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11/11/05 Protein Structure Prediction & Modeling

11/11/05 Protein Structure Prediction & Modeling . Bioinformatics Seminars. Nov 11 Fri 12:10 BCB Seminar in E164 Lago Building Supertrees Using Distances Steve Willson, Dept of Mathematics http://www.bcb.iastate.edu/courses/BCB691-F2005.html. Next week - Baker Center/BCB Seminars:

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11/11/05 Protein Structure Prediction & Modeling

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  1. 11/11/05Protein StructurePrediction & Modeling D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  2. Bioinformatics Seminars Nov 11 Fri 12:10 BCBSeminarin E164 Lago Building Supertrees Using Distances Steve Willson, Dept of Mathematics http://www.bcb.iastate.edu/courses/BCB691-F2005.html Next week - Baker Center/BCB Seminars: (seminar abstracts available at above link) Nov 14 Mon 1:10 PM Doug Brutlag, Stanford Discovering transcription factor binding sites Nov 15 Tues 1:10 PM Ilya Vakser, Univ Kansas Modeling protein-protein interactions both seminars will be in Howe Hall Auditorium D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  3. Protein Structure & Function:Analysis & Prediction Mon Protein structure: basics; classification,databases, visualization Wed Protein structure databases - cont. Thurs Lab Protein structure databases Visualization software Secondary structure prediction Fri Protein structure prediction Protein-nucleic acid interactions D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  4. Reading Assignment (for Mon-Fri) • Mount Bioinformatics • Chp 10 Protein classification & structure prediction http://www.bioinformaticsonline.org/ch/ch10/index.html • pp. 409-491 • Ck Errata:http://www.bioinformaticsonline.org/help/errata2.html D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  5. BCB 544 Additional Reading • Required: • Gene Prediction: • Burge & Karlin 1997 JMB 268:78 Prediction of complete gene structures in human genomic DNA • Optional: • Structure Prediction: • Schueler-Furman…Baker 2005 Science 310:638 Progress in modeling of protein structures and interactions D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  6. Review last lecture:Protein Structure: Databases, Classification & Visualization D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  7. Protein sequence databases • UniProt (SwissProt, PIR, EBI) http://www.pir.uniprot.org • NCBI Protein http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein • More on these later: protein function prediction D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  8. Protein sequence & structure: analysis • Diamond STING Millennium - many useful structure analysistools, includingProtein Dossierhttp://trantor.bioc.columbia.edu/SMS/ • SwissProt (UniProt) • protein knowledgebase • http://us.expasy.org/sprot • InterPRO • sequence analysis tools • http://www.ebi.ac.uk/interpro D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  9. Protein structure databases • PDBProtein Data Bank http://www.rcsb.org/pdb/ • (RCSB) - THE protein structure database • MMDBMolecular Modeling Database • http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure (NCBI Entrez) - has "added" value • MSD Molecular Structure Database http://www.ebi.ac.uk/msd Especially good for interactions, binding sites D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  10. Protein structure classification • SCOP = Structural Classification of Proteins Levels reflect both evolutionary and structural relationships http://scop.mrc-lmb.cam.ac.uk/scop • CATH = Classification by Class, Architecture, Topology & Homology http://cathwww.biochem.ucl.ac.uk/latest/ • DALI/FSSP (recently moved to EBI & reorganized) • fully automated structure alignments • DALI server http://www.ebi.ac.uk/dali/index.html • DALI Database (fold classification) http://ekhidna.biocenter.helsinki.fi/dali/start D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  11. Protein structure visualization • Molecular Visualization Freeware: • http://www.umass.edu/microbio/rasmol • MolviZ.Org • http://www.umass.edu/microbio/chime • Protein Explorer http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm • RASMOL (& many decendents: Protein Explorer,PyMol, MolMol, etc.) • http://www.umass.edu/microbio/rasmol/index2.htm • CHIME • http://www.umass.edu/microbio/chime/getchime.htm • Cn3Dhttp://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/ • Deep View = Swiss-PDB Viewer http://www.expasy.org/spdbv D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  12. Protein structure visualization • Superb interactive structure visualization software • by Jane & Dave Richardson, Duke University • KINIMAGE • http://kinemage.biochem.duke.edu/ • Fantastic research tools for structure analysis & refinement D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  13. RCSB PDB - Beta site http://pdbbeta.rcsb.org/pdb/Welcome.do D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  14. MMDBhttp://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  15. Cn3Dhttp://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  16. Cn3D : Displaying 2' Structures D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  17. Cn3D: Structural Alignments D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  18. SCOP - Structure Classificationhttp://scop.mrc-lmb.cam.ac.uk/scop D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  19. 