Proteomics Session 1 Introduction. Some basic concepts in biology and biochemistry.
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Transcript of Proteomics Session 1 Introduction. Some basic concepts in biology and biochemistry.
The bonds contribute to protein structure
1. Hydrogen bond
2. Hydrophobic interaction
3. Ionic bond
4. Disulfide bond
Proteins are the molecule tools for most cellular functions
TYPE FUNCTION EXAMPLE Structural proteins Support Collagen, Elastin,
Keratin Storage proteins Storage of amino acid Ovalbumin,
Casein Transport proteins Transport of other
substrate Hemoglobin
Hormonal proteins Coordination of and organism’s activities
Insulin
Receptors proteins Response of cell to chemical stimuli
Receptor in nerve transmit route
Contractile proteins Movement Actin, Myosin Defensive proteins Protecton against
disease Antibodys
Enzymatic proteins Selective acceleraton of chemical reactions
Trypsin, ATPase, GAPDH
What is “bioinformatics”?
(Molecular)(Molecular) BioBio – – informaticsinformatics
One idea for a definition?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 “Bioinformatics is “MISMIS” for Molecular Biology Information. It ” for Molecular Biology Information. It is a practical discipline with is a practical discipline with many many applicationsapplications..
Bioinformatics - History
1980
2005
2000
1990
1985
1995
Single StructuresModeling & GeometryForces & SimulationDocking
Sequences, Sequence-Structure Relationships
AlignmentStructure PredictionFold recognition
GenomicsDealing with many sequencesGene finding & Genome Annotation Databases
Integrative AnalysisExpression & Proteomics DataData miningSimulation again….
Growth of biological databases
1 2 3 5 10 16 24 35 49 72 101 157 217385
652
1,160
2,009
3,841
0
500
1,000
1,500
2,000
2,500
3,000
3,500
4,000
百萬
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
Source: GenBank
3D StructuresGrowth:
Source: http://www.rcsb.org/pdb/holdings.html
GenBank BASEPAIR GROWTH
Example: Drug Discovery
Target IdentificationTarget Identification– Which protein to inhibit?Which protein to inhibit?
Lead discovery & optimizationLead discovery & optimization– What sort of molecule will bind to this protein?What sort of molecule will bind to this protein?
ToxicologyToxicology– Side effects, target specificitySide effects, target specificity
PharmacokineticsPharmacokinetics– Metabolization and transportMetabolization and transport
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!$600-700 Million!
With the aid of bioinformatics
7-15 years
Drug lead screening
5,000 to 10,000 compounds screened
250 Lead Candidates in Preclinical Testing5 Drug Candidates
enter Clinical Testing; 80% Pass Phase I
One drug approved by the FDAOne drug approved by the FDA
30%Pass Phase II
80% Pass Phase III
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
Why proteomics becomes an important discipline
Significant DNA sequencing results: Significant DNA sequencing results: – 45 microorganism genomes have been sequenced 45 microorganism genomes have been sequenced
and 170 more are in progressand 170 more are in progress– 5 eukaryotes have been completed5 eukaryotes have been completed
Saccharomyces cerevisiaeSaccharomyces cerevisiaeSchizosaccharomyces pombeSchizosaccharomyces pombeArabodopsis thalianaArabodopsis thalianaCaenorhabditis elegansCaenorhabditis elegansDrosophilia melanogasterDrosophilia melanogasterRice, Mouse and Human are nearly doneRice, Mouse and Human are nearly done
However, However, 2/3 of all genes “identified” have 2/3 of all genes “identified” have no no known functionknown function
Only DNA sequence is not enough
StructureStructure
RegulationRegulation
InformationInformation
Computers cannot determine which of these 3 Computers cannot determine which of these 3 roles DNA play solely based on sequence roles DNA play solely based on sequence (although we would all like to believe they can)(although we would all like to believe they can)
Those are what we need to know about proteins
Introduction to Proteomics
DefinitionsDefinitions– 1. 1. Classical -Classical - restricted to large scale analysis of restricted to large scale analysis of
gene products involving only proteinsgene products involving only proteins (small view)(small view)– 2. 2. Inclusive -Inclusive - combination of protein studies with combination of protein studies with
analyses that have genetic components such as analyses that have genetic components such as mRNA, genomics, and yeast two-hybridmRNA, genomics, and yeast two-hybrid (bigger vi(bigger view)ew)
Don’t forget that the proteome is Don’t forget that the proteome is dynamicdynamic, changing to reflect the , changing to reflect the environment that the cell is inenvironment that the cell is in..
1 gene = 1protein?
1 gene is no longer equal to one protein1 gene is no longer equal to one protein
TThe definition of a gene is debatable..(ORF, he definition of a gene is debatable..(ORF, promoter, pseudogene, gene product, etc)promoter, pseudogene, gene product, etc)
1 gene1 gene == how many proteins?how many proteins? (never known) (never known)
Differential protein expression
Scenario 1: can be analyzed by microarray technology
DNA RNA Protein
Transcription Translation
x1 x4
DNA RNA Protein
Transcription Translation
x3
Stimulus
DNA RNA Protein
Transcription Translation
x3
Stimulus
Scenario 2: can be solved by proteomics technology
What proteomics can answer
Protein identification
Protein Expression Studies
Protein Function
Protein Post-Translational Modification
Protein Localization and Compartmentalization
Protein-Protein Interactions
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.