Peptide cleavage sites

Howe, C., and Wallace, T. (1990). Prediction of leader peptide cleavage sites for polypeptides of the thylakoid lumen. Nucl. Acids Res. 18, 3417-3417. 

Figure 12.15. Prediction of signal peptide cleavage site. The profile plot shows the prediction of signal peptide cleavage site of duck lysozyme by SignalP.

Nielsen, H Engelbrecht, J., von Heijne, G. Brunak, S. (1996). Defining a similarity threshold for a functional protein sequence pattern the signal peptide cleavage site. Proteins 24,165-77. (The data set is available from the FTP server at ftp //virus.cbs.dm.dk/pub/signalp). 

Thomas, G., Potter, L., and Cole, J. A., 1999,The periplasmic nitrate reductase from Escherichia coli a heterodimeric molyhdoprotein with a douhle-arginine signal sequence and an unusual leader peptide cleavage site, FEMS Microbiol. Lett. 174 167nl71. 

The following example shows how BioPerl can be used to read protein sequences from a FASTA file and find signal peptide cleavage sites. The file format is inferred from the file extension. fa. 

Fig. 3. NMR structures of PrP-sen. The refined NMR structure of (A) recombinant mouse PrP-sen from amino acid residues 121-231 (Riek et al., 1996) and (B) recombinant hamster PrP-sen from amino acid residues 23-231 (Liu et al, 1999). The structure of full-length mouse PrP-sen has been derived (Riek et al., 1997), but residues from the signal peptide cleavage site to the structure illustrated (i.e., 23-120) exist in a flexible, random coil-like state as shown for the hamster PrP-sen structure in (B). S, P strand H, a helix. Figure prepared with the program MOLMOL (Koradi et al, 1996).

A fragment of the lettuce VDE cDNA was amplified from lettuce cDNA by PCR and used to isolate a near full-length cDNA for lettuce VDE (Bugos and Yamamoto, 1996). The cDNA encoded a polypeptide of 473 amino acids with a calculated molecular mass of 54.4 kDa. This was confirmed from in vitro transcription/translation of the VDE cDNA which produced a 55 kDa polypeptide when analyzed by SDS-PAGE. The deduced preprotein contained a 125 amino acid bipartite transit peptide for transport into the chloroplast and thylakoid lumen. Based on the N-terminal sequence of the purified VDE from lettuce, which indicates the transit peptide cleavage site, the mature VDE protein is encoded by 348 amino acids with a calculated molecular mass of... 

Sequencing of the labelled mature soy a-CT and BCCP, isolated from pea stroma after import of corresponding precursors, allowed us to determine the position of the transit peptide cleavage site, which is for a-CT2... 

Technologies that offer the opportunity to use MS for intact protein mass determination allow rapid assessment of signal peptide cleavage sites and post-translational heterogeneity. A well-resolved mass spectrum of an intact protein defines its native covalent profile as well as its associated heterogeneity. A comprehensive mass spectrometric approach that integrates both intact protein molecular mass measurement (top-down) and proteolytic fragment identification (bottom-up) would represent a powerful approach for proteome/ protein characterization. 

Predict Peptide Cleavage Site Based on Subsite Coupling Model. 

BROEKMAN DC, FREI DM, GYLFASON GA, STEINARSSON A, JORNVALL H, AGERBERTH B, GUDMUNDSSON GH, MAIER VH (2011), Cod cathelicidin isolation of the mature peptide, cleavage site characterisation and developmental expression , Dev Comp... 

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