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BCB 444/544

BCB 444/544. Lecture 22 Secondary Structure Prediction Tertiary Structure Prediction #22_Oct10. Required Reading ( before lecture). Mon Oct 8 - Lecture 20 Protein Secondary Structure Prediction Chp 14 - pp 200 - 213 Wed Oct 10 - Lecture 21 Protein Tertiary Structure Prediction

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BCB 444/544

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  1. BCB 444/544 Lecture 22 • Secondary Structure Prediction • Tertiary Structure Prediction #22_Oct10 BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  2. Required Reading (before lecture) MonOct 8- Lecture 20 Protein Secondary Structure Prediction • Chp 14 - pp 200 - 213 Wed Oct 10 - Lecture 21 Protein Tertiary Structure Prediction • Chp 15 - pp 214 - 230 Thurs Oct 11 & Fri Oct 12- Lab 7 & Lecture 22 Protein Tertiary Structure Prediction • Chp 15 - pp 214 - 230 BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  3. Assignments & Announcements ALL: HomeWork #3 √Due: Mon Oct 8 by 5 PM • HW544: HW544Extra #1 √Due: Task 1.1 - Mon Oct 1 by noon Due: Task 1.2 & Task 2 - Fri Oct 12 by 5 PM • 444 "Project-instead-of-Final" students should also submit: • HW544Extra #1 • √Due: Task 1.1 - Mon Oct 8 by noon • Due: Task 1.2 - Fri Oct 12 by 5 PM <Task 2 NOT required for BCB444 students> BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  4. New Reading & Homework Assignment ALL: HomeWork #4 (posted online today) Due: Fri Oct 19 by 5 PM (one week from today) Read: Ginalski et al.(2005) Practical Lessons from Protein Structure Prediction, Nucleic Acids Res. 33:1874-91.http://nar.oxfordjournals.org/cgi/content/full/33/6/1874 (PDF posted on website) • Although somewhat dated, this paper provides a nice overview of protein structure prediction methods and evaluation of predicted structures. • Your assignment is to write a summary of this paper - for details see HW#4 posted online & sent by email on Fri Oct 12 BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  5. Seminars this Week - (yesterday) BCB List of URLs for Seminars related to Bioinformatics: http://www.bcb.iastate.edu/seminars/index.html • Oct 11 Thurs • Dr. Klaus Schulten (Univ of Illinois) - Baker Center Seminar The Computational Microscope2:10 PM in E164 Lagomarcinohttp://www.bioinformatics.iastate.edu/seminars/abstracts/2007_2008/Klaus_Schulten_Seminar.pdf • Dr. Dan Gusfield(UC Davis) - Computer Science ColloquiumReCombinatorics: Combinatorial Algorithms for Studying History of Recombination in Populations 3:30 PM in Howe Hall Auditorium http://www.cs.iastate.edu/~colloq/new/gusfield.shtml BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  6. Seminars this Week - Fri (today) BCB List of URLs for Seminars related to Bioinformatics: http://www.bcb.iastate.edu/seminars/index.html • Oct 12 Fri • Dr. Edward Yu(Physics/BBMB, ISU) - BCB Faculty Seminar TBA: "Structural Biology" (see URL below)2:10 PM in 102 Scihttp://webdev.its.iastate.edu/webnews/data/site_gdcb_dept_seminars/30/webnewsfilefield_abstract/Dr.-Ed-Yu.pdf • Dr. Srinivas Aluru (ECprE, ISU) - GDCB Seminar Consensus Genetic Maps: A Graph Theoretic Approach 4:10 PM in 1414 MBB http://webdev.its.iastate.edu/webnews/data/site_gdcb_dept_seminars/35/webnewsfilefield_abstract/Dr.-Srinivas-Aluru.pdf BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  7. Chp 12 - Protein Structure Basics SECTION V STRUCTURAL BIOINFORMATICS Xiong: Chp 12Protein Structure Basics • Amino Acids • Peptide Bond Formation • Dihedral Angles • Hierarchy • Secondary Structures • Tertiary Structures • Determination of Protein 3-Dimensional Structure • Protein Structure DataBank (PDB) BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  8. Experimental Determination of 3D Structure 2 Major Methods to obtain high-resolution structures • X-ray Crystallography(most PDB structures) • Nuclear Magnetic Resonance (NMR) Spectroscopy Note Advantages & Limitations of each method • (See your lecture notes & textbook) • For more info:http://en.wikipedia.org/wiki/Protein_structure • Other methods (usually lower resolution, at present): • Electron Paramagnetic Resonance (EPR - also called ESR, EMR) • Electron microscopy (EM) • Cryo-EM • Scanning Probe Microscopies (AFM - Atomic Force Microscopy) • http://www.uweb.engr.washington.edu/research/tutorials/SPM.pdf • Circular Dichroism (CD), several other spectroscopic methods BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  9. "Best" Resolution of Protein Structures • High-resolution methods • X-ray crystallography (< 1A) • NMR (~1 - 2.5A) • Lower-resolution methods • Cryo-EM (~10-15A) • Theoretical Models? • Usually low resolution, at present, but • Highly variable - & a few ~crystal data Baker & Sali (2000) Pevsner Fig 9.36 BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  10. Chp 13 - Protein Structure Visualization, Comparison & Classification SECTION V STRUCTURAL BIOINFORMATICS Xiong: Chp 13 Protein Structure Visualization, Comparison & Classification • Protein Structural Visualization • Protein Structure Comparison - later • Protein Structure Classification BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  11. 