1. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.1 11/9/05 Protein Structure Databases (continued) Prediction & Modeling

2. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.2 Bioinformatics Seminars Nov 10 Thurs 3:40 Com S Seminar in 223 Atanasoff Computational Epidemiology Armin R. Mikler, Univ. North Texas http://www.cs.iastate.edu/~colloq/#t3 Nov 10 Thurs 4:10 EEOB Seminar in 210 Bessey Diversity and Evolution of Plant Immunity Genes: Insights from Molecular Population Genetics Peter Tiffin, Univ. of Minnesota http://www.cbs.umn.edu/tiffin/index.html

3. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.3 Bioinformatics Seminars CORRECTION: Next week - Baker Center/BCB Seminars: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

4. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.4 Protein Structure & Function: Analysis & Prediction Mon Protein structure: basics; classification,databases, visualization Wed Protein structure databases - cont. Thurs Lab Protein structure databases Protein structure analysis & prediction Fri Protein structure prediction Protein-nucleic acid interactions

5. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.5 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 Additional reading assignments for BCB 544: Gene Prediction: Burge & Karlin 1997 JMB 268:78Burge & Karlin 1997 JMB 268:78 Prediction of complete gene structures in human genomic DNA Structure Prediction: Schueler-Furman…Baker, Science 310:638Schueler-Furman…Baker, Science 310:638 Progress in modeling of protein structures and interactions

6. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.6 Review last lecture: Protein Structure: Basics

7. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.7 Protein Structure & Function Amino acids characteristics Structural classes & motifs Protein functions & functional families ( not much - more on this later) Classification Databases Visualization

8. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.8 Amino Acids Each of 20 different amino acids has different "R-Group," side chain attached to C 

9. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.9 Peptide bond is rigid and planar

10. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.10 Hydrophobic Amino Acids

11. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.11 Charged Amino Acids

12. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.12 Polar Amino Acids

13. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.13 Certain side-chain configurations are energetically favored (rotamers) Ramachandran plot: "Allowable" psi & phi angles

14. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.14 Glycine is smallest amino acid R group = H atom Glycine residues increase backbone flexibility because they have no R group

15. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.15 Proline is cyclic Proline residues reduce flexibility of polypeptide chain Proline cis-trans isomerization is often a rate-limiting step in protein folding Recent work suggests it also may also regulate ligand binding in native proteins - Andreotti

16. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.16 Cysteines can form disulfide bonds Disulfide bonds (covalent) stabilize 3-D structures In eukaryotes, disulfide bonds are found only in secreted proteins or extracellular domains

17. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.17 Globular proteins have a compact hydrophobic core Packing of hydrophobic side chains into interior is main driving force for folding Problem? Polypeptide backbone is highly polar (hydrophilic) due to polar -NH and C=O in each peptide unit; these polar groups must be neutralized Solution? Form regular secondary structures, e.g.,  -helix,  -sheet, stabilized by H-bonds

18. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.18 Exterior surface of globular proteins is generally hydrophilic Hydrophobic core formed by packed secondary structural elements provides compact, stable core "Functional groups" of protein are attached to this framework; exterior has more flexible regions (loops) and polar/charged residues Hydrophobic "patches" on protein surface are often involved in protein-protein interactions

19. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.19 Protein Secondary Structures  Helices  Sheets Loops Coils

20. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.20  helix: stabilized by H-bonds between every ~ 4th residue in backbone C = black O = red N = blue

21. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.21 Certain amino acids are "preferred" & others are rare in  helices Ala, Glu, Leu, Met = good helix formers Pro, Gly Tyr, Ser = very poor Amino acid composition & distribution varies, depending on on location of helix in 3-D structure

22. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.22  -sheets - also stabilized by H-bonds between back bone atoms Anti-parallelParallel

23. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.23  Loops Connect helices and sheets Vary in length and 3-D configurations Are located on surface of structure Are more "tolerant" of mutations Are more flexible and can adopt multiple conformations Tend to have charged and polar amino acids Are frequently components of active sites Some fall into distinct structural families (e.g., hairpin loops, reverse turns)

24. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.24 Coils Regions of 2' structure that are not helices, sheets, or recognizable turns Intrinsically disordered regions appear to play important functional roles

25. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.25 Globular proteins are built from recurring structural patterns Motifs or supersecondary structures = combinations of 2' structural elements Domains = combinations of motifs Independently folding unit (foldon) Functional unit

26. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.26 Simple motifs combine to form domains

27. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.27 6 main classes of protein structure 1)  Domains Bundles of helices connected by loops 2)  Domains Mainly antiparallel sheets, usually with 2 sheets forming sandwich 3)  Domains Mainly parallel sheets with intervening helices, also mixed sheets 4)  Domains Mainly segregated helices and sheets 5) Multidomain (  Containing domains from more than one class 6 ) Membrane & cell-surface proteins

28. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.28  -domain structures: 4-helix bundles

29. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.29  -sheets: up-and-down sheets & barrels

30. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.30  -domains: leucine-rich motifs can form horseshoes

31. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.31 New today: Protein Structure Databases Classification Visualization Protein Structure Prediction Secondary structure Tertiary structure

32. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.32 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 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein More on these later: protein function prediction

33. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.33 Protein sequence & structure: analysis Diamond STING Millennium - many useful structure analysis tools, including Protein Dossier http://trantor.bioc.columbia.edu/SMS/ 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

34. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.34 Protein structure databases PDB Protein Data Bank http://www.rcsb.org/pdb/ http://www.rcsb.org/pdb/ (RCSB) - THE protein structure database MMDB Molecular 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 http://www.ebi.ac.uk/msd Especially good for interactions, binding sites

35. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.35 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/ http://cathwww.biochem.ucl.ac.uk/latest/ DALI/FSSP (recently moved to EBI & reorganized) fully automated structure alignments DALI serverhttp://www.ebi.ac.uk/dali/index.htmlhttp://www.ebi.ac.uk/dali/index.html DALI Database (fold classification) http://ekhidna.biocenter.helsinki.fi/dali/start http://ekhidna.biocenter.helsinki.fi/dali/start

36. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.36 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 Cn3D http://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/ http://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/ Deep View = Swiss-PDB Viewer http://www.expasy.org/spdbv

37. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.37 PDB (RCSB) http://www.rcsb.org/pdb http://www.rcsb.org/pdb

38. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.38 RCSB PDB - Beta site http://pdbbeta.rcsb.org/pdb/Welcome.do http://pdbbeta.rcsb.org/pdb/Welcome.do

39. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.39 RCSB PDB - New Tutorial http://core1.rcsb.org/tutorial http://core1.rcsb.org/tutorial

40. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.40 NCBI Structure http://www.ncbi.nlm.nih.gov/Structure http://www.ncbi.nlm.nih.gov/Structure

41. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.41 MMDB http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

42. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.42 Cn3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

43. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.43 MM MMDB: Molecular Modeling Data Base Derived PDB structure records Value added to PDB records including: Integration with other ENTREZ databases & tools Conversion to parseable ASN.1 data description language Correction of numbering discrepancies in structure vs sequence Validation Addition of explicit chemical graph information Structure neighbors determined by Vector Alignment Search Tool (VAST)

44. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.44 Searching MMDB 1CET

45. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.45 MMDB Structure Summary Cn3D viewer VAST neighbors BLAST neighbors

46. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.46 Cn3D : Displaying 2' Structures Chloroquine

47. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.47 Cn3D : Displaying 3' Structures Chloroquine

48. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.48 Cn3D: Structural Alignments Chloroquine NADH

49. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.49 Protein Explorer (RasMol/Chime)

50. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.50 Protein Explorer

51. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.51 SCOP - Structure Classification

52. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.52 CATH - Structure Classification

53. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.53 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

54. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.54 Structural Genomics Projects TargetDB: database of structural genomics targets http://targetdb.pdb.org Protein Structure Prediction?

55. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.55 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!

56. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.56 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

57. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.57 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

58. 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont.58 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