730.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAV97995.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
AAV98000.1      APATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDP
n6VXX_1|Ch      APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
QHR63300.2      APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
sp|P0DTC2|      APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
QHD43416.1      APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP
                ********* **:*:**:**************** *.*.* ********::* **:****
AAP50485.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTG
AAP30713.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTG
AAP13441.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTG
AAP41037.1      KTSEILDISPCAFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTG
AAU04664.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTLIHAEQLTPAWRIYSTG
AAV49730.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTLIHAEQLTPAWRIYSTG
AAV97995.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTLIHAEQLTPAWRIYSTG
AAV98000.1      KTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTLIHAEQLTPAWRIYSTG
n6VXX_1|Ch      QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTG
QHR63300.2      QTLEILDITPCSFGGVSVITPGTNASNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTG
sp|P0DTC2|      QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTG
QHD43416.1      QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTG
                :* *****:**:************:*.:***********:*.. ***:****:**:****
AAP50485.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLL----RSTSQKSIVAYTMSL
AAP30713.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLL----RSTSQKSIVAYTMSL
AAP13441.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLL----RSTSQKSIVAYTMSL
AAP41037.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLL----RSTSQKSIVAYTMSL
AAU04664.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSSL----RSTSQKSIVAYTMSL
AAV49730.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSSL----RSTSQKSIVAYTMSL
AAV97995.1      NNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSSL----RSTSQKSIVAYTMSL
AAV98000.1      NNVFQTQAGCLIGAEHVDSSYECDIPIGAGICASYHTVSSL----RSTSQKSIVAYTMSL 
n6VXX_1|Ch      SNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSL
QHR63300.2      SNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNS----RSVASQSIIAYTMSL
sp|P0DTC2|      SNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSL
QHD43416.1      SNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSL
                .*****.**********:.****************:* :       *.:.:**:******
AAP50485.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAP30713.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAP13441.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAP41037.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAU04664.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAV49730.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAV97995.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
AAV98000.1      GADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDCNMYICGDSTECANLLLQYGSF
n6VXX_1|Ch      GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSF
QHR63300.2      GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSF
sp|P0DTC2|      GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSF
QHD43416.1      GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSF
                **:.*:*****:*******:**:***::****:******.**********:*********
AAP50485.1      CTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIE
AAP30713.1      CTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIE
AAP13441.1      CTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIE
AAP41037.1      CTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFGGFNFSQILPDPLKPTKRSFIE
AAU04664.1      CRQLNRALSGIAAEQDRNTREVFVQVKQMYKTPTLKDFGGFNFSQILPDPLKPTKRSFIE
AAV49730.1      CRQLNRALSGIAAEQDRNTREVFVQVKQMYKTPTLKDFGGFNFSQILPDPLKPTKRSFIE
AAV97995.1      CRQLNRALSGIAAEQDRNTREVFVQVKQMYKTPTLKDFGGFNFSQILPDPLKPTKRSFIE
AAV98000.1      CRQLNRALSGIAAEQDRNTREVFVQVKQMYKTPTLKDFGGFNFSQILPDPLKPTKRSFIE
n6VXX_1|Ch      CTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIE
QHR63300.2      CTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIE
sp|P0DTC2|      CTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIE
QHD43416.1      CTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIE
                * ******:***.***.**.***.****:****.:* ************* **:******
AAP50485.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAP30713.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAP13441.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAP41037.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAU04664.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAV49730.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAV97995.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
AAV98000.1      DLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGLTVLPPLLTDDMIAAYTAALVS
n6VXX_1|Ch      DLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLA
QHR63300.2      DLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLA
sp|P0DTC2|      DLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLA
QHD43416.1      DLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLA
                **************:****:***** **********************:*** **:**::
AAP50485.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAP30713.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAP13441.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAP41037.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAU04664.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAV49730.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAV97995.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
AAV98000.1      GTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKQIANQFNKAISQIQESLT
n6VXX_1|Ch      GTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLS 
QHR63300.2      GTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLS
sp|P0DTC2|      GTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLS
QHD43416.1      GTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLS
                ** *:************************************* ******.**.:**:**:
AAP50485.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAP30713.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAP13441.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAP41037.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAU04664.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAV49730.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAV97995.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
AAV98000.1      TTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
n6VXX_1|Ch      STASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITG
QHR63300.2      STASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
sp|P0DTC2|      STASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
QHD43416.1      STASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITG
                :*::******************************************  ************
AAP50485.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAP30713.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAP13441.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAP41037.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAU04664.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAV49730.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAV97995.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
AAV98000.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQAAPHG
n6VXX_1|Ch      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG
QHR63300.2      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG
sp|P0DTC2|      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG
QHD43416.1      RLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG
                *******************************************************:****
AAP50485.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAP30713.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAP13441.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAP41037.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAU04664.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAV49730.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAV97995.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
AAV98000.1      VVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFNGTSWFITQRNFFSPQIITTDN
n6VXX_1|Ch      VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDN
QHR63300.2      VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDN
sp|P0DTC2|      VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDN
QHD43416.1      VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDN
                **********:**.**********:***:******** *** **:*****:.********
AAP50485.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDFGDISGINASVVNI
AAP30713.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAP13441.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAP41037.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAU04664.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAV49730.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAV97995.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
AAV98000.1      TFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
n6VXX_1|Ch      TFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
QHR63300.2      TFVSGSCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
sp|P0DTC2|      TFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
QHD43416.1      TFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNI
                *****.*******:********************************:*************
AAP50485.1      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAP30713.1      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAP13441.1      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAP41037.1      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAU04664.1      QEEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAV49730.1      QEEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAV97995.1      QEEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
AAV98000.1      QEEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWLGFIAGLIAIVMVTILLCCMTS
n6VXX_1|Ch      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGG---------------G
QHR63300.2      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIIMVTIMLCCMTS
sp|P0DTC2|      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTS
QHD43416.1      QKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTS
                *:****************************** .   .* * .*               .
AAP50485.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAP30713.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAP13441.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAP41037.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAU04664.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAV49730.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAV97995.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
AAV98000.1      CCSCLKGACSCGSCCKFDEDDSEPVLKGVKL------HYT
n6VXX_1|Ch      GSGYIPEAPRDGQA--YVRKDGEWVLLSTFLGHHHHHHHH
QHR63300.2      CCSCLKGCCSCGSCCKFDEDDSEPVLKGVKL------HYT
sp|P0DTC2|      CCSCLKGCCSCGSCCKFDEDDSEPVLKGVKL------HYT
QHD43416.1      CCSCLKGCCSCGSCCKFDEDDSEPVLKGVKL------HYT
                 .. :  .   *..  :  .*.* ** .. *      *:
  • This highlighted portion was the sequence that we chose because it showed the most amount of difference between the different strains of the virus.

