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Proteomics Module Proteomics Module

Proteomics OverviewProteomics Overview

““What is Proteomics ?”What is Proteomics ?”

or Proteome - “ics” ?or Proteome - “ics” ?or Protein - “omics” ?or Protein - “omics” ?

CREDIT: JOE SUTLIFF, Science 291: 1221. 2001

First let’s ask, “What is Genomics?” First let’s ask, “What is Genomics?”

or Genome - “ics” ?or Genome - “ics” ?or Gene - “omics” ?or Gene - “omics” ?

You have likely heard, that not long ago (2001) the You have likely heard, that not long ago (2001) the human genome was sequenced.human genome was sequenced.

What does this mean?What does this mean?

Genomics is the study of an Genomics is the study of an organism’s (sometimes a cell’s organism’s (sometimes a cell’s

or a tissue’s) DNA or a tissue’s) DNA (includes all genes) in its totality.(includes all genes) in its totality.

The Human Genome and the “Birth” of GenomicsThe Human Genome and the “Birth” of Genomics

The term “omics” is of recent origin butThe term “omics” is of recent origin butIs now used by biologists to refer to the study ofIs now used by biologists to refer to the study of

a type of molecule or compound in its totality a type of molecule or compound in its totality (or at least on a large scale)(or at least on a large scale)

Some examples of “omic” disciplines are: Some examples of “omic” disciplines are: genomics, lipidomics, metabolomics and genomics, lipidomics, metabolomics and

proteomics.proteomics.

“ “ OMICS ”OMICS ”

So, now, what is Proteomics?So, now, what is Proteomics?

Proteomics is the study of an organism’s Proteomics is the study of an organism’s

(or a cell’s or a tissue’s or an organelle’s)(or a cell’s or a tissue’s or an organelle’s)

Proteins in their totalityProteins in their totality

(or at least on a large scale).(or at least on a large scale).

So, a large-scale study of proteins is proteomics.So, a large-scale study of proteins is proteomics.

What can we learn from What can we learn from seeing things in their totality seeing things in their totality

that we can’t learn from that we can’t learn from seeing them individually?seeing them individually?

What things can we learn What things can we learn

from seeing things from seeing things individually that we can’t see individually that we can’t see

from seeing them in their from seeing them in their totality? totality?

““I can’t see the forest for the trees.”I can’t see the forest for the trees.” ““I can’t see the trees for the forest.”I can’t see the trees for the forest.”

Guard CellGuard Cell ChloroplastChloroplast

But I can see the trees!But I can see the trees! But I can see the forest!But I can see the forest!

Technological Advances Help Us See Both the Forest and the TreesTechnological Advances Help Us See Both the Forest and the Trees

Remembering the “Central Dogma” of biology and howRemembering the “Central Dogma” of biology and howInherited information is (most usually) interpreted by a cell.Inherited information is (most usually) interpreted by a cell.

Transcription

DNA

mRNA

Protein

Translation( Splicing )

Smith et al. 2000Ann. Rev. of Biochem.

Remembering what a protein is:Remembering what a protein is:

Proteins are Polymers of amino acids, whose unique sequence Proteins are Polymers of amino acids, whose unique sequence Gives them unique structures and thereby unique functions.Gives them unique structures and thereby unique functions.

Protein

Remembering what an amino acid is:Remembering what an amino acid is:

The Scope of Proteomics The Scope of Proteomics

In Humans there are ~20,000-25,000 genes (almost In Humans there are ~20,000-25,000 genes (almost all genes encode proteins).all genes encode proteins).

So humans haveSo humans have~ 20,000-25,000 basic protein “ types ”.~ 20,000-25,000 basic protein “ types ”.

However !!!However !!!

There can be great variability in proteins due to:There can be great variability in proteins due to:

The Scope of Proteomics The Scope of Proteomics

● ● Post Translational Modifications:Post Translational Modifications:● ● phosphorylationphosphorylation● ● methylation methylation ● ● glycosylation glycosylation ● ● ubiquitylationubiquitylation● ● acetylationacetylation

● ● Alternative SplicingAlternative Splicing

● ● Polymorphisms (Single Nucleotide Polymorphisms)Polymorphisms (Single Nucleotide Polymorphisms)● ● ProteolysisProteolysis

Humans Devote 653 Humans Devote 653 (roughly 3% of their genes) (roughly 3% of their genes)

to proteins that directly to proteins that directly add phosphate (add phosphate (KinasesKinases))

or remove phosphateor remove phosphate ((PhosphatasesPhosphatases). ).

