Methods for detecting the signal peptide in transmembrane and globular proteins

摘要

Signal peptides (SP) play an important role in protein transport and sorting to the different compartment of the cell. Although SPs have varying lengths and do not have a consensus sequence, almost all possess a common three-region structure: the positively charged n-region, the hydrophobic h-region, and the c-region where the cleavage site occurs. The presence of an SP in the sequence, if not properly addressed, affects the prediction accuracy of a membrane topology prediction method. For instance, in a recently published results of complete genomes' analysis, the discrimination performance between soluble and membrane proteins drops when SPs are present. Among transmembrane (TM) proteins, the effect becomes evident when predicting for the TM topology because almost all TM prediction methods have the tendency to predict SP as the first TM segment (paper under review). Thus, here, we present two methods, one to discriminate between a putative first TM segment and an SP among TM proteins, and theother one to detect the presence of an SP among globular proteins. The first method applies two discrimination parameters: the position of the first upstream charged residue scanned from the maximal average hydrophobicity region and the average hydrophobicity computed from a fixed number of residue positions from the N-terminal. The second method uses a combination of the occurrence of an uncharged region and the peak average hydrophobocity and its location.