1. Protein Folding Programs By Asım OKUR CSE 549 November 14, 2002

2. Protein Structure DNA Sequence  Protein Sequence  Structure  (Mis)function DNA Sequence  Protein Sequence  Structure  (Mis)function It is believed that all the information necessary to determine the structure of a protein is present in its primary sequence. It is believed that all the information necessary to determine the structure of a protein is present in its primary sequence.

3. Protein Folding Programs Protein folding is one of the biggest computational challenges Protein folding is one of the biggest computational challenges Different types of folding and structure predictions programs Different types of folding and structure predictions programs Simulations Simulations Homology Modeling Approaches Homology Modeling Approaches

4. Simulations Simulate the real behavior of proteins Simulate the real behavior of proteins High detail, short time scales High detail, short time scales 2 main simulation types 2 main simulation types Molecular Dynamics Molecular Dynamics Monte Carlo Monte Carlo

5. The Energy Function Calculate energies for each particle Calculate energies for each particle Since long range interactions important for each pair of particles the pair-wise interactions should be calculated Since long range interactions important for each pair of particles the pair-wise interactions should be calculated

6. Homology Modeling Template Selection and Fold Assignment Template Selection and Fold Assignment Target – Template Alignment Target – Template Alignment Model Building Model Building Loop Modeling Loop Modeling Sidechain Modeling Sidechain Modeling Model Evaluation Model Evaluation

7. Fold Assignment and Template Selection Identify all protein structures with sequences related to the target, then select templates Identify all protein structures with sequences related to the target, then select templates 3 main classes of comparison methods 3 main classes of comparison methods Compare the target sequence with each database sequence independently, pair-wise sequence – sequence comparison, BLAST and FASTA Compare the target sequence with each database sequence independently, pair-wise sequence – sequence comparison, BLAST and FASTA Multiple sequence comparisons to improve sensitivity, PSI-BLAST Multiple sequence comparisons to improve sensitivity, PSI-BLAST Threading or 3-D template matching methods Threading or 3-D template matching methods

8. Target – Template Alignment Most important step in Homology Modeling Most important step in Homology Modeling A specialized method should be used for alignment A specialized method should be used for alignment Over 40% identity the alignment is likely to be correct. Over 40% identity the alignment is likely to be correct. Regions of low local sequence similarity become common when overall sequence identity is under 40%. (Saqi et al., Protein Eng. 1999) Regions of low local sequence similarity become common when overall sequence identity is under 40%. (Saqi et al., Protein Eng. 1999) The alignment becomes difficult below 30% sequence identity. (Rost, Protein Eng. 1999) The alignment becomes difficult below 30% sequence identity. (Rost, Protein Eng. 1999)

9. Model Building Construct a 3-D model of the target sequence based on its alignment on template structures Construct a 3-D model of the target sequence based on its alignment on template structures Three different model building approaches Three different model building approaches Modeling by rigid body assembly Modeling by rigid body assembly Modeling by segment matching Modeling by segment matching Modeling by satisfaction of spatial restraints Modeling by satisfaction of spatial restraints Accuracies of these models are similar Accuracies of these models are similar Template selection and alignment have larger impact on the model Template selection and alignment have larger impact on the model

10. Swiss-MOD Web Server Screenshots from the Homology Modeling Server Swiss-Model Construct a framework using known protein structures Generate the location of the target amino acids on the framework If loop regions not determined, additional database search or short simulations

11. Procedure of the MODELLER program After obtaining restraints run a geometry optimization or real- space optimization to satisfy them

12. Errors in Homology Models a.Errors in sidechain packing b.Distortions and shifts in correctly aligned regions c.Errors in regions without a template

13. d. Errors due to misalignment e. Incorrect templates

14. Model Building Programs COMPOSERPwww-cryst.bioc.cam.ac.uk CONGENPwww.congenomics.com/congen/congen.html CPH modelsSwww.cbs.dtu.dk/services/CPHmodels/ DRAGONPwww.nimr.mrc.ac.uk/~mathbio/a-aszodi/dragon.html ICMPwww.molsoft.com InsightIIPwww.msi.com MODELLERPguitar.rockefeller.edu/modeller/modeller.html LOOKPwww.mag.com QUANTAPwww.msi.com SYBYLPwww.tripos.com SCWRLPwww.cmpharm.ucsf.edu/~bower/scrwl/scrwl.html SWISS-MODSwww.expasy.ch/swissmod WHAT IFPwww.sander.embl-heidelberg.de/whatif/

16. Applications

17. Critical Assessment of protein Structure Prediction (CASP) Venclovas et al. Proteins, 2001

18. Critical Assessment of protein Structure Prediction (CASP) Venclovas et al. Proteins, 2001

19. Conclusions Computer Simulations are powerful to show detailed motions but they cannot cover long enough time spans to simulate folding for large systems Computer Simulations are powerful to show detailed motions but they cannot cover long enough time spans to simulate folding for large systems Homology Modeling techniques can be successful if the target protein has a known fold Homology Modeling techniques can be successful if the target protein has a known fold The higher the sequence similarity the more likely the model will be successful The higher the sequence similarity the more likely the model will be successful With the implementation of better techniques the errors in fold assignment, alignment, and sidechain and loop modeling are decreasing With the implementation of better techniques the errors in fold assignment, alignment, and sidechain and loop modeling are decreasing Theoretically, if at least one member of every possible fold is known, it is possible to predict the structure of every coding sequence to within a certain accuracy Theoretically, if at least one member of every possible fold is known, it is possible to predict the structure of every coding sequence to within a certain accuracy