comparative genomics of zbtb7b between human and mouse

Comparative genomics of zbtb7b between human and mouse

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.

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

Core Proteome

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

Proteome Mining

Identifying as many as possible of the proteins in your sample

Protein Expression Profiling

Identification of proteins in a particular sample as a function of a particular state of the organism or cell

Functional proteomics

Post-translational modifications

Identifying how and where the proteins are modified

Protein-protein interactions Protein-network mappingDetermining how the proteins interact with each other in living systems

Structural Proteomics

Protein quantitation or differential analysis

Proteomics and biology /Applications

ExPaSy website (www.expasy.org)

Proteomics tools of ExPaSy

Protein characterization tools

ProtParam tool

Protparam output

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.

ProtParam explanation

Protein characterization tools

Peptide cutter tool

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Peptide cutter tool

Peptide cutter output

Post-translational modification

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).

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 phospho-serine 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.

Types of Glycosylation

If the G-score is >0.5 the residue is predicted as glycosylated; the higher the score the more confident the prediction.

NetOGlyc output

Graphical NetOGlyc output

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 N-glycosylation 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 N-glycosylation occuring within Asn-Xaa-Cys tripeptide where a cysteine is opposed to a serine/threonine e.g. plasma protein C, von Willebrand factor etc.

The Asn-Xaa-Ser/Thr sequon

Prediction of N-glycosylation sites in human proteins(NetNGlyc)

NetNGlyc output

Graphical 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

The Asn-Xaa-Ser/Thr sequon in NetNGlyc output

Prediction of Phosphorylation sites (NetPhos)

NetPhos output

Usually the threshold is set as 0.5 by default. In general, the higher the score the higher the confidence of the prediction.

NetPhos graphical output

FASTA input for signal peptide detection

Predicting signal sequence (SignalP)