Dear Modellers, Our lab is studying the structure of the rod and cone photoreceptor phosphodiesterase that is central to the visual signaling pathway. The rod enzyme contains a regulatory tandem GAF domain (GAFa-GAFb) and a catalytic domain, and exists as a heterodimer (PDE6A and PDE6B).
There are currently no full length crystal structures for this catalytic heterodimer, only a structure for the GAFa regulatory domain of cone PDE6C, the GAF domain that binds cGMP noncatalytically.
The most homologous protein to PDE6 is the PDE that is abundant in vascular smooth muscle and is the target for Viagra, PDE5 (a catalytic homodimer). There is a dimeric structure for the PDE5 tandem GAF domains (GAFa-GAFb) and for the isolated, monomeric catalytic domain, but no full-length structures. cGMP binds to the GAFa domain of PDE5, the same as PDE6.
A more distantly related PDE, PDE2, has a crystal structure of the nearly full-length, dimeric protein, but unfortunately the GAF domains of PDE2 occur in an opposite order compared to PDE5 and PDE6 (i.e., the cGMP binding site is in GAFb).
See the attached diagram for a visual description of the domain organization of the three PDEs.
We are trying to build a homology model for PDE6 heterodimer. The homology model when PDE6 is threaded onto the PDE2 structure is poor. In contrast, structural homology modeling of PDE6 GAF and catalytic domains using PDE5 as a template gives excellent results. Unfortunately, it is only in the PDE2 structure that the molecular architecture of the nearly full-length dimer has been determined, namely the region between the GAF and catalytic domains and the relationship of the two catalytic domains. Is there some way to rearrange (cut-and-past) the individual domains in the sequence alignment to allow PDE5 to serve for the template for those domains that have been determined, while still using the PDE2 template to thread the PDE6 linker region and to define the relationship of the two catalytic domains with each other?
Could you kindly give us some advice on how to do the alignment and build the model? I would greatly appreciate your help.
Best,
Xiongzhuo Gao
Molecular, Cellular and Biomedical Sciences Department
University of New Hampshire Durham, New Hampshire 03824 Phone: 603-862-3829
On 6/15/12 6:21 AM, Xiongzhuo Gao wrote: > Is there some way to rearrange (cut-and-past) the individual domains in > the sequence alignment to allow PDE5 to serve for the template for those > domains that have been determined, while still using the PDE2 template > to thread the PDE6 linker region and to define the relationship of the > two catalytic domains with each other?
One option would be to use PDE5 as a template, as you have done, but to extract a set of long-range domain-domain distance restraints from the PDE2 template. In principle Modeller could do this automatically with a carefully constructed alignment, but it would be tricky (first you'd have to reorder the domains so that you can align PDE2 with PDE5) so you might have more luck doing it manually (just add the linker region from PDE2 to your alignment). You can just measure a representative set of distances between domains in PDE2 (e.g. CA-CA distances) and then add them to your PDE5-based modeling as additional distance restraints: http://salilab.org/modeller/9.10/manual/node27.html