6 main classes of protein structure • 1) a Domains • Bundles of helices connected by loops • 2)  Domains • Mainly antiparallel sheets, usually with 2 sheets forming sandwich • 3) aDomains • Mainly parallel sheets with intervening helices, also mixed sheets • 4)  aDomains • Mainly segregated helices and sheets • 5) Multidomain (a   • Containing domains from more than one class • 6) Membrane & cell-surface proteins D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  20. CATH - Structure Classificationhttp://cathwww.biochem.ucl.ac.uk/latest/ D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  21. Structural Genomics • ~ 30,000 "traditional" genes in human genome • (not counting: ???) ~ 3,000 proteins in a typical cell > 2 million sequences in UniProt > 33,000 protein structures in the PDB • Experimental determination of protein structure lags far behind sequence determination! Goal: Determine structures of "all" protein folds in nature, using combination of experimental structure determination methods (X-ray crystallography, NMR, mass spectrometry) & structure prediction D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  22. Structural Genomics Projects TargetDB: database of structural genomics targets http://targetdb.pdb.org Protein Structure Prediction? D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  23. Protein Folding • "Major unsolved problem in molecular biology" • In cells: spontaneous • assisted by enzymes • assisted by chaperones • In vitro: many proteins fold spontaneously • & many do not! D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  24. Steps in Protein Folding • 1- "Collapse"- driving force is burial of hydrophobic aa’s • (fast - msecs) • 2- Molten globule - helices & sheets form, but "loose" • (slow - secs) • 3- "Final" native folded state - compaction, some 2' structures rearranged • Native state? - assumed to be lowest free energy • - may be an ensemble of structures D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  25. Protein Dynamics • Protein in native state is NOT static • Function of many proteins depends on conformational changes, sometimes large, sometimes small • Globular proteins are inherently "unstable" • (NOT evolved for maximum stability) • Energy difference between native and denatured state is very small (5-15 kcal/mol) • (this is equivalent to 1 or 2 H-bonds!) • Folding involves changes in both entropy & enthalpy D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  26. Protein Structure Prediction • Structure is largely determined by sequence BUT: • Similar sequences can assume different structures • Dissimilar sequences can assume similar structures • Many proteins are multi-functional • Protein folding: • determination of folding pathways • prediction of tertiary structure • still largely unsolved problems D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  27. New today: Protein Structure Prediction Secondary structure (text focuses on this - I won't)Tertiary structure (let's do this instead!) D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  28. Protein Structure Prediction or "Protein Folding" Problem given the amino acid sequence of a protein, predict its 3-dimensional structure (fold) • "Inverse Folding" Problem given a protein fold, identify every amino acid sequence that can adopt its 3-dimensional structure Deciphering the Protein Folding Code D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  29. Protein Structure Determination? • High-resolution structure determination • X-ray crystallography (<1A) • Nuclear magnetic resonance (NMR) (~1-2.5A) • Lower-resolution structure determination • Cryo-EM (electron-microscropy) ~10-15A • Theoretical Models? • Highly variable - now, some equiv to X-ray! D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  30. Tertiary Structure Prediction • Fold or tertiary structure prediction problem can be formulated as a search for minimum energy conformation • search space is defined by psi/phi angles of backbone and side-chain rotamers • search space is enormous even for small proteins! • number of local minima increases exponentially of the number of residues Computationally it is an exceedingly difficult problem! D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  31. Ab Initio Prediction • Develop energy function • bond energy • bond angle energy • dihedral angle energy • van der Waals energy • electrostatic energy • Calculate structure by minimizing energy function (usually Molecular Dynamics or Monte Carlo methods) • Ab initio prediction - not practical in general • Computationally?very expensive • Accuracy? Usually poor for all but short peptides (but see Baker review!) Provides both folding pathway & folded structure