plapa phosphate localization and prediction algorithm
TRANSCRIPT
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PLAPA
Phosphate Localization And Prediction Algorithm
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How does it work?
• Generates a surface using Matt’s surface generation tool in PLOP
• Places a phosphate “ball” of -2 charge at each point
• Minimizes the position of the ball• Calculates energy• Ranks all positions and chooses the
lowest energy point – no averages among points
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What Have I Done?
• Used five test cases to evaluate different strategies– 1gxc – FHA domain– 1g6g – FHA domain– 1fpr – SH2 domain– 1bm2 – SH2 domain– 1een – SH2 domain
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FHA Domain
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What Have I Done?
• Started by using a phosphate ball– This did not work at either of the trial radii of
1.4, 2.0, and 3.0 A, or the OPLSAA phosphate radius of 4.83 A
– Why?? (All following examples with 1BM2 only, Native is always BLUE, Decoy RED)
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Radius vs Distance from Native Post Minimization
Radius of Sphere in A
Dis
tanc
e fr
om N
ativ
e
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Energy of Native vs Decoy at Different Radii
Radius of Sphere in A
Ene
rgy
in K
cals
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Energy of Native vs Decoy After Subtraction of LJ
Radius of Sphere in A
Ene
rgy
in K
cals
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Energy of Native vs Decoy Using only Electrostatics
Radius of Sphere in A
Ene
rgy
in K
cals
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Another Issue, 1G6G
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1G6G Fix
• Added capping group (ACE)
• Lowest energy moved to within 5 A of native phosphate position in native vs decoy trials
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Final Output for 1BM2
Distance from Native in A
Ene
rgy
in K
cals
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Distance from Native with Minimization in GB and in vacuum
Protein With GB Vacuum
1BM2 0.278 0.361
1GXC 0.585 0.675
1EEN 0.805 1.966
1G6G 7.971 11.485
1FPR 11.453 6.116
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Future Directions
• Investigate the two examples that are not working, haven’t had time due to CASP…
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CASP Target T0196
Possible Elongation Factor from Pyrococcus furiosus
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Initial AlignmentP.abyssi MLG-FFRRKKKEE-EEKI---TGKPVGKVKVENILIVGFK-TVIICEVLEGMV P.horikoshi MFK-FFKRKGEDE--KDV---TGKPVGKVKVESILKVGFR-DVIICEVLEGIV 1 AHHHHHHGSGLFDFLKRKEVKE-EEKIEILSKKPAGKVVVEEVVNIMGK-DVIIGTVESGMI TARGET 189 ----------AKILELAGFLDSYIPEPERAIDKP-FLLPIEDVFSISGRGTVVTGRVERGII 1dg1 210 ----------YNGPTLEEYLDQ-LELPPKPVDKP-LRIPIQDVYSISGVGTVPVGRVESGVL 1jny DKIWELLDAIDEYIPTPVRDVDKP-FLMPVEDVFTITGRGTVATGRIERGKV 1aipA DKIWELLDAIDEYIPTPVRDVDKP-FLMPVEDVFTITGRGTVATGRIERGKV 1b23 DKIWELLDAIDEYIRTRVRDVDKR-FLMRVEDVFTITGRGTVATGRIERGKV 1mj1 VKGKTLLEAIDA-IEQPSRPTDKP-LRLPLQDVYKIGGIGTVPVGRVETGVI 1f60 KSVQKLLDAVDTYIPVPTRDLEKP-FLLPVESVYSIPGRGTVVTGTLERGIL 1d2e ANIDVLVKAIEDFIPTPKRDPNKPMLVLRSFDVNKPKLVGGVLDGSIVQGKL 1kjz P.ab KVGYKVRK-GKK---VAGIVSMEREHK-KVEFAIPGDKIGIMLEKN-IGAEK-GDILEVFIV P.ho KVGYKVKK-GKK---VAGIVSMEREHK-KIEFAIPGDRVGMMLEKN-INAEK-DDILEVYLV 61 GVGFKVKG-PSG---IGGIVRIERNRE-KVEFAIAGDRIGISIEGK-IGKVKKGDVLEIYQT TARGET 238 KVGEEVEIVGIKET-QKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGT 1dg1 260 KVGDKIVFMPAG---KVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNN 1jny KVGDEVEIVGLAPETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGS 1iapA KVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGS 1b23 KVGDEVEIVGLARETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKRGS 1mj1 KPGMVVTFAPAG---VTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN 1f60 KKGDECEFLGHSKN-IRTVVTGIEMFHKSLDRAEAGDNLGALVRGLKREDLRRGLVMAKPGS 1d2e KVGDEIEIRPGVPEPITTEIVSLQAGGQFVEEAYPGGLVGVGTKLD--PYLTKGDLMAGNVV 1kjz
* Poly His at the beginning of a sequence is usually a His tag…
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Secondary Structure Prediction With and Without His Tag
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Superposition on 1JNY
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Ok, so it doesn’t quite match
• Genomic search – is it only a piece?
