Antitopes Define Preferential Proteasomal Cleavage Site Usage

The VHSE-Based Prediction of Proteasomal Cleavage Sites

Prediction of proteasomal cleavage sites has been a focus of computational biology. Up to date, the predictive methods are mostly based on nonlinear classifiers and variables with little physicochemical meanings. In this paper, the physicochemical properties of 14 residues both upstream and downstream of a cleavage site are characterized by VHSE (principal component score vector of hydrophobic,...

Predicting proteasomal cleavage sites: a comparison of available methods.

The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced ...

Proteasomal cleavage site prediction of protein antigen using BP neural network based on a new set of amino acid descriptor.

The accurate identification of cytotoxic T lymphocyte epitopes is becoming increasingly important in peptide vaccine design. The ubiquitin-proteasome system plays a key role in processing and presenting major histocompatibility complex class I restricted epitopes by degrading the antigenic protein. To enhance the specificity and efficiency of epitope prediction and identification, the recogniti...

Preferential cleavage in pre-ribosomal RNA byprotein B23 endoribonuclease.

Protein B23 is an abundant nucleolar protein and a putative ribosome assembly factor which possesses an intrinsic ribonuclease activity. In the current work, the effects of RNA sequence and secondary structure on the cleavage preference by protein B23 were studied. Protein B23 ribonuclease preferentially cleaved the single-stranded homopolymers poly(A), poly(U) and poly(C). However, double-stra...

Virus-Specific CTL Response Preferential HLA Usage in the Influenza