Download Homology modeling with SWISS

Homology modeling with
SWISS-MODEL
Building of hER-beta in agonist
conformation
Robert Dilis
Homology Modeling
• Homology modeling allows to build the structure of a
protein when only its amino acid sequence and the
complete atomic structure of at least one other reference
protein is known
• The reference protein must be structurally homologous to
the model protein being build. Structural segments, which
are thought to be conserved within the family of
homologous proteins are taken directly from the reference
protein
Homology Modeling with SWISS-MODEL
• SWISS-MODEL is a fully automated protein structure
homology modeling server
• Accessible via the ExPASy Molecular Biology web server
(http://www.expasy.org/)
• Also accessible from DeepView (Swiss Pdb-Viewer)
program
• DeepView provides manual control during homology
modeling and tools for analyzing generated models
Swiss-model provides two ways of doing
homology modeling
• First approach mode
fully automatic procedure
http://www.expasy.org/swissmod/SWISS-MODEL.html
• Optimize Mode
manually optimized sequence alignment via
DeepView program(Swiss Pdb-Viewer)
Performing Homology modeling with SWISSMODEL
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Search for suitable templates
Check sequence identity with target
Create ProModII jobs
Generate models with ProModII
This step involves several procedures performed
by server:
Performing Homology modeling with SWISSMODEL
• Superposition of related 3D-structures
• Generation of a multiple alignment with the sequence to be
modeled
• Generation of a framework for the new sequence
• Rebuilding lacking loops
• Completion and correction of backbone
• Verification of model structure quality and packing
• Energy minimization with Cromos96
Oestrogen receptor
• The sex steroid hormone oestrogen exerts a wide variety of
tissue-specific effects during growth and development
• These effects are mediated by the oestrogen receptor (ER)
– a ligand-inducible transcription factor belonging to the
nuclear receptor (NR) superfamily
• Such receptors share a common structural organization
with distinct domains associated with DNA binding and
hormone recognition
• Hormone binding initiates a series of conformational
changes within the receptor and enables ER to interact
efficiently with its specific DNA response element and to
recruit components of the transcriptional machinery
Oestrogen receptor
• Two isoforms of ER are known: ER- α and ER-
• They exhibit overlapping but distinct tissue distribution
patterns and differ in their ligand binding affinity and
transactivational properties
• ER-α and ER- share modest overall sequence identity
(47%)
• little homology between N-terminal transactivation (AF-1)
domains
• well conserved DNA- and ligand-binding domains
• The C-terminal ligand-binding domain is multifunctional
and in addition to a ligand binding cavity, contains region
for receptor dimerization and ligand depended (AF-2)
transactivation
Homology modeling of hER- LBD in
agonist conformation using hER-α LBD
template
• First step is obtaining sequence in FASTA format of hER 
LBD (1L2J:A)
Can be obtained in Protein Data Bank
(http://www.rcsb.org/pdb)
• Next step is obtaining template structure in agonist
conformation (1G50:A)
Can be obtained with Search template option in SWISSMODEL (http://www.expasy.org/swissmod/SWISSMODEL.html)