I have a question about modelling dimers. What I am trying to do is model a homodimer. I have tried to few things that might work, but I am not really sure. What I did: 1. Edited the pdb file for the template, making it all one subunit 2. My alignment file has the 60 amino acids from the first dimer then chain of glycines then next 60 amino acids from the second dimer. 3. After I model, remove the chain of glycines and add back the B domain letter to the pdb file.
The models look good. What does the group think? Will these models be accurate? Will the restraints between the two dimers be included in the models? Can I edit the restraints to remove the bad restraints located at the end of the first dimer and beginning of the second?
Below is the alignment: I edited the 1a0a template change B domain to A and adjusting the amino acid numbers. >P1;1a0aSP structureX:1a0aSP:1:A:112:A:Pho4:yeast: 2.00:-1.00 MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTVEAACRYIRHLQQNGST--------------MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTV* >P1;1hlo sequence:1hloModel: : : ::Max:Human: 2.00:-1.00 DKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQILDKATEYIQYMGGGGGGGGGGGGGGGGGGGGDKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQIL*
************************************************ Michael Buck NCSU Genetics mjbuck@unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************
Hi Michael
I think a more elegant solution is to treat the chains separately. If you want them to stay the same you can apply restraints. Thus the alignment file might look like this
>P1;candida_dimer_1st sequence:candida_dimer_1st:::: ----------------------M KIVLVL------YDAGKHAADE-EKLYGCTENKLGIANWLKDQGHELITT SDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVG SDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVVMTMLVLVRNFVPAHEQ IINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYY DYQALPKDAEEKVGARRVENIEELVAQADIVTVNAPLHAGTKGLINKELL SKFKKGAWLVNTARGAICVAEDVAAALESGQLR GYGGDVWFPQTAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAQG TKNILESFFTGKFDYRPQDIILLNGEYVTKAYGKHDKK------- / ----------------------M KIVLVL------YDAGKHAADE-EKLYGCTENKLGIANWLKDQGHELITT SDKEGGNSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVG SDHIDLDYINQTGKKISVLEVTGSNVVSVAEHVVMTMLVLVRNFVPAHEQ IINHDWEVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYY DYQALPKDAEEKVGARRVENIEELVAQADIVTVNAPLHAGTKGLINKELL SKFKKGAWLVNTARGAICVAEDVAAALESGQLR GYGGDVWFPQTAPKDHPWRDMRNKYGAGNAMTPHYSGTTLDAQTRYAQG TKNILESFFTGKFDYRPQDIILLNGEYVTKAYGKHDKK------- * >P1;2nad_doubleA_noHET structureX:2nad_doubleA_noHET:1:A:391:B AKVLCVLYDDPVDGYPKTYARDD LPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVT SDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIG SDHVDLQSAID--RNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEW ARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFD-VHLHYT DRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETL KLFKRGAYIVNTARGKLCDRDAVARALESGRLA GYAGDVWFPQPAPKDHPWRTMP-----YNGMTPHISGTTLTAQARYAAG TREILECFFEGR-PIRDEYLIVQGGALAGTGAHSYSKGNATGGSE / AKVLCVLYDDPVDGYPKTYARDD LPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVT SDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIG SDHVDLQSAID--RNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEW ARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFD-VHLHYT DRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETL KLFKRGAYIVNTARGKLCDRDAVARALESGRLA GYAGDVWFPQPAPKDHPWRTMP-----YNGMTPHISGTTLTAQARYAAG TREILECFFEGR-PIRDEYLIVQGGALAGTGAHSYSKGNATGGSE
and at the end of your top file you put something like this
SUBROUTINE ROUTINE = 'special_restraints'
# Try to put symmetry restraints here # This is called from __homcsr after other restraints set up
SET RES_TYPES = 'ALL' SET ATOM_TYPES = 'ALL' SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_SEARCH = 'SEGMENT'
SET SYMMETRY_WEIGHT = 0.5 PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '364:' PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '365:' '728:' DEFINE_SYMMETRY ADD_SYMMETRY = on off
RETURN END_SUBROUTINE
Residues 1-364 are the first chain and 365-728 the second chain of the output homodimer.
Good luck
Daniel
+-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+
On Thu, 25 Jul 2002, Michael Buck wrote:
> I have a question about modelling dimers. What I am trying to do is model > a homodimer. I have tried to few things that might work, but I am not > really sure. What I did: > 1. Edited the pdb file for the template, making it all one subunit > 2. My alignment file has the 60 amino acids from the first dimer > then chain of glycines then next 60 amino acids from the second dimer. > 3. After I model, remove the chain of glycines and add back the B > domain letter to the pdb file. > > The models look good. What does the group think? Will these models be > accurate? Will the restraints between the two dimers be included in the > models? Can I edit the restraints to remove the bad restraints located at > the end of the first dimer and beginning of the second? > > > > > > Below is the alignment: I edited the 1a0a template change B domain to A and > adjusting the amino acid numbers. > >P1;1a0aSP > structureX:1a0aSP:1:A:112:A:Pho4:yeast: 2.00:-1.00 > MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTVEAACRYIRHLQQNGST--------------MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTV* > >P1;1hlo > sequence:1hloModel: : : ::Max:Human: 2.00:-1.00 > DKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQILDKATEYIQYMGGGGGGGGGGGGGGGGGGGGDKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQIL* > > > > > > > > ************************************************ > Michael Buck > NCSU Genetics > mjbuck@unity.ncsu.edu > Phone (919)515-5759 > Fax (919)515-3355 > http://www4.ncsu.edu/~mjbuck > ************************************************* > >
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