Lecture 5 - Proteomics & Epigenomics

<Proteomics & Epigenomics>
Interaction proteomics => protein -protein association
Protein family - protein mother, father

 

The first person who identify the sequence of amino acid in protein. - Sanger(insulin)

 

Pfam - the data base of protein family
PDB - protein data bank
scop - classification
swiss porf - protein data base from swiss
UNIPROT - protein data base 
interproscan
NCBI NR(non-redundant) db ->largest data base -> check the redundancy

 

The level of any protein in the cell of 
1. rate of transcription of the gene
2. the efficiency of translation of mRNA into protein
3. the rate of degradation into half life of mRNA

 

In my opinion, the number of possilble kinds of protein is 20^300(The number of type of amino acid is 20, and the average length of protein is 300aa ->20*20*20*......*20 ) -> protein space

 

The number of protein types -> about 100,000 
The number of type of protein structure -> 4000~1000

 

secondary structure - alpha helix/ beta sheet

Starting point of polypeptide - N - terminus
End point of polypeptide - C -terminus

domain - area/region of protein

determining protein structure
1. X-ray crystallography
2. NMR -> sensor using magnetic radiation
3. protein prediction program - computer

structure & function
Hydrophobicity is determined by the primary and secondary structure

sequence-(not 1:1)- structure -(1:1)- fuction

There is no method to analyze the amino acid sequence
So we use indirect way to the protein such as Mass spectrometry, 2D gel electrophoresis, 2 type of MS, MALDI-TOF

 

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