Dear Sir,
I read the modeller forum for multichain proteins however I am not sure whether I have understood correctly. I am a novice in the area of structural biology and hence have lots of queries.
1) In case of a homomeric protein.
For example protein with id 1sv6 is my template which has 5 chains (A-E). In order to align my target protein with this template, I copied and pasted the sequence of my target 5 times separated by the delimiter '/'.
The alignment of the template (1SV6) with my target gene ABM40476.1 gave the following result. Is this the right way to proceed in case of homomeric proteins?
>P1;1sv6.pdb
structureX:1sv6.pdb: 1 :A:+1305:E:MOL_ID 1; MOLECULE 2-KETO-4-PENTENOATE HYDRATASE; CHAIN A, B, C, D, E; SYNONYM 2-HYDROXYPENTADIENOIC ACID HYDRATASE; EC 4.2.1.-; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC ESCHERICHIA COLI; ORGANISM_TAXID 562; GENE MHPD, B0350; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562: 2.90: 0.24
MT--KHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLG
VDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWS
IQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLR
TGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS/
MT--KHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVD
QPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDT
VADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILT-G
ALGPMVAVNAGDRFEAHIEGIGSVAATFSS/
MTKHTLEQLAADLRRAAEQGEAIAPLRD XXXXXXXXXXX repetition of the chain XXXXXXXXXXXXX*
>P1;ABM40476.1_-_Acidovorax_sp._JS42
sequence:ABM40476.1_-_Acidovorax_sp._JS42: : : : ::: 0.00: 0.00
MTMTPALIEQLGDELYQALTQRRMLEPLTNRHADITIDDAYAIQQKMLARRLAAGEKVVGKKIGVTSKAVMDMLG
VFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIAFVLKKTLKGPGITAADVLAATEGVMACFEIVDSRIRDWK
IKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMVLEKNGDIVATGAGAA------------------------
--------ALGH-PA-NA-------------------V/
MTMTPALIEQLGDELYQALTQRRMLEPLTNRHADIT
IDDAYAIQQKMLARRLAAGEKVVGKKIGVTSKAVMDMLGVFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIA
FVLKKTLKGPGITAADVLAATEGVMACFEIVDSRIRDWKIKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMV
LEKNGDIVATGAGAAALGHPANA----------------------V/
MTMTPALIEQLGDE-------------LYQA-LTQR---RMLEPLTNR------HADIT----IDD---AYAIQQKMLARRLAAGEKVVGK
KIGVTSKAVMDMLGVFQPDFGWLTDGMVFNEGQAVQANTLIQPKAEGEIAFVLKKTLKGPGITAADVLAATEGVM
ACFEIVDSRIRDWKIKIQDTVADNASCGVFVLGDRLVDPRDVDLGTCGMVLEKNGDIVATGAGAAALGHPANA--------------
--------V/
(XXXX and so on )--------*
2.) In order to further model this protein should I be using MyModel instead of automodel?
If so do I need to make changes in this part of the code as per the number of chains in the template (highlighted below)?
s1 = selection(self.chains['A']).only_atom_types('CA')
s2 = selection(self.chains['B']).only_atom_types('CA') #Should the C,D,E chains be appended to self.restraints.symmetry?
self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
3). I also have a heteromeric protein such as 1O7G which has a large and small subunit as chain A and B.
The target gene that I want to model shows sequence similarity only with chain A. How should my alignment file be in this case?
for example if the template is
>P1;1o7g
structure::::
MNOPTHSWYRTY....XXXXXXXXX...../
MRSF...........*
then should my target gene which has aligned to only chainA be depicted as
>P1,TargetGene
sequence:::::::
MNOPTYIKL--DFT--WANH--XXX--/
-----------------------------------------------*
Sir , request you to please guide me in this issue as I am stuck and unable to proceed further.
Thanks & Regards
Anwesha