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Introduction to Proteomics

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Title: Introduction to Proteomics Author: Zhu GuoPing Last modified by: Zhu GuoPing Created Date: 6/12/2007 3:29:37 PM Document presentation format – PowerPoint PPT presentation

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Title: Introduction to Proteomics


1
Chapter 8 New Research Field in Molecular
Biology
2
8.1 Bioinformatics
3
  1. What is bioinformatics? Bioinformatics and
    computational biology involve the use of
    techniques including applied mathematics,
    informatics, statistics, computer science,
    artificial intelligence, chemistry, and
    biochemistry to solve biological problems usually
    on the molecular level.

4
2. Major research fields (1) Sequence
analysis (3) Computational evolutionary
biology (4) Measuring biodiversity (5) Analysis
of gene expression (6) Analysis of
regulation (7) Analysis of protein
expression (8) Analysis of mutations in
cancer (9) Prediction of protein structure (10)
Comparative genomics (11) Modeling biological
systems (12) High-throughput image analysis
5
3. Databases ?BLAST ACCESS ?dbEST /
Expressed Sequence Tags database ?ceDB
databases ? Phenotypic databases
?LIMS ?BASE ?MOLCAS ..
6
8.2 Proteome Proteomics
7
1. What is Proteome?
  • Proteome - All the proteins expressed by a cell ,
    tissue or organism at a particular time and under
    specific conditions.

8
2. What is Proteomics?
  • Proteomics is the systematic study of all of the
    proteins in a cell, tissue, or organism. The
    analysis includes the identification, expression,
    localizations, functions (physiological and
    pathophysiological functions), and interactions
    of proteomes.

9
4. Branches of Proteomics
  • Expressional Proteomics
  • Functional Proteomics
  • Structural Proteomics

10
Protein Microarrays
11
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12
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13
Different Kinds of Protein Arrays
Antibody Array Antigen Array
Ligand Array
Detection by SELDI MS, fluorescence, SPR,
electrochemical, radioactivity, microcantelever
14
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15
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  • (Surface enhanced laser desorption/ionization,
    SELDI)
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  • (atomic force microscope, AFM )
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16
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Problems
  • Expensive
  • Standard
  • Specificity
  • Sensitivity

18
Functional Proteomics (in vitro)
  • Multi-well plate readers
  • Full automation/robotics
  • Fluorescent and/or chemi-luminescent detection
  • Small volumes (mL)
  • Up to 1536 wells/plate
  • Up to 200,000 tests/day
  • Mbytes of data/day

19
  • In silico methods (bioinformatics)
  • Genome-wide Protein Tagging
  • Genome-wide Gene Deletion or Knockouts
  • Random Tagged Mutagenisis or Transposon Insertion
  • Yeast two-hybrid Methods
  • Protein (Ligand) Chips

20
Structural Proteomics
High Throughput protein structure determination
via ? X-ray crystallography ? NMR ?
spectroscopy ? comparative molecular modeling
21
Structural Proteomics The Goal
22
Why Structural Proteomics?
  • Structure Function
  • Structure Mechanism
  • Structure-based Drug Design
  • Solving the Protein Folding Problem

23
Bioinformatics Proteomics
24
8.3 Metabonome Metabonomics
25
1. What is Metabonome ? - It refers the
complete set of metabologically regulated
elements in cells.
26
2. What is Metabonomics Metabonomics is
the branch of science concerned with the
quantitative understandings of the metabolite
complement of integrated living systems and its
dynamic responses to the changes of both
endogenous factors and exogenous factors.
27
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28
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By the end...
Systems Biology
31
Final Exam
32
Thank You Very Much
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