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Hsueh-Fen Juan ( 阮雪芬 ) NTUT Oct 9, 2003 Bioinformatics Data Analysis in Proteomics.

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Presentation on theme: "Hsueh-Fen Juan ( 阮雪芬 ) NTUT Oct 9, 2003 Bioinformatics Data Analysis in Proteomics."— Presentation transcript:

1 Hsueh-Fen Juan ( 阮雪芬 ) NTUT Oct 9, 2003 Bioinformatics Data Analysis in Proteomics

2 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

3 Yuki Juan’s Systems Biology Lab Proteomics Network Identify Proteins Drug Discovery Structures Protein-Protein Interactions Pathways Protein Functions

4 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

5 Yuki Juan’s Systems Biology Lab What Is Proteomes ?

6 Yuki Juan’s Systems Biology Lab Proteomes Gene + Chromosome  Genome Protein +Genome  Proteome Proteomes are dynamics Proteome changes as a function of: time development extracellular condition intracellular condition

7 Yuki Juan’s Systems Biology Lab Definitions of Proteomics First coined in 1995 by Wilkins Be defined as the large-scale characterization of the entire protein complement of a cell line, tissue, or organism. The study of proteomes Goal: -To obtain a more global and integrated view of biology by studying all the proteins of a cell rather than each one individually.

8 Yuki Juan’s Systems Biology Lab Proteomics Origins In 1975, the introduction of the 2D gel by O’Farrell who began mapping proteins from E. coli. The first major technology to emerge for the identification of proteins was the sequencing of proteins by Edman degradation  picomole MS technology has replaced Edman degradation to identify proteins  femtomole

9 Yuki Juan’s Systems Biology Lab How Proteomics Can Help Drug Development http://www.sciam.com.tw/read/readshow.asp?FDocNo=63&CL=18

10 Yuki Juan’s Systems Biology Lab Types of Proteomics and Their Applications to Biology

11 Yuki Juan’s Systems Biology Lab Mechanisms by Which a Single Gene Can Give Rise to Multiple Gene Products In bacteria, 1 or 2 proteins/gene In yeast, 3 proteins/gene In human, 3 or more proteins/gene Glycosylation

12 Yuki Juan’s Systems Biology Lab Two-dimensional Gel Approach Nature 2000, 405, 837-846

13 Yuki Juan’s Systems Biology Lab 3.510 42 60 70 150 kDa pH Increase of 50% Decrease of 50% Unmatched spots Matched spots Image Matching

14 Yuki Juan’s Systems Biology Lab www.expasy.ch/ch2d

15 Yuki Juan’s Systems Biology Lab

16 http://www.expasy.ch/melanie/

17 Yuki Juan’s Systems Biology Lab

18 Standard Proteome Analysis by 2DE-MS Current Opinion in Chemical Biology 2000, 4:489–494 Mass Fingerprint Searching in http://www.expas y.ch/tools/peptide nt.html

19 Yuki Juan’s Systems Biology Lab ControlTreated sample Example: Gel

20 Yuki Juan’s Systems Biology Lab + - gel membrane Transfer proteins from gel to PVDF membrane Sequencing (Very time-Consuming)

21 Yuki Juan’s Systems Biology Lab Mass spectrometry

22 Yuki Juan’s Systems Biology Lab For peptide mass fingerprint data

23 Yuki Juan’s Systems Biology Lab Species pI and MW

24 Yuki Juan’s Systems Biology Lab Peptide Mass Fingerprinting

25 Yuki Juan’s Systems Biology Lab World Wide Web Tools for Searching Databases Site nameURLInformation available MOWSE http://srs.hgmp.mrc.ac.uk/cgi-bin/mowsePeptide mass mapping and sequencing ProFoundhttp://prowl.rockefeller.edu/cgi- bin/ProFound Peptide mass mapping and sequencing PeptIdenthttp://www.expasy.ch/tools/peptident.Peptide mass mapping and sequencing PepSeahttp://195.41.108.38/PepSeaIntro.htmlPeptide mass mapping and sequencing MASCOThttp://www.matrixscience.com/Peptide mass mapping and sequencing PepFraghttp://www.proteometrics.com/Peptide mass mapping and sequencing Protein Prospectorhttp://prospector.ucsf.edu/Peptide mass mapping and sequencing FindModhttp://www.expasy.ch/tools/findmod/Posttranslational modification SEAQUESThttp://fields.scripps.edu/sequest/Uninterpreted MS/MS searching FASTA Search Programs http://fasta.bioch.virginia.edu/Protein and nucleotide database searching Cleaved Radioactivity of Phosphopeptides http://fasta.bioch.virginia.edu/crpProtein phosphorylation site mapping

26 Yuki Juan’s Systems Biology Lab The Information Stored in Genes Is Expressed by a Multistage Process

27 Yuki Juan’s Systems Biology Lab DNA 和蛋白質合成的地方 DNA Proteins Sugar Chain

28 Yuki Juan’s Systems Biology Lab Post-translational Modification Genomics provides comprehensive data-bases of sequence information, DNA and mRNA provide no information concerning the activities and post- translational modifications of proteins. The number of documented protein co- and post- translational modifications now exceeds 400 (http: / / abrf.org / index-.cfm/dm.home). The elucidation of protein post-translational modifications is perhaps the most important justification for proteomics as a scientific endeavor.

