Modelado Molecular.Parte 2

MMKKALLLALALSLPGAAFAAEYPIGKPAEKGGMEIGAVYLQPIEMDPPGMMRAAKDSDVHLEADIHATAGNATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLDGPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGPWFEPFDLEYEFVFAGTGKKGGY

Encontrar un modelo estructural de la siguientesecuencia:

Fold assignment

Alineamiento

ClustalXProfile-ProfileHMM-HMM

Modeller

Para usar con el Modeller tiene que estar en formato Pir

2O6D_A 30 .[4].EFPIGEDRDVG PLHVGGVYFQPVEMHP.[1].PG.[1].QPSKEEADCHIEADIHANEAGKD.[1].GYG 91query 18 .[4].EYPIGKPAEKG GMEIGAVYLQPIEMDP PG.[1].MRAAKDSDVHLEADIHATAGNAT GFP 77gi 123058371 21 .[4].EYPIGKPQLMN GMEVAAVYLQPIEMEP AH.[1].MRPAADSDVHLEADIHATRDNAN GFA 80gi 123321076 20 .[4].EYPIGKPQKVD.[2].GFEVAAVYLQPIDMEP PG.[1].MRPAAESDVHLEADIKALKGNKN GYA 81gi 123545787 22 .[4].EIPIGKPQLLG GMEIAAVYLQPIEMEP EG.[1].MRPAKDSDVHLEADIKAAKDNTN GFA 81gi 81684265 22 .[4].EYPIGKHQIQG GMEIGAVYLQPITMDP EG.[1].MRKASDSDIHLEADIHAVKNNPT GFA 81gi 123746954 21 .[4].EYPIGVPQQRN GMEIAAVYLQPVEMEP EG.[1].MKKASDSDIHLEADIHALANNPN GFE 80gi 81656749 21 .[4].EYPIGKPALKN GMEIGAVYLQPTKMEP DG.[1].MLKPEASDIHLEADIHATKNNPN GFE 80gi 123026006 20 .[4].EYPIGKPKTLA GMEIAAVYLQPVTMDP DG ACDIKDADVHLEADIKATKDNKN GFA 78gi 122519528 19 .[4].EYPLGQPVLKN GMEIQGVYLQPITMDT EG.[5].SLSAKDSDVHLEADIHAAEENPN GFA 82

2O6D_A 92 VGDFVPYLRVVAFLQKHG.[1].EKVQKVMFAPMNAGDGPHYGANVKF.[1].EGLGTYKVRFEIAAPSH DEYSL 158query 78 EGEWVPYLVVKYEVQKVG.[1].DKVQKGTFMPMVANDGPHYGDNVKL DGPGKYKLKYTIMPPTA.[3].NHFGR 146gi 123058371 81 EGDWIPNLTIEYTLTKLD.[1].NGQTGGVFMPMVASDGPHYGDNVKL MGAGKYRLVYKIASVAP.[3].SHFGR 149gi 123321076 82 EGDWVGYLKITYELTKAG.[1].AEAIKGDAMPMVASDGPHYGDNVKL AGPGKYTLKFNISPPGS.[4].SHFGR 151gi 123545787 82 EGDWVPYLVVSYELTHLD.[1].GKVQKGDFMPMVANDGPHYGDNVKL DGPGKYKLKLFVSPPSA.[3].AHFGR 150gi 81684265 82 EGDWMPYLQVTYKLTKQG.[2].KWAAQGDLMGMVASDGPHYGDNVKL NGPGKYHLTLVVKPPMQ.[3].MAFGR 151gi 123746954 81 EGAWMPYLAIKFEVSKIG.[1].DFKVSGDFMPMVANDGPHYGDNVKL AGPGKYKVKYTILPPSA.[3].SHFGR 149gi 81656749 81 EGAWMPYLVVKYELTKVG GKTQKGELMPMVANDGPHYGDNIKL QGPGKYKLKYTIMPPTA.[3].AHFGR 148gi 123026006 79 EGDWVPYLFIKYELTKEG.[1].AEPTKGEFLAMVASDGPHYGENVKL SGPGKYKLKFTIAPPSE.[3].AAFHR 147gi 122519528 83 EGDWMPYLTIKYSVDKLG.[2].KPAQTGEFMPMVASDGPHYGKNIKL DGNGKYKVTFTIYPPSY.[3].AMFGR 152

