Re: [modeller_usage] How to create a Pentameric Channel?

[Michael Accardi <>]

Hello Mr. Webb,

On May 16th I had asked how to form a pentamer, but I have settled for tackling the dimer situation first. As you suggested, I have included the chain break (/) character in my alignment. I have also tried using both automodel and the mymodel subclass inputs I obtained from http://salilab.org/modeller/9v8/manual/node28.html.

Unfortunately, my resulting dimer does not look good. The automodel commands (#3; see below) produce a better model but with that said, one subunit appears to be normal where as the second subunit appears to have no structure whatsoever. Additionally, the subunit that appears to be 'normal' does not look as it would if I were to perform a single subunit model generation as some loops are slightly shifted. 

The alignment I have been using is as follows:

 >P1;1I9B
structureX:1I9B.pdb:   1 :A:+205 :A:MOL_ID  1; MOLECULE  ACETYLCHOLINE BINDING PROTEIN; CHAIN  A, B, C, D, E; SYNONYM  ACHBP; ENGINEERED  YES; MUTATION  YES:MOL_ID  1; ORGANISM_SCIENTIFIC  LYMNAEA STAGNALIS; ORGANISM_COMMON  GREAT POND SNAIL; ORGANISM_TAXID  6523; EXPRESSION_SYSTEM  PICHIA PASTORIS; EXPRESSION_SYSTEM_TAXID  4922; EXPRESSION_SYSTEM_STRAIN  GS 115; EXPRESSION_SYSTEM_VECTOR_TYPE  PLASMID; EXPRESSION_SYSTEM_PLASMID  PPIC9: 2.70:-1.00
------F-----------DRA---DILYNIRQTSRP-D-----VIPTQR------DRPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTLAWNS-----SHSPDQVSVPIS---SLWVPDLAAYNAI-SKPEVLTP--QLARVVSDGEVLYMPSIRQRFSCDVS-GVDTESGATCRIKIGSWTHHSREISVDPTTENSDDSEYFSQYSRFEILDVTQKKNSVTYS---CCPEAYEDVEVSLNFRKK-G-*

>P1;HcoUnc49B.B99990038
sequence:HcoUnc49B.B99990038:1:A:508:B:::0.00: 0.00
MRISDLFLFATTATFYHVSRAQEDDIIVDTSQLSTVLDRLTNKTIYDKRLRPRYGDKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGTLDLGIAKQITSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIDSDGTVYTSQRLTVTATCPMKLQLFPMDSQRCKLEIESYGYTMADIDYFWGRQRSDPRQSAVVFGNFMLPQFKQTCYHVNYTQATTSSGSYRRLYFEILLVRNMGF/MRISDLFLFATTATFYHVSRAQEDDIIVDTSQLSTVLDRLTNKTIYDKRLRPRYGDKPVDVGITIHVSSISAVSEVDMDFTLDFYMRQTWQDPRLAFGTLDLGIAKQITSLTVGVDYLDRLWKPDTFFPNEKKSFFHLATTHNSFLRIDSDGTVYTSQRLTVTATCPMKLQLFPMDSQRCKLEIESYGYTMADIDYFWGRQRSDPRQSAVVFGNFMLPQFKQTCYHVNYTQATTSSGSYRRLYFEILLVRNMGF*

HcoUnc49B.B99990038 - denotes a pdb file I created when I formed just a single subunit model. 

I subsequently ran the above alignment file (named: HcoUnc49B_two.ali) in one of the following three commands:

1) Cut and paste The input command from node 28 (link above) and changed the following three lines:

alnfile  = 'HcoUnc49B_two.ali' ,     # alignment filename
knowns   = '1i9b',              # codes of the templates
sequence = 'HcoUnc49B.B99990038')              # code of the target

2) Cut and paste the same input as #1 (with corrections) but instead wrote automodel where node28 insisted the user use 'MyModel'

(i.e. # Be sure to use 'MyModel' rather than 'automodel' here!)

3) The following input which was in a file I created called 'model.py':

from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='HcoUnc49B_two.ali',
knowns='1I9B', sequence='HcoUnc49B.B99990038')
assess_methods=(assess.DOPE, assess.GA341)
a.starting_model = 1
a.ending_model = 5
a.make()

Do you see any roadblocks in my commands, that may be preventing me from producing two nice looking (possibly interacting) subunits?

Ideally what I would like to create is a dimer that looks like two of my HcoUnc49B.B99990038.pdb files positioned beside each other so that one loop (i.e. amino acids 187-190 in the above sequence) on the primary subunit is adjacent to another loop (i.e. amino acids 84-86) on the corresponding subunit.

I apologize for the length of the email. Any advice is greatly appreciated. 

Thank you in advance,
All the best,
Mike