Ben Webb, Modeller Caretaker
Dear Modeller community,
I am trying to model a protein (i.e. a polymerase) with magnesium and a nucleotide in its active site. The problem is that after calculations, unless metals and ligand are well localized in the active site , a meaningless fragment -SCC(N)CO(O) like a cystein- is linked to the last aminoacid ( a cystein)of my protein. the last part of my sequence alignment looks like that:
> P1;unknown sequence:UL54: 1: :1000: :: : 0.00: 0.00 AKKRARKPPSVVCNYEVAEDPSYVREHGVPIHADKYFE-QVLKAVTNVLSPVFPGGETARKDKFLHMVLPRRLHLEPAFLPYSVKAHECC/ ....* > P1;template1 structureX:template1: 60:B: 2020:B: : :-1.00:-1.00 ARLAALRELDKLLVSELAEDPAYAIAHGVALNTDYYFS-HLLGAACVTFKALF-GNNAKITESLLKRFIPEVWH----------------/ ....*
> P1;template2 structureX:template2:1223:B:1242:B: : :-1.00:-1.00 ----------------------------------------------------------------------RRLHLEPAFLPYSVKAHECC/ ----*
"...." are for the BLK residues nucleotide and the 3 Mg2+, respectively
the end of the PDB file of template2 which BLK residues belongs to:
[...] ATOM 8153 N TRP B1196 65.776 26.703 9.332 1.00 58.52 N ATOM 8154 CA TRP B1196 64.810 27.441 10.157 1.00 58.00 C ATOM 8155 C TRP B1196 63.752 28.162 9.304 1.00 58.04 C ATOM 8156 O TRP B1196 62.939 28.970 9.795 1.00 56.87 O ATOM 8157 CB TRP B1196 65.546 28.462 11.019 1.00 57.75 C ATOM 8158 CG TRP B1196 66.438 27.901 12.067 1.00 56.58 C ATOM 8159 CD1 TRP B1196 66.411 26.651 12.577 1.00 56.98 C ATOM 8160 CD2 TRP B1196 67.457 28.604 12.773 1.00 55.70 C ATOM 8161 CE2 TRP B1196 68.016 27.709 13.699 1.00 56.89 C ATOM 8162 CE3 TRP B1196 67.959 29.909 12.707 1.00 57.14 C ATOM 8163 NE1 TRP B1196 67.363 26.516 13.550 1.00 57.61 N ATOM 8164 CZ2 TRP B1196 69.070 28.063 14.552 1.00 56.64 C ATOM 8165 CZ3 TRP B1196 68.999 30.278 13.572 1.00 57.29 C ATOM 8166 CH2 TRP B1196 69.538 29.349 14.485 1.00 57.02 C ATOM 8167 N HIS B1197 63.763 27.835 8.020 1.00 58.43 N ATOM 8168 CA HIS B1197 62.788 28.344 7.087 1.00 58.51 C ATOM 8169 C HIS B1197 61.503 27.591 7.340 1.00 59.34 C ATOM 8170 O HIS B1197 60.736 28.030 8.189 1.00 60.44 O ATOM 8171 CB HIS B1197 63.284 28.126 5.657 1.00 58.57 C ATOM 8172 CG HIS B1197 64.495 28.937 5.314 1.00 57.60 C ATOM 8173 CD2 HIS B1197 65.285 29.727 6.080 1.00 57.68 C ATOM 8174 ND1 HIS B1197 64.992 29.031 4.036 1.00 57.71 N ATOM 8175 CE1 HIS B1197 66.042 29.834 4.032 1.00 57.32 C ATOM 8176 NE2 HIS B1197 66.250 30.258 5.263 1.00 54.79 N TER 8177 HIS B1197 HETATM 8178 PA BLK B2017 52.886 71.468 10.308 1.00 21.91 P HETATM 8179 PB BLK B2017 52.583 74.293 10.892 1.00 21.14 P HETATM 8180 PG BLK B2017 54.870 74.729 12.687 1.00 21.92 P HETATM 8181 C5' BLK B2017 51.878 71.976 7.940 1.00 18.42 C HETATM 8182 O5' BLK B2017 51.853 71.173 9.113 1.00 20.44 O HETATM 8183 C4' BLK