Homology modeling with SWISSMODEL

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Homology modeling with SWISS-MODEL

• Building of hER-beta in agonist conformation
• Robert Dilis

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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

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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

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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)

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Performing Homology modeling with SWISS-MODEL

• Search for suitable templates
• Check sequence identity with target
• Create ProModII jobs
• Generate models with ProModII
  This step involves several procedures performed
  by server

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Performing Homology modeling with SWISS-MODEL

• 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

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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

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Oestrogen receptor

• Two isoforms of ER are known ER- a and ER-?
• They exhibit overlapping but distinct tissue
  distribution patterns and differ in their ligand
  binding affinity and transactivational properties
  
• ER-a 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

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Homology modeling of hER-? LBD in agonist
conformation using hER-a LBD template

• First step is obtaining sequence in FASTA format
  of hER ? LBD (1L2JA)
  Can be
  obtained in Protein Data Bank (http//www.rcsb.org
  /pdb)
• Next step is obtaining template structure in
  agonist conformation (1G50A)
  
  Can be obtained with Search template option in
  SWISS-MODEL (http//www.expasy.org/swissmod/SWISS-
  MODEL.html)