Task 3: Sequence-based predictions

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Revision as of 19:54, 25 May 2011 by Pfeiffenberger (talk | contribs) (Task 3.3: Prediction of transmembrane alpha-helices and signal peptides)

Task description

The full description of this task can be found here.


Task 3.1: Secondary structure prediction

Task 3.2: Prediction of disordered regions

Task 3.3: Prediction of transmembrane alpha-helices and signal peptides

General Questions to prediction of transmembrane alpha-helices and signal peptides

Why is the prediction of transmembrane helices and signal peptides grouped together here?

Description of different signal peptides

Signalpeptides for the import to the endoplasmic reticulum (ER)

The import to the ER is usually required for the secretory pathway (to export proteins out of a cell). The import process can occur either co-translational (the nascent protein chain is translocated together with the ribosome) or post-translational (only the fully synthesized protein is transported to the ER). However, for both cases the SEC-pathway is mostly used.

The co-translational transport to the ER is done by the signal recognition particle (SRP). This particle recognizes the N-terminal signal-sequence of the nascent polypeptide chain and then transports it to the ER membrane where the complex, consisting of SRP, polypeptide chain and ribosome, is recognized by the ER membrane bound signal recognition particle receptor (SR). After this recognition the polypeptide chain is imported into the ER lumen via the SEC channel in an ATP dependent process.

The post-translational import to the ER lumen is done by chaperons which guide the polypeptide chain to the SEC channel which is then imported in an ATP dependent process.

However, not only the import to the ER lumen is possible, an import to the ER membrane is possible as well. So far, 5 different types of import to the ER membrane are known.

Type 1 requires an N-terminal signal sequence and an intrinsic stop transfer anchor sequence which will be the part which is inserted in the membrane.

Type 2 and 3 do not require a N-terminal signal sequence only a intrinsic signal anchor sequence is required. The difference between type 2 and 3 is that type 2 has positively charged residues before the signal anchor sequence (on the N-Terminal side) and type 3 has positively charged residues after the signal anchor sequence (on C-Terminal side). These charged residues of trans-membrane protein are always in the cytosol. Thus, type 2 inserted proteins have their N-terminal end residing in the cytosol whereas type 3 inserted proteins have a C-terminal end in the cytosol.

Type 4-A and 4-B insertion is also known as multipass membrane insertion. These proteins have not one trans-membrane helix like the proteins imported via Type 1,2 and 3, instead they have several trans-membrane helices. Hence, they consist of multiple internal stop-transfer anchor sequences and internal signal-anchor sequences. The difference between type 4-A and 4-B is that in type 4-A the N and C terminal ends are located in the cytosol whereas type 4-B import results in a N-terminal end residing in the ER lumen and a C-terminal end residing in the cytosol.

In addition to the N-terminal import of trans-membrane proteins there is also the possiblity for a C-terminal import. Obviously, these proteins are imported post-translation.

Signalpeptides for the import to the mitochondrion
Signalpeptides for the import to the chloroplast
Signalpeptides for the import to the peroxisome
Signalpeptides for the import to the nucleus

TMHMM

Phobius and PolyPhobius

OCTOPUS and SPOCTOPUS

SignalP

TargetP

Task 3.4: Prediction of GO terms

GOPET

Pfam

ProtFun 2.2