Screen Shot 2020-04-29 at 9.26.40 PM.png

Phylogenetic Tree

  • Used www.phylogeny.fr
    • Generated a tree using the protein sequences of the 12 different strains of the SARS virus
    • Uploaded the FASTA sequences of each of the strains in to the "One Click" option on the www.phylogeny.fr website.
    • This tree shows that the sequences from each strain cluster together

SARS Phylogenetic Tree BIOL368 Final Project.PNG

3D structures of SARS RBD binding to Host ACE2

Final Research Project S Protein with RBD Highlighted.PNG

  • This figure shows the different areas that have differences in amino acid sequence in specifically the 2019-SARS-CoV virus (Walls, 2020).
  • Structures of the spike protein receptor binding domain interacting with the host ACE2 protein:
    • The highlighted regions show the areas in which there was noticeable variability in the amino acid sequences of the different SARS spike proteins.
  • These figures show close up of Protein 6M17 from Yan et al. (2020)

Final Research Project RBD-ACE2 Interaction.PNG

Final Research Project RBD-ACE2 N-terminus Interaction.PNG

Final Research Project RBD-ACE2 Beta Loop Interaction.PNG

Data and Files

Scientific Conclusion

From the results of this project, we determined that due to the lack of differences between the initial SARS-CoV epidemic strain and the reemergence strain, that the overall pathogenicity of the virus is not driven by ACE2 interactions between the spike protein and the host ACE2. We also showed that pathological differences between the viruses is driven by the different polar resides that they contain.

Link to Presentation

File:Coronavirus Structure Research Project.pdf

Acknowledgements

I worked with homework partners Jack P. Menzagopian and Nicholas D. Yeo on 4/23/2020. We worked on the project and presentation via zoom meeting.

I copied and modified the BIOL368/S20:Week 14 assignment page.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Dcartmel (talk) 22:00, 29 April 2020 (PDT)

References

NCBI. NCBI Structure Databases. (2020). Retrieved April 29, 2020, from NCBI Structure Database

OpenWetWare. (2020). BIOL368/S20:Week 14. Retrieved April 29, 2020 from https://openwetware.org/wiki/BIOL368/S20:Week_14.

OpenWetWare. (2020). BIOL368/S20:Week 13. Retrieved April 29, 2020 from https://openwetware.org/wiki/BIOL368/S20:Week_13.

Phylogeny.fr. (2020). Retrieved April 29, 2020 from Retrieved April 27, 2020 from http://www.phylogeny.fr/.

Kan, B., Wang, M., Jing, H., Xu, H., Jiang, X., Yan, M., ... & Cui, B. (2005). Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. Journal of virology, 79(18), 11892-11900. Retrieved April 29 2020 from https://jvi.asm.org/content/jvi/79/18/11892.full.pdf.

Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science, 367(6485), 1444-1448. Retrived April 29, 2020 from https://science.sciencemag.org/content/367/6485/1444.abstract?casa_token=bW_84xnDVnQAAAAA:5eHy_ZFt26coQNxNw7PPxWkaGkIKd2vPtrjNMftJVlRezkzKPkufC9T4fi1GtWrlC0g_XlI9IxQiFEA

Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. Retrieved April 29, 2020 from https://www.sciencedirect.com/science/article/pii/S0092867420302622.