[PyMOL] [Fwd: Re: Symmetry Mates Problem]
Docking is very non-reliable. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Maia humayun scherrif wrote: Hello, Thank you for detailed explanation, surely it is helping me to sort out the possibilities. As per your query a) There are many references that the protein is a Hexamer, but I am considering, because the domain which I have got structure, interacts with other proteins to make a biological complex, their interaction could be important for biological hexamerization of the whole complex ( those interacting proteins also exist as hexamer in complex with my protein ) b) I coudnt find any hexameric homologue (although there are some good homologue structures but they mostly exist as dimer or monomer) c) the structure is not yet been solved and not reported as yet. So according your reply, does that mean the only possibility left is docking ? because others are not working for me at all. Thank you again for suggestions. On Wed, May 19, 2010 at 6:31 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Humayun, Crystallograpic symmetries are often not of much help to construct biologically relevant complexes. Do you have (a) a reference of the hexameric structure, or (b) of a hexameric homologue, or (c) is it only known to form hexamers and is the structure still unsolved? In case of (a), the structure is likely to have a recipe to build the biological unit (possibly as REMARK 350 in the PDB file). In case of (b), you can try to fit copies of the structure onto each chain of the homologue, being aware that that will give you a crude approximation as starting point for further work. And in case of (c), you might want to consider doing some docking. Hope it helps, Tsjerk On Wed, May 19, 2010 at 10:26 AM, humayun scherrif hum@gmail.com mailto:hum@gmail.com wrote: Thank you all for the replies. The protein itself makes hexamer which is well documented and proved structural evidence from other cytoplasmic domains ( my structure is also a domain). I have run PISA, but the online PISA server didnt give me output like standalone PISA in CCP4 (result is mentioned below). Online PISA results show that there are not significant dimer interfaces and thus the trimer structure is because of only crystal packing result For homology modeling I didnt get any proper homologs which have hexameric assembly (I@ Bryn: I cant send you PDB id since its not submitted yet) Analysis of protein interfaces suggests that the following quaternary structures are stable in solution (I wonder the DGdiss is positive value, is it significant to make Hexamer assembly because I couldnt find any help to find out about the allowed values) .-.---.--- Set | No | Size Id ASA BSADGdiss | Formula +-+---+--- 1 | 1 | 60 19917.75536.3 3.8 | A(2)B(2)C(2) +-+---+--- 2 | 2 | 31 10722.92004.1 6.2 | ABC +-+---+--- 3 | 3 | 42 14004.23014.9 0.5 | A(2)B(2) | 4 | 134217.5 0.0 -0.0 | A +-+---+--- 4 | 5 | 247506.21003.3 7.0 |AB | 6 | 134217.5 0.0-0.0 |A +-+---+--- 5 | 7 | 257443.81000.8 6.8 | AB | 8 | 164282.4 0.0 -0.0 | A +-+---+--- 6 | 9 | 277556.51008.3 2.0 | A(2) | 10 | 184227.1 0.0 -0.0 |A | 11 | 134217.5 0.0 -0.0 |A '-'---'--- Waiting for your reply Thanks H On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick robert.fenw...@irbbarcelona.org mailto:robert.fenw...@irbbarcelona.org wrote: Also, if you would like to try homology modelling then that could work. However you would need a couple of hexamer strucutres to start with. It would probably take some tinkering with current tools. I would probably use an MD approach
Re: [PyMOL] [Fwd: Re: Symmetry Mates Problem]
But maybe you can have a try: HADDOCK seems to give good results, once you have defined the symmetry of your complex... See: Mol. Cell. Proteomics 2010 'Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multi-body docking server' Karaca E. et al. Cheers, Annalisa - Annalisa Bordogna PhD. Student Università degli Studi di Milano - Bicocca Milano (Italy) 2010/5/19 Maia Cherney ch...@ualberta.ca Docking is very non-reliable. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303 Maia humayun scherrif wrote: Hello, Thank you for detailed explanation, surely it is helping me to sort out the possibilities. As per your query a) There are many references that the protein is a Hexamer, but I am considering, because the domain which I have got structure, interacts with other proteins to make a biological complex, their interaction could be important for biological hexamerization of the whole complex ( those interacting proteins also exist as hexamer in complex with my protein ) b) I coudnt find any hexameric homologue (although there are some good homologue structures but they mostly exist as dimer or monomer) c) the structure is not yet been solved and not reported as yet. So according your reply, does that mean the only possibility left is docking ? because others are not working for me at all. Thank you again for suggestions. On Wed, May 19, 2010 at 6:31 PM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi Humayun, Crystallograpic symmetries are often not of much help to construct biologically relevant complexes. Do you have (a) a reference of the hexameric structure, or (b) of a hexameric homologue, or (c) is it only known to form hexamers and is the structure still unsolved? In case of (a), the structure is likely to have a recipe to build the biological unit (possibly as REMARK 350 in the PDB file). In case of (b), you can try to fit copies of the structure onto each chain of the homologue, being aware that that will give you a crude approximation as starting point for further work. And in case of (c), you might want to consider doing some docking. Hope it helps, Tsjerk On Wed, May 19, 2010 at 10:26 AM, humayun scherrif hum@gmail.com mailto:hum@gmail.com wrote: Thank you all for the replies. The protein itself makes hexamer which is well documented and proved structural evidence from other cytoplasmic domains ( my structure is also a domain). I have run PISA, but the online PISA server didnt give me output like standalone PISA in CCP4 (result is mentioned below). Online PISA results show that there are not significant dimer interfaces and thus the trimer structure is because of only crystal packing result For homology modeling I didnt get any proper homologs which have hexameric assembly (I@ Bryn: I cant send you PDB id since its not submitted yet) Analysis of protein interfaces suggests that the following quaternary structures are stable in solution (I wonder the DGdiss is positive value, is it significant to make Hexamer assembly because I couldnt find any help to find out about the allowed values) .-.---.--- Set | No | Size Id ASA BSADGdiss | Formula +-+---+--- 1 | 1 | 60 19917.75536.3 3.8 | A(2)B(2)C(2) +-+---+--- 2 | 2 | 31 10722.92004.1 6.2 | ABC +-+---+--- 3 | 3 | 42 14004.23014.9 0.5 | A(2)B(2) | 4 | 134217.5 0.0 -0.0 | A +-+---+--- 4 | 5 | 247506.21003.3 7.0 |AB | 6 | 134217.5 0.0-0.0 |A +-+---+--- 5 | 7 | 257443.81000.8 6.8 | AB | 8 | 164282.4 0.0 -0.0 | A +-+---+--- 6 | 9 | 277556.51008.3 2.0 | A(2) | 10 | 184227.1 0.0 -0.0 |A | 11 | 134217.5 0.0 -0.0 |A