• Bacterial gene prediction
• Operon search (functional proteins are grouped onto operons in prokaryotes)
• Similar operons = more sequences for the alignment
• It’s a real protein…
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Structural Alignment
• Schrodinger Structural Alignment Tool– ~jacobson/bin/dinger/utilities/structalign pdb1 pdb2 pdbN– Must use PDB files with only one chain– ~jacobson/bin/dinger/utilities/getpdb pdbID:chain (CAPS)– BUGS
• Rotation matrix a bit screwy for some pdbs• Some of your pdbs will appear in alignment but will not
appear as files at the end of the run• This can be fixed by creating a .fasta file with the
structural alignment, loading into chimera, and aligning the structures
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Structural Alignment
• Whole protein structural alignment performed with CE and Schrodinger– CE provided a good alignment, but output pdb
file useless since the other domains influenced position
– Schrodinger script could not handle this
• Domain only alignment based on sequence alignment– CE could not do this– Schrodinger could…with bugs
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Domain Alignment
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Domain Alignment
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Domain Alignment without 1KJZ
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Domain Alignment without 1KJZ
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Interlude
• Here is where I bitch about how chimera crashed my system about 5 times so I downloaded the linux version, in which I could not figure out how to change the background to white…so its black.
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No Gaps: 1B23, 1MJ1, 1AIP
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One Gap: 1DG1, 1D2E, 1EFC
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Two Gaps: 1JNY, 1F60
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Different Full Templates
Template After Min
1b23 -5800.713823
1mj1 -5779.877660
1jny -5764.675874
1aip -5759.879378
1d2e -5753.214127
1efc -5747.859993
1f60 -5693.832217
1dg1 -5601.769850
1kjz -3393.077255
Template After Min
1b23 -4390.297563
1jny -4388.786342
1d2e -4351.241514
1aip -4345.402888
1dg1 -4327.787431
1f60 -4212.589465
1efc -4187.567498
1mj1 -4151.266300
1kjz -1905.964341
Different Partial Templates
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AlignmentP.abyssi MLG-FFRRKKKEE-EEKI---TGKPVGKVKVENILIVGFK-TVIICEVLEGMV P.horikoshi MFK-FFKRKGEDE--KDV---TGKPVGKVKVESILKVGFR-DVIICEVLEGIV 1 AHHHHHHGSGLFDFLKRKEVKE-EEKIEILSKKPAGKVVVEEVVNIMGK-DVIIGTVESGMI TARGET 189 ----------AKILELAGFLDSYIPEPERAIDKP-FLLPIEDVFSISGRGTVVTGRVERGII 1dg1 210 ----------YNGPTLEEYLDQ-LELPPKPVDKP-LRIPIQDVYSISGVGTVPVGRVESGVL 1jny DKIWELLDAIDEYIPTPVRDVDKP-FLMPVEDVFTITGRGTVATGRIERGKV 1aipA DKIWELLDAIDEYIPTPVRDVDKP-FLMPVEDVFTITGRGTVATGRIERGKV 1b23 DKIWELLDAIDEYIRTRVRDVDKR-FLMRVEDVFTITGRGTVATGRIERGKV 1mj1 VKGKTLLEAIDA-IEQPSRPTDKP-LRLPLQDVYKIGGIGTVPVGRVETGVI 1f60 KSVQKLLDAVDTYIPVPTRDLEKP-FLLPVESVYSIPGRGTVVTGTLERGIL 1d2e ANIDVLVKAIEDFIPTPKRDPNKPMLVLRSFDVNKPKLVGGVLDGSIVQGKL 1kjz P.ab KVGYKVRK-GKK---VAGIVSMEREHK-KVEFAIPGDKIGIMLEKN-IGAEK-GDILEVFIV P.ho KVGYKVKK-GKK---VAGIVSMEREHK-KIEFAIPGDRVGMMLEKN-INAEK-DDILEVYLV 61 GVGFKVKG-PSG---IGGIVRIERNRE-KVEFAIAGDRIGISIEGK-IGKVKKGDVLEIYQT TARGET 238 KVGEEVEIVGIKET-QKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGT 1dg1 260 KVGDKIVFMPAG---KVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNN 1jny KVGDEVEIVGLAPETRRTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGS 1iapA KVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGS 1b23 KVGDEVEIVGLARETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKRGS 1mj1 KPGMVVTFAPAG---VTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN 1f60 KKGDECEFLGHSKN-IRTVVTGIEMFHKSLDRAEAGDNLGALVRGLKREDLRRGLVMAKPGS 1d2e KVGDEIEIRPGVPEPITTEIVSLQAGGQFVEEAYPGGLVGVGTKLD--PYLTKGDLMAGNVV 1kjz
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All Models
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No Gaps: 1B23, 1MJ1, 1AIP
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One Gap: 1DG1, 1D2E, 1EFC
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Two Gaps: 1JNY, 1F60
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Two Lowest Energy Models
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1JNY and 1B23 structures
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Further Directions
• Build longer models
• Look over surface of final model to see whether there is a hydrophobic patch for helix packing
• Get your suggestions…
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