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 & Homologyhttp://cathwww.biochem.ucl.ac.uk/latest/ • DALI -(recently moved to EBI & reorganized) DALI Database (fold classification)http://ekhidna.biocenter.helsinki.fi/dali/start Each method has strengths & weaknesses…. BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  12. Chp 14 - Secondary Structure Prediction SECTION V STRUCTURAL BIOINFORMATICS Xiong: Chp 14 Protein Secondary Structure Prediction • Secondary Structure Prediction for Globular Proteins • Secondary Structure Prediction for Transmembrane Proteins • Coiled-Coil Prediction BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  13. Secondary Structure Prediction Has become highly accurate in recent years (>85%) • Usually 3 (or 4) state predictions: • H = -helix • E = -strand • C = coil (or loop) • (T = turn) BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  14. Secondary Structure Prediction Methods • 1st Generation methods Ab initio - used relatively small dataset of structures available Chou-Fasman - based on amino acid propensities (3-state) GOR - also propensity-based (4-state) • 2nd Generation methods based on much larger datasets of structures now available GOR II, III, IV, SOPM, GOR V, FDM • 3rd Generation methods Homology-based & Neural network based PHD, PSIPRED, SSPRO, PROF, HMMSTR, CDM • Meta-Servers combine several different methods Consensus & Ensemble based JPRED, PredictProtein, Proteus BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  15. Secondary Structure Prediction Servers Prediction Evaluation? • Q3 score - % of residues correctly predicted (3-state) in cross-validation experiments Best results? Meta-servers • http://expasy.org/tools/(scroll for 2' structure prediction) • http://www.russell.embl-heidelberg.de/gtsp/secstrucpred.html • JPred www.compbio.dundee.ac.uk/~www-jpred • PredictProteinhttp://www.predictprotein.org/Rost, Columbia Best "individual" programs? ?? • CDM http://gor.bb.iastate.edu/cdm/ Sen…Jernigan, ISU • FDM (not available separately as server) Cheng…Jernigan, ISU • GOR Vhttp://gor.bb.iastate.edu/ Kloczkowsky…Jernigan, ISU BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  16. Consensus Data Mining (CDM) • Developed by Jernigan Group at ISU • Basic premise: combination of 2 complementary methods can enhance performance by harnessing distinct advantages of both methods; combines FDM & GOR V: • FDM - Fragment Data Mining - exploits availability of sequence-similar fragments in the PDB, which can lead to highly accurate prediction - much better than GOR V - for such fragments, but such fragments are not available for many cases • GOR V - Garnier, Osguthorpe, Robson V - predicts secondary structure of less similar fragments with good performance; these are protein fragments for which FDM method cannot find suitable structures • For references & additional details: http://gor.bb.iastate.edu/cdm/ BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  17. Where Find "Actual" Secondary Structure? In the PDB BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  18. How Does Predicted Secondary Structure Compare? e.g., from CMD DSSP Author Query MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEE GOR V CCCCHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCC FDM CCCCCCCCCCCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHHHHHCCC CDM CCCCHHHHHHCCCCCCCEECCCCCCCCCHHHCCCCCCEECCCCCCCCCCHHHHHHHHCCC BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  19. Secondary Structure Prediction: for Different Types of Proteins/Domains For Complete proteins: Globular Proteins - use methods previously described Transmembrane (TM) Proteins - use special methods (next slides) For Structural Domains:many under development: Coiled-Coil Domains (Protein interaction domains) Zinc Finger Domains (DNA binding domains), others… BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  20. SS Prediction for Transmembrane Proteins Transmembrane (TM) Proteins • Only a few in the PDB - but ~ 30% of cellular proteins are membrane-associated ! • Hard to determine experimentally, so prediction important • TM domains are relatively 'easy' to predict! Why? constraints due to hydrophobic environment 2 main classes of TM proteins: -helical - barrel BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  21. SS Prediction for TM -Helices -Helical TM domains: • Helices are 17-25 amino acids long (span the membrane) • Predominantly hydrophobic residues • Helices oriented perpendicular to membrane • Orientation can be predicted using "positive inside" rule Residues at cytosolic(inside or cytoplasmic) side of TM helix, near hydrophobic anchor are more positively charged than those on lumenal (inside an organelle in eukaryotes) or periplasmicside (space between inner & outer membrane in gram-negative bacteria) • Alternating polar & hydrophobic residues provide clues to interactions among helices within membrane Servers? • TMHMM or HMMTOP - 70% accuracy - confused by hydrophobic signal peptides (short hydrophobic sequences that target proteins to the endoplasmic reticulum, ER) • Phobius - 94% accuracy - uses distinct HMM models for TM helices & signal peptide sequences BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  22. SS Prediction for TM -Helices -Helical TM domains: • Helices