B2017 50.438 72.342 7.584 1.00 18.78 C HETATM 8184 O4' BLK B2017 49.619 71.166 7.552 1.00 17.55 O HETATM 8185 C3' BLK B2017 49.744 73.248 8.586 1.00 17.53 C HETATM 8186 O3' BLK B2017 50.110 74.645 8.523 1.00 16.04 O HETATM 8187 C2' BLK B2017 48.281 72.991 8.232 1.00 15.82 C HETATM 8188 C1' BLK B2017 48.276 71.490 7.958 1.00 17.68 C HETATM 8189 N1 BLK B2017 47.947 70.834 9.243 1.00 19.13 N HETATM 8190 O1A BLK B2017 54.256 71.815 9.770 1.00 20.91 O1- HETATM 8191 O1B BLK B2017 51.239 74.950 10.958 1.00 21.71 O1- HETATM 8192 O1G BLK B2017 54.925 74.009 14.011 1.00 20.37 O HETATM 8193 C2 BLK B2017 46.600 70.860 9.679 1.00 20.99 C HETATM 8194 O2 BLK B2017 45.732 71.415 8.949 1.00 18.60 O HETATM 8195 O2A BLK B2017 52.799 70.342 11.279 1.00 21.10 O HETATM 8196 O2B BLK B2017 53.419 74.703 9.682 1.00 20.26 O HETATM 8197 O2G BLK B2017 55.058 76.214 12.843 1.00 20.21 O1- HETATM 8198 N3 BLK B2017 46.249 70.310 10.877 1.00 20.67 N HETATM 8199 O3A BLK B2017 52.247 72.737 11.034 1.00 21.93 O HETATM 8200 O3B BLK B2017 53.302 74.613 12.284 1.00 21.91 O HETATM 8201 O3G BLK B2017 55.666 74.057 11.600 1.00 22.00 O HETATM 8202 C4 BLK B2017 47.185 69.723 11.660 1.00 22.30 C HETATM 8203 N4 BLK B2017 46.816 69.177 12.845 1.00 21.81 N HETATM 8204 C5 BLK B2017 48.526 69.686 11.242 1.00 22.38 C HETATM 8205 C6 BLK B2017 48.883 70.260 10.012 1.00 19.16 C HETATM 8206 MG MG B2018 55.475 73.776 9.310 1.00 20.18 MG2+ HETATM 8207 MG MG B2019 55.986 70.196 8.530 1.00 43.33 MG2+ HETATM 8208 MG MG B2020 39.276 55.436 40.480 1.00 55.02 MG2+ END
and the end of the .pdb of one of the generated model (non expected atoms are highlighted by "<<<<<<<"):
[...] ATOM 16741 N CYS D1055 67.146 39.478 18.616 1.00217.11 N ATOM 16742 H CYS D1055 66.718 39.397 17.719 1.00217.11 H ATOM 16743 CA CYS D1055 67.047 40.695 19.336 1.00217.11 C ATOM 16744 HA CYS D1055 67.914 40.758 19.976 1.00217.11 H ATOM 16745 CB CYS D1055 66.972 41.938 18.439 1.00217.11 C ATOM 16746 HB3 CYS D1055 66.744 42.815 19.083 1.00217.11 H ATOM 16747 HB2 CYS D1055 66.136 41.824 17.716 1.00217.11 H ATOM 16748 SG CYS D1055 68.544 42.217 17.575 1.00217.11 S ATOM 16749 HG CYS D1055 68.158 43.350 17.007 1.00217.11 H ATOM 16750 C CYS D1055 65.855 40.722 20.171 1.00217.11 C ATOM 16751 O CYS D1055 64.729 40.723 19.679 1.00217.11 O ATOM 16752 N CYS D1056 66.137 40.806 21.477 1.00115.72 N ATOM 16753 H CYS D1056 67.077 40.820 21.811 1.00115.72 H ATOM 16754 CA CYS D1056 65.129 40.891 22.465 1.00115.72 C ATOM 16755 HA CYS D1056 65.583 40.633 23.404 1.00115.72 H ATOM 16756 CB CYS D1056 64.539 42.290 22.571 1.00115.72 C ATOM 16757 HB3 CYS D1056 65.305 42.969 22.999 1.00115.72 H ATOM 16758 HB2 CYS D1056 63.717 42.241 23.317 1.00115.72 H ATOM 16759 SG CYS D1056 63.907 43.004 21.019 1.00115.72 S ATOM 16760 HG CYS D1056 63.496 44.140 21.564 1.00115.72 H ATOM 16761 C CYS D1056 64.051 39.882 22.170 1.00115.72 C ATOM 16762 O CYS D1056 64.442 38.722 21.891 1.00115.72 O ATOM 16763 OXT CYS D1056 62.846 40.235 22.229 1.00115.72 O TER 16764 CYS D1056 HETATM16765 N BLK E1057 67.782 36.707 25.725 1.00216.72 