2O6D_A 159 HIDEQTGVSG.[2].WSEPLVAEW.[1].DFEWKG 186query 147 HIDKETGVGP WFEPFDLEY EFVFAG 171gi 123058371 150 HVDKETGVGA WPETFTVEY EFTYAG 174gi 123321076 152 HVDKETGVGP WFKPFTVQY DFTFAG 176gi 123545787 151 HVDKETGVGP WFKPVTAEY EFVYAG 175gi 81684265 152 HVDKETGVGA WFKPITLEY DFPFAG 176gi 123746954 150 HTDRATGVRP WFKPFEVEY EFTYVG 174gi 81656749 149 HVDKETGVAA WFKPFDLNY EFTFAG 173gi 123026006 148 HTDKETGVAE WFKTFSVDY EFTFAG 172gi 122519528 153 HIDKETGVAP WFKPFDVSW EFNYAG 177

from modeller import *

env = environ()aln = alignment(env)mdl = model(env, file='2o6e', model_segment=('FIRST:A','LAST:A'))aln.append_model(mdl, align_codes='2o6eA', atom_files='2o6e.pdb')aln.append(file='seq.fasta', align_codes='eug')aln.align2d()aln.write(file='eug-2o6e.ali', alignment_format='PIR')aln.write(file='eug-2o6e.pap', alignment_format='PAP')

Script del Modeller: align2d.py

>P1;2o6estructureX:2o6e:29:A:182:A:::1.50:0.20DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDE---YSLHIDEQTGVSGRFWSEPLVAEWDDFEWKG*>P1;irp1sequence:irp1:1::242::::0.00:0.00AEYPIGKPAEKGGMEIGAVYLQPIEMDPP-GMMRAAKDSDVHLEADIHATAGN-ATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLD-GPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGP--WFEPFDLEY-EFVFAG*

Construcción de modelos usando Modeller

# Homology modeling with multiple templatesfrom modeller import * # Load standard Modeller classesfrom modeller.automodel import * # Load the automodel class

log.verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in

# directories for input atom filesenv.io.atom_files_directory = './:../atom_files'env.io.hetatm = True

a = automodel(env,alnfile = 'irp1.pir', # alignment filenameknowns = ('2o6e'), # codes of the templatessequence = 'irp1') # code of the target

a.starting_model= 1 # index of the first modela.ending_model = 100 # index of the last model

# (determines how many models to calculate)a.make() # do the actual homology modeling

EXPDTA THEORETICAL MODEL, MODELLER 9v5 2009/06/07 23:12:58REMARK 6 MODELLER OBJECTIVE FUNCTION: 901.9978REMARK 6 MODELLER BEST TEMPLATE % SEQ ID: 45.695ATOM 1 N ALA 1 8.223 43.424 83.299 1.00 9.31 NATOM 2 CA ALA 1 7.210 43.168 82.252 1.00 9.31 CATOM 3 CB ALA 1 5.914 43.937 82.556 1.00 9.31 CATOM 4 C ALA 1 7.711 43.602 80.915 1.00 9.31 CATOM 5 O ALA 1 8.912 43.573 80.651 1.00 9.31 OATOM 6 N GLU 2 6.784 44.008 80.027 1.00 28.50 NATOM 7 CA GLU 2 7.178 44.433 78.718 1.00 28.50 CATOM 8 CB GLU 2 6.539 43.605 77.587 1.00 28.50 CATOM 9 CG GLU 2 7.015 42.149 77.558 1.00 28.50 CATOM 10 CD GLU 2 6.318 41.432 76.408 1.00 28.50 CATOM 11 OE1 GLU 2 5.497 42.087 75.712 1.00 28.50 OATOM 12 OE2 GLU 2 6.592 40.217 76.215 1.00 28.50 OATOM 13 C GLU 2 6.727 45.848 78.554 1.00 28.50 CATOM 14 O GLU 2 5.738 46.269 79.152 1.00 28.50 OATOM 15 N TYR 3 7.467 46.633 77.744 1.00 47.64 NATOM 16 CA TYR 3 7.098 48.002 77.532 1.00 47.64 CATOM 17 CB TYR 3 8.164 48.997 78.015 1.00 47.64 CATOM 18 CG TYR 3 8.256 48.807 79.492 1.00 47.64 CATOM 19 CD1 TYR 3 7.345 49.406 80.332 1.00 47.64 CATOM 20 CD2 TYR 3 9.249 48.025 80.036 1.00 47.64 CATOM 21 CE1 TYR 3 7.425 49.230 81.694 1.00 47.64 CATOM 22 CE2 TYR 3 9.333 47.844 81.397 1.00 47.64 CATOM 23 CZ TYR 3 8.420 48.448 82.228 1.00 47.64 CATOM 24 OH TYR 3 8.505 48.265 83.624 1.00 47.64 OATOM 25 C TYR 3 6.887 48.181 76.059 1.00 47.64 CATOM 26 O TYR 3 7.593 47.599 75.239 1.00 47.64 OATOM 27 N PRO 4 5.889 48.945 75.705 1.00 86.04 NATOM 28 CA PRO 4 5.568 49.116 74.310 1.00 86.04 CATOM 29 CD PRO 4 4.715 49.079 76.549 1.00 86.04 C

