Lecture22 - Lecture 22 Protein Structure Prediction II T e...

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Lecture 22: Protein Structure Prediction II § Tertiary (3D) Structure Prediction • Homology Modeling • Fold Recognition • Protein Threading Ab initio structure prediction § Quaternary Structure Some slides adapted from slides originally created by Dr. Keith Dunker
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Protein Threading • 3D profiles • methods with pair- wise interactions YES Protein Structure Prediction Flow Chart Protein Sequence Sequence alignment (BLAST or PSI-BLAST) Homolog of known structure? Homology Modeling NO Fold Recognition Known Fold? NO YES Ab initio structure prediction Model of 3D structure Adapted in part from figure in http://www.cs.wright.edu/~mraymer/cs790/Homology_Modeling.ppt
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Homology (or Comparative) Modeling § Definition: Predicting the tertiary structure of an unknown protein using, as a template, a known 3D structure of protein(s) with homologous sequence • Method based on observation that protein structure is typically more conserved than sequence § Important to use as a template homologous proteins whose structure was determined using high resolution experimental methods (i.e., X-ray crystallography or NMR) § Homology modeling is based on the assumption that homologous protein sequences will likely have a very similar 3D structure • For this reason, 3D models generated using homology modeling typically have high resolution and good accuracy • As more 3D structures are solved experimentally, there is a better likelihood of finding a homologous template structure Some of the material from this section is from: http://www.cs.wright.edu/~mraymer/cs790/Homology_Modeling.ppt
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Homology Modeling Procedure § 1. Search databases for homologous protein sequences of known structure to use as templates • 1.B. Select the best template(s) to use for modeling § 2. Align sequence of interest with homologous template(s) of known structure § 3. Build a model of the structure of the protein of interest using the known structure(s) of homologous template(s) § 4. Evaluate and refine model structure Adapted in part from http://www.cs.sunysb.edu/~skiena/549/presentations/protein-folding.ppt
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Examples of Model Building Programs 3D-JIGSAW http://bmm.cancerresearchuk.org/~3djigsaw/ CONGEN www.congenomics.com/congen/congen.html CPH models www.cbs.dtu.dk/services/CPHmodels/ ICM www.molsoft.com MODELLER http://salilab.org/modeller/modeller.html SYBYL www.tripos.com SWISS-MODEL http://swissmodel.expasy.org/ PHYRE http://www.sbg.bio.ic.ac.uk/phyre/ Adapted from http://www.cs.sunysb.edu/~skiena/549/presentations/protein-folding.ppt
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Step 1: Searching for homologous template(s) § Use sequence alignment search programs (e.g., BLAST) to identify homologous sequences with known 3D structure • Typically search for sequences in a protein structure database - Protein Data Bank (PDB): http://www. pdb .org/ - Structural Classification of Proteins (SCOP): http: //scop . mrc-lmb .cam.ac. uk/scop/ - Protein Structure Classification (CATH): http://www. cathdb .info/ § Profile-based search methods (e.g., PSI-BLAST) are commonly used to
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Lecture22 - Lecture 22 Protein Structure Prediction II T e...

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