N <<<<<<< HETATM16766 CA BLK E1057 67.537 35.764 26.809 1.00216.72 C <<<<<<< HETATM16767 C BLK E1057 68.587 34.650 27.038 1.00216.72 C <<<<<<< HETATM16768 O BLK E1057 69.332 34.143 26.193 1.00216.72 O <<<<<<< HETATM16769 CB BLK E1057 66.140 35.141 26.779 1.00216.72 C <<<<<<< HETATM16770 SG BLK E1057 64.838 36.192 27.419 1.00216.72 S <<<<<<< HETATM16771 OXT BLK E1057 68.789 34.157 28.153 1.00216.72 O <<<<<<< HETATM16772 PA BLK E1057 58.705 76.985 10.592 1.00216.72 P HETATM16773 PB BLK E1057 58.489 79.812 11.194 1.00216.72 P HETATM16774 PG BLK E1057 60.725 80.154 13.073 1.00216.72 P HETATM16775 C5' BLK E1057 57.796 77.547 8.203 1.00216.72 C HETATM16776 O5' BLK E1057 57.704 76.739 9.365 1.00216.72 O HETATM16777 C4' BLK E1057 56.386 77.969 7.800 1.00216.72 C HETATM16778 O4' BLK E1057 55.526 76.827 7.730 1.00216.72 O HETATM16779 C3' BLK E1057 55.694 78.895 8.784 1.00216.72 C HETATM16780 O3' BLK E1057 56.116 80.277 8.750 1.00216.72 O HETATM16781 C2' BLK E1057 54.237 78.701 8.378 1.00216.72 C HETATM16782 C1' BLK E1057 54.183 77.201 8.094 1.00216.72 C HETATM16783 N1 BLK E1057 53.784 76.548 9.361 1.00216.72 N HETATM16784 O1A BLK E1057 60.097 77.267 10.138 1.00216.72 O HETATM16785 O1B BLK E1057 57.169 80.521 11.219 1.00216.72 O HETATM16786 O1G BLK E1057 60.705 79.423 14.394 1.00216.72 O HETATM16787 C2 BLK E1057 52.421 76.623 9.750 1.00216.72 C HETATM16788 O2 BLK E1057 51.606 77.216 8.995 1.00216.72 O HETATM16789 O2A BLK E1057 58.537 75.854 11.560 1.00216.72 O HETATM16790 O2B BLK E1057 59.381 80.198 10.018 1.00216.72 O HETATM16791 O2G BLK E1057 60.968 81.626 13.239 1.00216.72 O HETATM16792 N3 BLK E1057 52.012 76.082 10.932 1.00216.72 N HETATM16793 O3A BLK E1057 58.087 78.270 11.312 1.00216.72 O HETATM16794 O3B BLK E1057 59.172 80.099 12.615 1.00216.72 O HETATM16795 O3G BLK E1057 61.531 79.449 12.025 1.00216.72 O HETATM16796 C4 BLK E1057 52.894 75.450 11.741 1.00216.72 C HETATM16797 N4 BLK E1057 52.464 74.912 12.908 1.00216.72 N HETATM16798 C5 BLK E1057 54.250 75.364 11.367 1.00216.72 C HETATM16799 C6 BLK E1057 54.668 75.934 10.156 1.00216.72 C HETATM16800 MG MG E1058 61.402 79.397 9.419 1.00 32.87 MG HETATM16801 MG MG E1059 61.943 75.542 9.040 1.00 19.54 MG HETATM16802 MG MG E1060 45.100 60.452 39.519 1.00 3.68 MG END
I precise that the .py works well.
By advance, Thanks for your help.
Anthony
On 7/25/12 2:29 AM, Anthony Couvreux wrote: > I am trying to model a protein (i.e. a polymerase) with magnesium and a > nucleotide in its active site. The problem is that after calculations, > unless metals and ligand are well localized in the active site , a > meaningless fragment -SCC(N)CO(O) like a cystein- is linked to the last > aminoacid ( a cystein)of my protein.
Sorry, but without seeing all your input files I cannot reproduce your problem, so I can't tell where this extra CYS is coming from. But it looks like an alignment error, such that the '.' in your sequence is aligned with a CYS in your template rather than a ligand.
Ben Webb, Modeller Caretaker
-
Anthony Couvreux -
Modeller Caretaker -
Xiongzhuo Gao