1. Proteomics Session 1 Introduction

2. Some basic concepts in biology and biochemistry

3. The hierarchy of biological organism From “molecule” to “organism”

4. The micro environment: Cell

5. DNA vs. chromosome DNA Chromosome

6. Central dogma: the story of life RNA DNA Protein

7. DNA structure Atomic structure Double helix

8. The basic unit in DNA A T GC

9. From DNA to Protein 1. Transcription 2. Translation

10. Step1: Transcription, generation of mRNA

11. Amino acid carrier: tRNA Step2: Translation, protein assembly

12. Peptide bond formation Peptide Chain

13. Protein structure Primary Secondary Tertiary Quaternary

14. The bonds contribute to protein structure 1. Hydrogen bond 2. Hydrophobic interaction 3. Ionic bond 4. Disulfide bond

15. Proteins are the molecule tools for most cellular functions

16. What is “bioinformatics”? Let’s take minutes to see the hot topic” bioinformatics

17. What is “bioinformatics”? (Molecular) Bio – informatics One idea for a definition? Bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical-chemistry) and then applying “informatics” techniques (derived from disciplines such as applied math and statistics) to understand and organize the information associated with these molecules, on a large-scale. Bioinformatics is “MIS” for Molecular Biology Information. It is a practical discipline with many applications.

18. Bioinformatics - History 1980 2005 2000 1990 1985 1995 Single Structures Modeling & Geometry Forces & Simulation Docking Sequences, Sequence-Structure Relationships Alignment Structure Prediction Fold recognition Genomics Dealing with many sequences Gene finding & Genome Annotation Databases Integrative Analysis Expression & Proteomics Data Data mining Simulation again….

19. Growth of biological databases Source: GenBank 3D Structures Growth: Source: http://www.rcsb.org/pdb/ holdings.html GenBank BASEPAIR GROWTH

20. What bioinformatics can do for us?

21. Example: Drug Discovery Target Identification –Which protein to inhibit? Lead discovery & optimization –What sort of molecule will bind to this protein? Toxicology –Side effects, target specificity Pharmacokinetics –Metabolization and transport

22. Drug Development Life Cycle Years 0 2 4 6 8 10 12 14 16 Discovery (2 to 10 Years) Preclinical Testing (Lab and Animal Testing) Phase I (20-30 Healthy Volunteers used to check for safety and dosage) Phase II (100-300 Patient Volunteers used to check for efficacy and side effects) Phase III (1000-5000 Patient Volunteers used to monitor reactions to long-term drug use) FDA Review & Approval Post-Marketing Testing $600-700 Million! With the aid of bioinformatics 7-15 years

23. Drug lead screening 5,000 to 10,000 compounds screened 250 Lead Candidates in Preclinical Testing 5 Drug Candidates enter Clinical Testing; 80% Pass Phase I One drug approved by the FDA 30%Pass Phase II 80% Pass Phase III

24. Complementarily –Shape –Chemical –Electrostatic ? ? Drug Lead Screening & Docking

25. Introduction to proteomics

26. What’s “proteomics” ? "The analysis of the entire protein complement expressed by a genome, or by a cell or tissue type.“ Wasinger VC et al Progress with gene-product mapping of the mollicutes: Mycoplasma genitalium. Electrophoresis 16 (1995) 1090-1094 Two most applied technologies: 1. 2-D electrophoresis: separation of complex protein mixtures 2. Mass spectrometry: Identification and structure analysis

27. Why proteomics becomes an important discipline Significant DNA sequencing results: –45 microorganism genomes have been sequenced and 170 more are in progress –5 eukaryotes have been completed Saccharomyces cerevisiae Schizosaccharomyces pombe Arabodopsis thaliana Caenorhabditis elegans Drosophilia melanogaster Rice, Mouse and Human are nearly done However, 2/3 of all genes “identified” have no known function However, 2/3 of all genes “identified” have no known function

28. Only DNA sequence is not enoughStructureRegulationInformation Computers cannot determine which of these 3 roles DNA play solely based on sequence (although we would all like to believe they can) Those are what we need to know about proteins

29. Introduction to ProteomicsDefinitions –1. Classical - restricted to large scale analysis of gene products involving only proteins (small view) –2. Inclusive - combination of protein studies with analyses that have genetic components such as mRNA, genomics, and yeast two-hybrid (bigger view) Don’t forget that the proteome is dynamic, changing to reflect the environment that the cell is in.

30. 1 gene = 1protein? 1 gene is no longer equal to one protein The definition of a gene is debatable..(ORF, promoter, pseudogene, gene product, etc) 1 gene = how many proteins? (never known)

31. Why Proteomics?

32. Differential protein expression Scenario 1: can be analyzed by microarray technology DNA RNAProtein Transcription Translation x1 x4 DNA RNAProtein Transcription Translation x3 Stimulus DNA RNAProtein Transcription Translation x3 Stimulus Scenario 2: can be solved by proteomics technology

33. Co- and Post-translational modification Co-translational modifiedPost-translational modified

34. What proteomics can answer Protein identification Protein Expression Studies Protein Function Protein Post-Translational Modification Protein Localization and Compartmentalization Protein-Protein Interactions

35. General classification for Proteomics Protein Expression comparison (beginning) – –Quantitative study of protein expression between samples that differ by some variable Structural Proteomics (simulation) – –Goal is to map out the 3-D structure of proteins and protein complexes Functional Proteomics (everything) – –To study protein-protein interaction, 3-D structures, cellular localization and PTMS in order to understand the physiological function of the whole set of proteome.