17.06.07
Lecture 5. Proteomics
* Protein
- Protein is polymer and has diverse of shape
- Protein switching > state change
- How many protein species? ▶ we don't know.
** Prediction **
20,000 genes ▶ 7-8 alternative splicing per gene ▶ a few 100,000 ~ 200,000 proteins
- How many structure in 100,000 proteins ▶ more than 100,000 : I think there is alternative form in one sequence.
- How many structure type (protein family ▶ have well conserved structure)
** Prediction **
<100,000 ▶ 4,000 (by Professor)
* The level of protein in the cell at any given time is controlled by
1. Rate of transcription of the gene
2. The efficiency of translation of mRNA into protein
3. The rate of degradation (half-life) of protein in the cell
* Protein structure
- Primary structure : sequence of specific amino acid
- Secondary structure : the primary polypeptide chain gets properly folded in of alpha-helix, beta pleated sheet, random coils and turns. (The reason that there is no gamma structure - all of protein structure is consisted of similar alpha and beta structure)
- Tertiary structure : secondary structure interact with each other chemically to form the 3 dimensional shape of proteins. (start : N terminal, end : C terminal)
- quaternary structure : interaction between different polypeptide unit
** Sequence-structure relationship - same structure from different sequences
- Protein domain : Discrete portions of the proteins that fold independently from the rest of protein and they have their own function and serve as one of the building blocks of that proteins.
* Determining the protein structure/polypeptide sequence by
1. X-ray crystallogrphy
2. Nuclear magnetic resonance
3. Protein predicting programmes - computer based (hard about long sequences)
* Relationship between structure and function
- 1:1 relationship
- In sepcific environment, there can be many functions in one structure
- How can we predict function of protein? ▶ predict structure based on sequence ▶ predict function based on structure
- ex) hydrophobicity is determined by primary and secondary structure
* Post translational modifications
- glycosylation
- phosphorylation
- sulfation
* Three major areas of proteomics
- Mass sepc, protein chip, protein interaction (function analysis) + protein sequencing (early stage)
* Type of proteomics
1. Interation proteomics ▶ protein-protein interaction
- proteins always work with interaction
- ligand : anything binding to a protein (ex. cofactor)
2. Expression proteomics ▶ protein quantification
* Protein database
- PDB, Pfam, SCOP (classification), Swissprot, UNIPROT, Interproscan (protein domain), NCBI NR (compaction of proteins based on similarity), etc.
* Protein and peptide separations done by one-dimensional / two-dimensional SDS-PAGE
- 2D : run the gel vertically ▶ run the gel horizontally
* We cannot sequencing protein. So, we predict by mass sepctrometer
- Mass spectrometry
: Identify proteins which separates charged particles or ions according to mass.
: 2 types ▶ MALDI-TOF, ESI-MS-MS
* Protein Microarrays
- Target : something that we like to catch
- a very small amount of different purified proteins are placed on a glass slide in a pattern of rows and columns. Followed addition of various types of the probe molecules, that are fluorescent dye labeled to the array ▶ count amount of dye (intensity of light) ▶ we can get information about protein type and amount
Lecture 6. Epigenomics
* Epigenetic modification - something change open structure on the DNA, reversible.
* Epigenetic modification play an important role in gene expression
- DNA methylation (suppress gene expression)
- DNA acetylation (activate gene expression)
▶ regulate chromatin accessibility
▶ methylation is usually occurred in CpG site
▶ DNA methyltransferase
▶ natural role : imprinting, x chromosome inactivation, heterochromatin maintenance, developmental controls, tissue specific expression controls
▶ cancer : there is different pattern of methylation (different epigenetic pathway)
▶ methylation and aging : getting order, higher methylation
- Histone modification
▶ histone : open up when acetylation is occurred
▶ different residue of histone detected by different epigenetic marker
- RNA interference
▶ siRNA mediated heterochromatin maintenance
* Studying about epigenetics
- 'Bisulfite treatment of cytosine'
1. Obtain blood (control) and tissue (test) from cancer person
2. Obtain sequence and do bisulfite treatment
3. Unmethylated C is changed to U (bisulfite conversion)
4. We can find original methylated C
▶ tissue specific methylation pattern study, cancer marker finding
▶ different with genomic sequencing
