Protein Structure Databases: Prediction and Modeling - Prof. Drena Leigh Dobbs, Lab Reports of Bioinformatics

Download Protein Structure Databases: Prediction and Modeling - Prof. Drena Leigh Dobbs and more Lab Reports Bioinformatics in PDF only on Docsity! Protein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 1 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 1 11/9/05 Protein Structure Databases (continued) Prediction & Modeling 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 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 3 Bioinformatics Seminars CORRECTION: 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 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 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 268:78 Prediction of complete gene structures in human genomic DNA • Structure Prediction: Schueler-Furman…Baker, Science 310:638 Progress in modeling of protein structures and interactions 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 6 Review last lecture: Protein Structure: Basics Protein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 2 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 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 Cα 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 9 Peptide bond is rigid and planar 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 10 Hydrophobic Amino Acids 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 11 Charged Amino Acids 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 12 Polar Amino Acids Protein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 5 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 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 26 Simple motifs combine to form domains 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 27 6 main classes of protein structure 1) α Domains • Bundles of helices connected by loops 2) β Domains • Mainly antiparallel sheets, usually with 2 sheets forming sandwich 3) α/β Domains • Mainly parallel sheets with intervening helices, also mixed sheets 4) α+β Domains • Mainly segregated helices and sheets 5) Multidomain (α & β) • Containing domains from more than one class 6) Membrane & cell-surface proteins 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 28 α-domain structures: 4-helix bundles 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 29 β-sheets: up-and-down sheets & barrels 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 30 α/β-domains: leucine-rich motifs can form horseshoes Protein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 6 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 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 More on these later: protein function prediction 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/ • SwissProt (UniProt) protein knowledgebase http://us.expasy.org/sprot • InterPRO sequence analysis tools http://www.ebi.ac.uk/interpro 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/ (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 Especially good for interactions, binding sites 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/ • 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 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/ • Deep View = Swiss-PDB Viewer http://www.expasy.org/spdbv Protein Structure Databases, cont. 11/09/05 D Dobbs ISU - BCB 444/544X 7 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 37 PDB (RCSB) http://www.rcsb.org/pdb 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 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 39 RCSB PDB - New Tutorial http://core1.rcsb.org/tutorial 11/09/05 D Dobbs ISU - BCB 444/544X: Protein Structure Databases - cont. 40 NCBI Structure http://www.ncbi.nlm.nih.gov/Structure 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 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