Phosphorylation is a Common Protein ModificationPhosphorylation is a Common Protein Modification

The Complexity of Protein PhosphorylationThe Complexity of Protein Phosphorylation

About 22,000 proteins encoded in the human genomeAbout 22,000 proteins encoded in the human genome

About 10,000 proteins made in a given cell typeAbout 10,000 proteins made in a given cell type

Rough estimates are 1/3 of proteins are phosphorylatedRough estimates are 1/3 of proteins are phosphorylatedat a given time.at a given time.

If phosphorylated a protein may average If phosphorylated a protein may average 3 phosphorylation sites 3 phosphorylation sites

There may be then ~10,000 Phosphorylation Sites / Cell !There may be then ~10,000 Phosphorylation Sites / Cell !

Upper limit for humans? Estimates are between 66,000 – 500,000 ?Upper limit for humans? Estimates are between 66,000 – 500,000 ?

Is Protein Modification Important?Is Protein Modification Important?

ab/ab

ab/ab =2 tyrosine tophenylalaninemutations, or loss of only 2hydroxyl groups!

Feng and Cooper. MCB 2009

MSTETELQVAVKTSAKKDSRKKGQDRSEATLIKRFKGEGVRYKAKLIGIDEVSAARGDKLCQDSMMKLKGVVAGARSKGEHKQKIFLTISFGGIKIFDEKTGALQHHHAVHEISYIAKDITDHRAFGYVCGKEGNHRFVAIKTAQAAEPVILDLRDLFQLIYELKQREELEKKAQKDKQCEQAVYQTILEEDVEDPVYQYIVFEAGHEPIRDPETEENIYQVPTSQKKEGVYDVPKSQPVSAVTQLELFGDMSTPPDITSPPTPATPGDAFLPSSSQTLPGSADVFGSMSFGTAAVPSGYVAMGAVLPSFWGQQPLVQQQIAMGAQPPVAQVIPGAQPIAWGQPGLFPATQQAWPTVAGQFPPAAFMPTQTVMPLAAAMFQGPLTPLATVPGTNDSARSSPQSDKPRQKMGKESFKDFQMVQPPPVPSRKPDQPSLTCTSEAFSSYFNKVGVAQDTDDCDDFDISQLNLTPVTSTTPSTNSPPTPAPRQSSPSKSSASHVSDPTADDIFEEGFESPSKSEEQEAPDGSQASSTSDPFGEPSGEPSGDNISPQDGS

Is Protein Modification Important?Is Protein Modification Important?Red Ys

Red Ys

Examples of Proteomics Studies—What Proteins Examples of Proteomics Studies—What Proteins Are Differentially Produced to Govern Behavior?Are Differentially Produced to Govern Behavior?

Phosphoproteomics—What Proteins are Phosphorylated Following Phosphoproteomics—What Proteins are Phosphorylated Following Various Treatments or In Different Cell Types or States?Various Treatments or In Different Cell Types or States?

Identification of Proteins in Embryonic Cerebral Spinal Fluid—What Proteins are in What Tissues?

Zappaterra et al, Journal of Proteome Research, 2007

Cellular Fractionation—What Proteins are in What Organelles?Cellular Fractionation—What Proteins are in What Organelles?

Proteomic Scientists often seek to understand and monitor how Proteomic Scientists often seek to understand and monitor how proteins behave collectively inside a cell—Protein Networks.proteins behave collectively inside a cell—Protein Networks.

Protein-Protein Interactions in Drosophila (“ Interactomes ”)

2346/~ total 5000 proteins

Science 302:1727 - 1736Science 302:1727 - 1736

Two Essential Partner Tools in ProteomicsTwo Essential Partner Tools in Proteomics

Mass SpectrometryMass SpectrometryGel ElectrophoresisGel Electrophoresis