29 Yuki Juan’s Systems Biology Lab Chemical modification Covalent linkage of chemical group to amino acid in protein Several types: Acetylation (common on first amino acid) Phosphorylation (often involved in regulation) Lipidation (attachment to membrane) Glycosylation (common outside cell)

30 Yuki Juan’s Systems Biology Lab Processing Removal of part of protein by either: Cleavage (protease cuts protein into smaller pieces) Splicing (self-removal and rejoining of ends)

31 Yuki Juan’s Systems Biology Lab

32 Post-translational Modification

33 Yuki Juan’s Systems Biology Lab Post-translational Modification Glycosylation Mass spectrometric “sequencing” of oligosaccharides Increase the complexity of the proteome

34 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

35 Yuki Juan’s Systems Biology Lab Protein Functions Gene Ontology http://www.geneontology.org/ GoMiner http://discover.nci.nih.gov/gominer

36 Yuki Juan’s Systems Biology Lab Gene Ontology

37 Yuki Juan’s Systems Biology Lab Gene Ontology

38 Yuki Juan’s Systems Biology Lab GoMiner

39 Yuki Juan’s Systems Biology Lab GoMiner Genome Biology 2003, 4:R28

40 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

41 Yuki Juan’s Systems Biology Lab Protein-protein Interactions Introduction Mass Spectrometry Yeast Two-hybrid Assay

42 Yuki Juan’s Systems Biology Lab Introduction Kanehisa (2000)said: Interaction NetworkFunction Post-genome informatics (2000)

43 Yuki Juan’s Systems Biology Lab Introduction Protein-protein interactions are intrinsic to every cellular process. Form the basis of phenomena DNA replication and transcription Metabolism Signal transduction Cell cycle control Secretion

44 Yuki Juan’s Systems Biology Lab Introduction Knowledge of interacting proteins Provide insight into the function of important genes Elucidates relevant pathways Facilitates the identification of potential drug targets Use in developing novel therapeutics

45 Yuki Juan’s Systems Biology Lab Interaction Discovery Methods TiBS(2003), 27(12), 633-638.

46 Yuki Juan’s Systems Biology Lab Structural Biology of Interactions and Complexes X-ray crystallography Nuclear Magnetic Resonance (NMR) Electron microscopy (EI)

47 Yuki Juan’s Systems Biology Lab Examples of Three-dimensional Protein Interactions and Complexes TiBS(2003), 27(12), 633-638.

48 Yuki Juan’s Systems Biology Lab The Study of Protein-protein Interaction by Mass Spectrometry bait S14 ? ? ? ? ** ** SDS- PAGE MASS

49 Yuki Juan’s Systems Biology Lab Peptide Mass Fingerprinting

50 Yuki Juan’s Systems Biology Lab Detecting Protein-protein Interactions by Protein Microarray Science, 2000, 289, 1761-1763

51 Yuki Juan’s Systems Biology Lab Yeast Two-hybrid System Useful in the study of various interactions The technology was originally developed during the late 1980's in the laboratory Dr. Stanley Fields (see Fields and Song, 1989, Nature).

52 Yuki Juan’s Systems Biology Lab Yeast Two-hybrid Assay GAL4 DNA- binding domain GAL4 DNA- activation domain Nature, 2000

53 Yuki Juan’s Systems Biology Lab Yeast Two-hybrid Assay Library-based yeast two-hybrid screening method Nature, 2000

54 Yuki Juan’s Systems Biology Lab Information Extraction (IE) A vast amount of data on protein- protein interactions residues in the published literature, which never been entered into databases. IE have been applied to gaining information on protein-protein interactions.

55 Yuki Juan’s Systems Biology Lab Mining Literature for Protein-protein Interactions

56 Yuki Juan’s Systems Biology Lab Mining Literature for Protein-protein Interactions

57 Yuki Juan’s Systems Biology Lab Protein-protein Interactions on the Web Yeast http://depts.washington.edu/sfields/yplm/data/index.html http://portal.curagen.com http://mips.gsf.de/proj/yeast/CYGD/interaction/ http://www.pnas.org/cgi/content/full/97/3/1143/DC1 http://dip.doe-mbi.ucla.edu/ http://genome.c.kanazawa-u.ac.jp/Y2H C. Elegans http://cancerbiology.dfci.harvard.edu/cancerbiology/ResLabs/Vid al/ H. Pylori http://pim/hybrigenics.com Drosophila http://gifts.univ-mrs.fr/FlyNets/Flynets_home_page.html

