Prediction of Signal Peptide Cleavage Sites with Subsite-Coupled and Template Matching Fusion Algorithm

2014 ◽  
Vol 33 (3) ◽  
pp. 230-239 ◽  
Author(s):  
Shao-Wu Zhang ◽  
Ting-He Zhang ◽  
Jun-Nan Zhang ◽  
Yufei Huang
Keyword(s):  
Signal Peptide ◽  
Template Matching ◽  
Cleavage Sites ◽  
Fusion Algorithm ◽  
Peptide Cleavage

scholarly journals Serum Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) Level as a Potential Biomarker of Cholangiocarcinoma

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 413 ◽  
Author(s):  
Doungdean Tummanatsakun ◽  
Tanakorn Proungvitaya ◽  
Sittiruk Roytrakul ◽  
Temduang Limpaiboon ◽  
Sopit Wongkham ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Transmembrane Helix ◽  
Control Group ◽  
Cleavage Sites ◽  
Dot Blot ◽  
Peptide Cleavage ◽  
Potential Biomarker ◽  
Predicted Signal Peptide ◽  
Healthy Control ◽  
Dot Blot Analysis

Diagnostic and/or prognostic biomarkers for cholangiocarcinoma (CCA) are still insufficient with poor prognosis of patients. To discover a new CCA biomarker, we constructed our secretome database of three CCA cell lines and one control cholangiocyte cell line using GeLC-MS/MS. We selected candidate proteins by five bioinformatics tools for secretome analysis. The inclusion criteria were as follows: having predicted signal peptide or being predicted as non-classically secreted protein; together with having no transmembrane helix and being previously detected in plasma and having the highest number of signal peptide cleavage sites. Eventually, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) was selected for further analysis. To validate APEX1 as a bio-marker for CCA, serum APEX1 levels of 80, 39, and 40 samples collected from CCA, benign biliary diseases (BBD), and healthy control groups, respectively, were measured using dot blot analysis. The results showed that serum APEX1 level in CCA group was significantly higher than that in BBD or healthy control group. Among CCA patients, serum APEX1 level was significantly higher in patients having metastasis than in those without metastasis. The higher level of serum APEX1 was correlated with the shorter survival time of the patients. Serum APEX1 level might be a diagnostic and prognostic biomarker for CCA.

scholarly journals Structure of the Human Signal Peptidase Complex Reveals the Determinants for Signal Peptide Cleavage

2021 ◽  
Author(s):  
A. Manuel Liaci ◽  
Barbara Steigenberger ◽  
Sem Tamara ◽  
Paulo Cesar Telles de Souza ◽  
Mariska Gröllers-Mulderij ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Signal Peptidase ◽  
Peptide Cleavage ◽  
Human Signal

Processing of Escherichia coli alkaline phosphatase: role of the primary structure of the signal peptide cleavage region 1 1Edited by A. R. Fersht

1998 ◽  
Vol 277 (4) ◽  
pp. 859-870 ◽  
Author(s):  
Andrew L Karamyshev ◽  
Zemphyra N Karamysheva ◽  
Andrey V Kajava ◽  
Vladimir N Ksenzenko ◽  
Marina A Nesmeyanova
Keyword(s):  
Escherichia Coli ◽  
Alkaline Phosphatase ◽  
Signal Peptide ◽  
Primary Structure ◽  
Peptide Cleavage

scholarly journals Sequences in rotavirus glycoprotein VP7 that mediate delayed translocation and retention of the protein in the endoplasmic reticulum.

1990 ◽  
Vol 111 (4) ◽  
pp. 1343-1350 ◽  
Author(s):  
S C Stirzaker ◽  
D Poncet ◽  
G W Both
Keyword(s):  
Signal Peptide ◽  
Glycosylation Site ◽  
Peptide Cleavage ◽  
Cos Cells ◽  
Chase Period ◽  
Hybrid Proteins ◽  
Rate Limiting Step ◽  
Necessary And Sufficient ◽  
Rate Limiting

Glycosylation and translocation of the simian rotavirus protein VP7, a resident ER protein, does not occur co-translationally in vivo. In pulse-chase experiments in COS cells, nonglycosylated VP7 was still detectable after a 25-min chase period, although the single glycosylation site was only 18 residues beyond the signal peptide cleavage site. After labeling, glycosylated and nonglycosylated VP7 was recovered in microsomes but the latter was sensitive to trypsin (i.e., the nascent protein became membrane associated) but most of it entered the ER posttranslationally because of a rate-limiting step early in translocation. In contrast with the simian protein, bovine VP7 was glycosylated and translocated rapidly. Thus, delayed translocation per se was not required for retention of VP7 in the ER. By constructing hybrid proteins, it was further shown that the signal peptide together with residues 64-111 of the simian protein caused delayed translocation. The same sequences were also necessary and sufficient for retention of simian VP7 in the ER. The data are consistent with the idea that certain proteins are inserted into the ER membrane in a loop configuration.

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