Transcript Core Proteome

Comparative genomics of zbtb7b between
human and mouse
Proteome
 The entire complement of proteins in a cell or organism.
 An order or magnitude more complex than the genome.
 Derived from genome
– The entire complement of genetic information in the cell.
 May comprise tens or even hundreds of thousands of
different proteins.
 The exact nature of the cellular proteome depends on the
cell type and its environment.
Core Proteome
 All cells contain
– A core proteome comprising housekeeping proteins that
are essential for survival
– An additional set of proteins conferring specialized
functions
 The cellular proteome is in a state of dynamic flux and can
be perturbed by changes in cell state of the environment
Proteomics
 The study of proteome
 The study of protein structure and behavior
 Encompassing
– Identification of proteins in tissues
– Characterization of the physicochemical properties of
proteins (e.g., protein sequences and post-translational
modifications)
– Description of their behavior (e.g., what function a
protein performs and how proteins interact with one
another and the environment)
Proteomics and biology /Applications
Protein Expression Profiling
Proteome Mining
Identifying as many as
possible of the proteins in
your sample
Identification of proteins in a particular
sample as a function of a particular
state of the organism or cell
Post-translational
modifications
Identifying how and
where the proteins are
modified
Functional
proteomics
Protein quantitation or
differential analysis
Protein-protein
interactions Proteinnetwork mapping
Structural
Proteomics
Determining how the
proteins interact with
each other in living
systems
ExPaSy website (www.expasy.org)
Proteomics tools of ExPaSy
Protein characterization tools
ProtParam tool
Protparam output
ProtParam explanation
Extinction coefficient: The absorption coefficient or
extinction coefficient is a measurement of how strongly a
protein absorbs light at a given wavelength.
Unit: M-1 cm-1
Instability: This parameter is a crude estimate of your
protein stability. When index below 40, the protein is usually
stable. Above 40 is a probable indication of unstability.
Half-life: The half-life is a crude prediction of the time it
takes for half of the amount of your protein present in a cell
to disappear completely after its synthesis.
Protein characterization tools
Peptide cutter tool
Peptide cutter tool
Continued…
Peptide cutter output
Post-translational modification
Glycosylation
 Glycosylation is the enzymatic process that links saccharides to
produce glycans, attached to proteins, lipids or other organic molecules.
 Glycosylation is a form of co-translational and post-translational
modification.
 Glycans serve as a variety of structural and functional roles in
membrane and secreted proteins.
 It is an enzyme-directed site-specific process.
 The carbohydrate chains attached to the target proteins serve various
functions.
i) Some proteins do not fold correctly unless they are
glycosylated first.
ii) Polysaccharides linked at the amide nitrogen of asparagine in
the protein confer stability on some secreted glycoproteins.
iii) The unglycosylated protein degrades quickly.
iv) Glycosylation may play a role in cell-cell adhesion (a
mechanism employed by cells of the immune system).
Types of Glycosylation
Five classes of glycans are produced:
 N-linked glycans attached to a nitrogen of asparagine or
arginine side chains
 O-linked glycans attached to the hydroxy oxygen of serine,
threonine, tyrosine, hydroxylysine, or hydroxyproline side
chains, or to oxygens on lipids such as ceramide
 Phospho-glycans linked through the phosphate of a phosphoserine
 C-linked glycans, a rare form of glycosylation where a sugar
is added to a carbon on a tryptophan side chain
 Glypiation, which is the addition of a GPI anchor that links
proteins to lipids through glycan linkages.
Post-translational modification
NetOGlyc output
If the G-score is >0.5 the residue is predicted as glycosylated; the higher the score
the more confident the prediction.
Graphical NetOGlyc output
Post-translational modification
The Asn-Xaa-Ser/Thr sequon
 N-glycosylation is known to occur on Asparagines, which
occur in the Asn-Xaa-Ser/Thr stretch (Xaa is considered as any
amino acid except Proline).
 Although this consensus tripeptide (also called the Nglycosylation sequon) best fit with the requirement, it is not
always sufficient for the Asparagine to be glycosylated.
 Furthermore, there are a very few known instances of Nglycosylation occuring within Asn-Xaa-Cys tripeptide where a
cysteine is opposed to a serine/threonine e.g. plasma protein C,
von Willebrand factor etc.
Prediction of N-glycosylation sites in human proteins
(NetNGlyc)
NetNGlyc output
Graphical NetNGlyc output
The Asn-Xaa-Ser/Thr sequon in NetNGlyc output
 By default, predictions are only shown on Asn-Xaa-Ser/Thr
sequons because so far Asn-Xaa-Ser/Thr (and in some cases
Asn-Xaa-Cys) are N-glycosylated in vivo.
 In the sequence output above, Asn-Xaa-Ser/Thr sequons are
highlighted in blue and N-glycosylated Asparagines are red.
+ - potential> 0.5
++ - Potential > 0.5 And Jury agreement (9/9) or potential > 0.75
+++ - Potential > 0.75 and Jury agreement
++++ - Potential > 0.90 and Jury agreement
Post-translational modification
Prediction of Phosphorylation sites (NetPhos)
NetPhos output
NetPhos graphical output
Usually the threshold is set as 0.5 by default. In general, the
higher the score the higher the confidence of the prediction.
FASTA input for signal peptide detection
Predicting signal sequence (SignalP)