58 Yuki Juan’s Systems Biology Lab Yeast Protein Linkage Map Data New protein-protein interactions in yeast Stanley Fields Lab http://depts.washington.edu/sfields/yplm/data List of interactions with links to YPD

59 Yuki Juan’s Systems Biology Lab Yeast Protein Linkage Map Data

60 Yuki Juan’s Systems Biology Lab GeneScape PathwayCalling: Protein interaction and pathway Analysis http://portal.curagen.com PATHCALLING YEAST DATABASE

61 Yuki Juan’s Systems Biology Lab GeneScape

62 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

63 Yuki Juan’s Systems Biology Lab Biological Pathways

64 Yuki Juan’s Systems Biology Lab Biological Pathways Metabolic and biochemical Transcription, regulation and protein synthesis Signal transduction

65 Yuki Juan’s Systems Biology Lab Metabolic and Biochemical Pathway The synthesis of fatty acids

66 Yuki Juan’s Systems Biology Lab Transcription, Regulation and Protein Synthesis Transcription Initiation Elongation Termination

67 Yuki Juan’s Systems Biology Lab Initiation of Transcription

68 Yuki Juan’s Systems Biology Lab The Elongation of Transcrption

69 Yuki Juan’s Systems Biology Lab The Termination of Transcription

70 Yuki Juan’s Systems Biology Lab Transcription, Regulation and Protein Synthesis Translation Initiation Elongation Termination

71 Yuki Juan’s Systems Biology Lab 30S Subunit and Shine-Dalgarno Sequence IF: Initiating protein factor E: Exit site P: Peptide site A: Aminoacyl site

72 Yuki Juan’s Systems Biology Lab Initiation of Translation in E. coli

73 Yuki Juan’s Systems Biology Lab The Elongation Process in Protein Synthesis EF-Tu: Elongation Factor Peptide transferase

74 Yuki Juan’s Systems Biology Lab Termination of Protein Synthesis Stop codon: UAG, UAA, UGA Cytoplasmic protein release factor

75 Yuki Juan’s Systems Biology Lab Signal Transduction EDF signaling pathway Protein kinase

76 Yuki Juan’s Systems Biology Lab Pathway Conservation

77 Yuki Juan’s Systems Biology Lab Databases of Pathways---KEGG http://www.genome.ad.jp/kegg/

78 Yuki Juan’s Systems Biology Lab Glycolysis

79 Yuki Juan’s Systems Biology Lab Pathway Software BIOCARTA http://biocarta.com/ Browse all pathway

80 Yuki Juan’s Systems Biology Lab Pathway Software BIOCARTA

81 Yuki Juan’s Systems Biology Lab Pathway Result 1: Enolase Glycolysis Pyruvate Acetyl-CoA ethanol lactate Cancer cells BIOCARTA

82 Yuki Juan’s Systems Biology Lab Pathway Result 2 : Retinoic Acid Receptor RXR-alpha BIOCARTA

83 Yuki Juan’s Systems Biology Lab Development of the Network- based Pathway Paradigm Ti BS (2003), 28(5), 250-258

84 Yuki Juan’s Systems Biology Lab Development of the Network- based Pathway Paradigm Ti BS (2003), 28(5), 250-258

85 Yuki Juan’s Systems Biology Lab BIND http://bind.mshri.on.ca/

86 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

87 Yuki Juan’s Systems Biology Lab

88 Protein Structure Data Bank- PDB http://www.rcsb.org/pdb/

89 Yuki Juan’s Systems Biology Lab Therapeutic Target Classes

90 Yuki Juan’s Systems Biology Lab Examples of Structure-based Drug Design HIV protease with the inhibitor amprenavir (Agenerase) bound Close-up of zanamivir (Relenza) bound to influenza neuraminidase

91 Yuki Juan’s Systems Biology Lab Outline Introduction to proteomics Protein Functions Protein-protein interactions Pathways Protein Structures and Drug Discovery Bioinformatics on the Web

92 Yuki Juan’s Systems Biology Lab Useful Bio Websites PROSITE http://tw.expasy.org/prosite/ Amos' WWW links page http://tw.expasy.org/alinks.html Phosphoprotein Database (PPDB) http://www- lmmb.ncifcrf.gov/phosphoDB/

93 Yuki Juan’s Systems Biology Lab PROSITE is a database of protein families and domains. http://tw.expasy.org/prosite/

94 Yuki Juan’s Systems Biology Lab

95 http://tw.expasy.org/alinks.html

96 Yuki Juan’s Systems Biology Lab http://tw.expasy.org/alinks.html#PTM

97 Yuki Juan’s Systems Biology Lab http://www.cbs.dtu.dk/databases/PhosphoBase/

98 Yuki Juan’s Systems Biology Lab

99

100 Proteomics Network Identify Proteins Drug Discovery Structures Protein-Protein Interactions Pathways Protein Functions

101 Yuki Juan’s Systems Biology Lab Thank You!

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