Sandbox6 Eric Martz: Difference between revisions
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<span style="font-size:150%"><font color="red">Please do not edit this page. Eric Martz, February 2011.</font></span> | <span style="font-size:150%"><font color="red">Please do not edit this page. Eric Martz, February 2011.</font></span> | ||
===Homology Model for 83-341=== | |||
<Structure size='450' frame='true' align='right' scene='Sandbox6_Eric_Martz/83-341/1' /> | <Structure size='450' frame='true' align='right' scene='Sandbox6_Eric_Martz/83-341/1' /> | ||
*Homology model of 83-341 on template chain A of [[3e4c]], 52% sequence identity (<scene name='Sandbox6_Eric_Martz/83-341/1'>restore initial scene</scene>). | *Homology model of 83-341 on template chain A of [[3e4c]], 52% sequence identity (<scene name='Sandbox6_Eric_Martz/83-341/1'>restore initial scene</scene>). Confidence in this model is high because of the 52% sequence identity and sequence alignment with only one 10-residue gap. | ||
{{Template:ColorKey_Amino2CarboxyRainbow}} | |||
*<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>. | |||
*The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain rotamer positions are incorrect in a homology model. | |||
<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | |||
*The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain rotamer positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>. | |||
* The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_conservation/1'>highly conserved</scene>, even based upon a multiple sequence alignment that includes mostly types other than 12<ref>ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.</ref> <scene name='Sandbox6_Eric_Martz/83-341_conservation/2'>Hide 141-341</scene>. | |||
<center>{{Template:ColorKey_ConSurf_NoGray}}</center> | |||
* When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a <scene name='Sandbox6_Eric_Martz/83-341_conservation/3'>few on the outside face are highly conserved</scene>, namely Asn130, Val135, Val136, Glu139, Asn140. <scene name='Sandbox6_Eric_Martz/83-341_conservation/4'>Hide 141-341</scene>. | |||
*The homology model can be downloaded from [[:Image:Caspase12-homology-model-83-341-on-3e4c-a.pdb|homology-model-83-341]]. | |||
===Homology Model for 2-88=== | |||
* Swiss-Model produced a <scene name='Sandbox6_Eric_Martz/2-88/1'>homology model for residues 2-88</scene> using chain A of [[1dgn]] as template. Confidence in this model is low because the sequence alignment had only 19% identity. | |||
* This model shows a <scene name='Sandbox6_Eric_Martz/2-88_charge/1'>noteworthy separation of charges</scene>, with a large region containing only negative charges. | |||
<center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | |||
*Analysis of evolutionary conservation for 2-88 is difficult because not enough related sequences are available in Uniprot. Thus most of the residues have "insufficient data" (yellow). Despite the paucity of information, there appears to be a <scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>conserved patch</scene> that may be of interest<ref>ConSurf run with E value cutoff rat default 0.001, Uniref-90 database, 2 PSI-BLAST iterations, 18 sequences after filtration (35%/95%), average pairwise distance in the multiple sequence alignment 1.09, 57 yellow residues. Number of yellow residues was not reduced in a separate run with the E value raised to 0.03, Uniprot database, 3 PSI-BLAST iterations, and filtration at 25%/98%. This gave 22 sequences, APD 0.90, but 65 yellow residues.</ref> (To identify the conserved residues, toggle spinning off, then touch each residue with the mouse, and observe the popup "hover" report.) | |||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/2'>Cartoon</scene><table align="right"><tr><td>{{Template:ColorKey_ConSurf_NoGray}}</td></tr></table> | |||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/3'>Cartoon decorated with conserved residues</scene> | |||
**<scene name='Sandbox6_Eric_Martz/2-88_conservation/1'>Spacefilling</scene> | |||
*This model can be downloaded from [[:Image:Caspase12-homology-model-2-88-on-1dgn-a.pdb|model-2-88]]. | |||
===Notes=== | |||
<references /> | |||