are 17-25 amino acids long (span the membrane) • Predominantly hydrophobic residues • Helices oriented perpendicular to membrane • Orientation can be predicted using "positive inside" rule Residues at cytosolic(inside or cytoplasmic) side of TM helix, near hydrophobic anchor are more positively charged than those on lumenal (inside an organelle in eukaryotes) or periplasmicside (space between inner & outer membrane in gram-negative bacteria) • Alternating polar & hydrophobic residues provide clues to interactions among helices within membrane Servers? • TMHMM or HMMTOP - 70% accuracy - confused by hydrophobic signal peptides (short hydrophobic sequences that target proteins to the endoplasmic reticulum, ER) • Phobius - 94% accuracy - uses distinct HMM models for TM helices & signal peptide sequences BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  23. SS Prediction for TM -Barrels -Barrel TM domains:  • -strands are amphipathic(partly hydrophobic, partly hydrophilic) • Strands are 10 - 22 amino acids long • Every 2nd residue is hydrophobic, facing lipid bilayer • Other residues are hydrophilic, facing "pore" or opening Servers?Harder problem, fewer servers… TBBPred - uses NN or SVM (more on these ML methods later) Accuracy ? BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  24. Prediction of Coiled-Coil Domains Coiled-coils • Superhelical protein motifs or domains, with two or more interacting -helices that form a "bundle" • Often mediate inter-protein (& intra-protein) interactions 'Easy' to detect in primary sequence: • Internal repeat of 7 residues (heptad) • 1 & 4 = hydrophobic (facing helical interface) • 2,3,5,6,7 = hydrophilic (exposed to solvent) • Helical wheel representation - can be used manually detect these, based on amino acid sequence Servers? Coils, Multicoil -probability-based methods 2Zip - for Leucine zippers = special type of CC in TFs: characterized by Leu-rich motif: L-X(6)-L-X(6)-L-X(6)-L BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  25. Chp 15 - Tertiary Structure Prediction SECTION V STRUCTURAL BIOINFORMATICS Xiong: Chp 15 Protein Tertiary Structure Prediction • Methods • Homology Modeling • Threading and Fold Recognition • Ab Initio Protein Structural Prediction • CASP BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  26. Structural Genomics - Status & Goal ~ 20,000 "traditional" genes in human genome (recall, this is fewer than earlier estimate of 30,000) ~ 2,000 proteins in a typical cell > 4.9 million sequences in UniProt (Oct 2007) > 46,000 protein structures in the PDB (Oct 2007) 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 BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  27. Structural Genomics Projects TargetDB: database of structural genomics targets http://targetdb.pdb.org BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  28. Protein Sequence & Structure: Analysis • Diamond STING Millennium- Many useful structure analysis tools, including Protein Dossier http://trantor.bioc.columbia.edu/SMS/ • SwissProt (UniProt) Protein knowledgebase http://us.expasy.org/sprot • InterPro Sequence analysis tools http://www.ebi.ac.uk/interpro BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  29. Protein Structure Prediction or Protein Folding Problem "Major unsolved problem in molecular biology" In cells: spontaneous assisted by enzymes assisted by chaperones In vitro: many proteins can fold to their "native" states spontaneously & without assistance but, many do not! BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  30. 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 that 3-dimensional structure Deciphering the Protein Folding Code BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  31. 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 2 Major Protein Folding Problems: 1- Determination of folding pathway 2- Prediction of tertiary structure from sequence Both still largely unsolved problems BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  32. 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 & rearrangement of some 2' structures Native state? - assumed to be lowest free energy - may be an ensemble of structures BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  33. Protein Dynamics • Protein in native state is NOT static • Function of many proteins requires 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 ~ 2 H-bonds!) • Folding involves changes in both entropy & enthalpy BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  34. Difficulty of Tertiary Structure Prediction Folding 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 with number of residues Computationally it is an exceedingly difficult problem! BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

  35. From Thursday's Lab: • Homology Modeling - using SWISS-MODEL • http://swissmodel.expasy.org//SWISS-MODEL.html • Threading - using 3-D JURY(BioinfoBank, a METAserver) • http://meta.bioinfo.pl/submit_wizard.pl • Be sure to take a look at CASP contest: • http://predictioncenter.gc.ucdavis.edu/ • CASP7 contest in 2006 • http://www.predictioncenter.org/casp7/Casp7.html BCB 444/544 F07 ISU Dobbs #22 - Secondary & Tertiary Structure Prediction

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