D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  32. Comparative Modeling • Two primary methods • 1) Homology modeling 2) Threading (fold recognition) • Note: both rely on availability of experimentally determined structures that are "homologous" or • at least structurally very similar to target Provide folded structure only D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  33. Homology Modeling • Identify homologous protein sequences • PSI-BLAST • multiple sequence alignment (MSA) • Among those with available structures, choose closest sequence match for template • Build model by placing residues into corresponding positions of homologous structure models & refine by "tweaking" • Homology modeling - works "well" • Computationally?not very expensive • Accuracy? higher sequence identity  better model Requires >30% sequence identity D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  34. Threading - Fold Recognition • Identify “best” fit between target sequence & template structure • Develop energy function • Develop template library • Align target sequence with each template & score • Determine best score (1D to 3D alignment) • Build refine structure as in homology modeling • Threading - works "sometimes" • Computationally? Can be expensive or cheap, depends on energy function & whether "all atom" or "backbone only" threading • Accuracy? in theory, should not depend on sequence identity (should depend on quality of template library & "luck") • But, usually higher sequence identity  better model D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  35. Threading - a "local" example Target Sequence ALKKGF…HFDTSE Structure Templates Align target sequence with template structures (fold library) from the Protein Data Bank (PDB) Calculate energy (score) to evaluate goodness of fit between target sequence & template structure Rank models based on energy scores D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  36. Threading Goals & Issues Find “correct” sequence-structure alignment of a target sequence with its native-like fold in PDB • Structure database- must be complete: no decent model if no good template in library! • Sequence-structure alignment algorithm: • Bad alignment  Bad score! • Energy function (scoring scheme): • must distinguish correct sequence-fold alignment from incorrect sequence-fold alignments • must distinguish “correct” fold from close decoys • Prediction reliability assessment- how determine whether predicted structure is correct (or even close?) D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  37. Threading – Structure database • Build a template database • (e.g., ASTRAL domain library derived from PDB) Supplement with additional decoys, e.g., generated using ab initio approach such as Rosetta (Baker) D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  38. Threading - Energy function • Two main methods (and combinations of these) • Structural profile (environmental) physico-chemical properties of aa’s • Contact potential (statistical) based on contact statistics from PDB (Miyazawa & Jernigan - Jernigan now at ISU) D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  39. What is "probability" that two specific residues are in contact? How well does a specific residue fit structural environment? Alignment gap penalty? Total energy: E_p + E_s + E_g Find a sequence-structure alignment that minimizing the energy function Protein Threading – typical energy function MTYKLILNGKTKGETTTEAVDAATAEKVFQYANDNGVDGEWTYTE D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  40. A Rapid Threading Approach for Protein Structure Prediction Kai-Ming Ho, Physics Haibo CaoYungok Ihm Zhong Gao James Morris Cai-zhuang WangDrena Dobbs, GDCBJae-Hyung Lee Michael Terribilini Jeff Sander D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  41. Performance Evaluation? "Blind Test" CASP5 Competition (Critical Assessment of Protein Structure Prediction) Given: Amino acid sequence Goal: Predict 3-D structure (beforeexperimental results published) D Dobbs ISU - BCB 444/544X: Protein Structure Prediction

  42. Actual Structure T174_1 Predicted Structure T174_2 Typical Results:well, actually, BEST Results:HO = #1 ranked CASP prediction for this target • Target 174 • PDB ID = 1MG7

  43. Overall Performance in CASP5 Contest (M. Levitt, Stanford) • FR Fold Recognition • (targets manually assessed by Nick Grishin) • ----------------------------------------------------------- • Rank Z-Score Ngood Npred NgNW NpNW Group-name • 1 24.26 9.00 12.00 9 12 Ginalski • 2 21.64 7.00 12.00 7 12 Skolnick Kolinski • 3 19.55 8.00 12.50 9 14 Baker • 4 16.88 6.00 10.00 6 10 BIOINFO.PL • 5 15.25 7.00 7.00 7 7 Shortle • 6 14.56 6.50 11.50 7 13 BAKER-ROBETTA • 7 13.49 4.00 11.00 4 11 Brooks • 8 11.34 3.00 6.00 3 6 Ho-Kai-Ming • 9 10.45 3.00 5.50 3 6 Jones-NewFold • ----------------------------------------------------------- • FR NgNW - number of good predictions without weighting for multiple models • FR NpNW - number of total predictions without weighting for multiple models

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