Evaluación con DOPE

from modeller import *from modeller.scripts import complete_pdb

log.verbose() # request verbose outputenv = environ()env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topologyenv.libs.parameters.read(file='$(LIB)/par.lib') # read parameters

# read model filemdl = complete_pdb(env, 'irp1.B99990005.pdb')

# Assess with DOPE:s = selection(mdl) # all atom selections.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='eug.profile',

normalize_profile=True, smoothing_window=15)

-6.00E-02

-5.00E-02

-4.00E-02

-3.00E-02

-2.00E-02

-1.00E-02

0.00E+00

1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96 101

106

111

116

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126

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136

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151

Profile DOPE del mejor modelo

# Loop refinement of an existing modelfrom modeller import *from modeller.automodel import *

log.verbose()env = environ()

# directories for input atom filesenv.io.atom_files_directory = './:../atom_files'

# Create a new class based on 'loopmodel' so that we can redefine# select_loop_atoms (necessary)class myloop(loopmodel):

# This routine picks the residues to be refined by loop modelingdef select_loop_atoms(self):

# 10 residue insertionreturn selection(self.residue_range('25', '35'))

m = myloop(env,inimodel='irp1.B99990005.pdb', # initial model of the targetsequence='eug') # code of the target

m.loop.starting_model= 1 # index of the first loop modelm.loop.ending_model = 10 # index of the last loop modelm.loop.md_level = refine.very_fast # loop refinement method

m.make()

Modelado de múltiples cadenas

>P1;2o6estructureX:2o6e:29:A:305:B:182:1.50:0.20DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDE---YSLHIDEQTGVSGRFWSEPLVAEWDDFEWKG/DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDE---YSLHIDEQTGVSGRFWSEPLVAEWDDFEWKG*>P1;irp1sequence:irp1:1::242::::0.00:0.00AEYPIGKPAEKGGMEIGAVYLQPIEMDPP-GMMRAAKDSDVHLEADIHATAGN-ATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLD-GPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGP--WFEPFDLEY-EFVFAG/AEYPIGKPAEKGGMEIGAVYLQPIEMDPP-GMMRAAKDSDVHLEADIHATAGN-ATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLD-GPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGP--WFEPFDLEY-EFVFAG*

Modelado con consideración explícita de ligandos y heteroátomos

>P1;2o6estructureX:2o6e:29:A:305:B:305:1.50:0.20DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDE---YSLHIDEQTGVSGRFWSEPLVAEWDDFEWKG/DEFPIGEDRDVGPLHVGGVYFQPVEMHPAPGAQPSKEEADCHIEADIHANEAGKDLGYGVGDFVPYLRVVAFLQKHGSEKVQKVMFAPMNAGDGPHYGANVKFEEGLGTYKVRFEIAAPSHDE---YSLHIDEQTGVSGRFWSEPLVAEWDDFEWKG..*>P1;irp1sequence:irp1:1::242::::0.00:0.00AEYPIGKPAEKGGMEIGAVYLQPIEMDPP-GMMRAAKDSDVHLEADIHATAGN-ATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLD-GPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGP--WFEPFDLEY-EFVFAG/AEYPIGKPAEKGGMEIGAVYLQPIEMDPP-GMMRAAKDSDVHLEADIHATAGN-ATGFPEGEWVPYLVVKYEVQKVGSDKVQKGTFMPMVANDGPHYGDNVKLD-GPGKYKLKYTIMPPTADKMNHFGRHIDKETGVGP--WFEPFDLEY-EFVFAG..*

# Homology modeling with multiple templatesfrom modeller import * # Load standard Modeller classesfrom modeller.automodel import * # Load the automodel class

log.verbose() # request verbose outputenv = environ() # create a new MODELLER environment to build this model in

# directories for input atom filesenv.io.atom_files_directory = './:../atom_files'env.io.hetatm = True

a = automodel(env,alnfile = 'irp1M.pir', # alignment filenameknowns = ('2o6e'), # codes of the templatessequence = 'irp1') # code of the target

a.starting_model= 1 # index of the first modela.ending_model = 5 # index of the last model

# (determines how many models to calculate)a.make() # do the actual homology modeling

http://www.bmm.icnet.uk/~3djigsaw/

http://swissmodel.expasy.org//SWISS-MODEL.html

http://salilab.org/modeller/