Computational analysis and modeling of cleavage by the immunoproteasome and the constitutive proteasome

Abstract

BackgroundProteasomes play a central role in the major histocompatibility class I (MHCI) antigen processing pathway. They conduct the proteolytic degradation of proteins in the cytosol, generating the C-terminus of CD8 T cell epitopes and MHCI-peptide ligands (P1 residue of cleavage site). There are two types of proteasomes, the constitutive form, expressed in most cell types, and the immunoproteasome, which is constitutively expressed in mature dendritic cells. Protective CD8 T cell epitopes are likely generated by the immunoproteasome and the constitutive proteasome, and here we have modeled and analyzed the cleavage by these two proteases.ResultsWe have modeled the immunoproteasome and proteasome cleavage sites upon two non-overlapping sets of peptides consisting of 553 CD8 T cell epitopes, naturally processed and restricted by human MHCI molecules, and 382 peptides eluted from human MHCI molecules, respectively, using N-grams. Cleavage models were generated considering different epitope and MHCI-eluted fragment lengths and the same number of C-terminal flanking residues. Models were evaluated in 5-fold cross-validation. Judging by the Mathew's Correlation Coefficient (MCC), optimal cleavage models for the proteasome (MCC = 0.43 ± 0.07) and the immunoproteasome (MCC = 0.36 ± 0.06) were obtained from 12-residue peptide fragments. Using an independent dataset consisting of 137 HIV1-specific CD8 T cell epitopes, the immunoproteasome and proteasome cleavage models achieved MCC values of 0.30 and 0.18, respectively, comparatively better than those achieved by related methods. Using ROC analyses, we have also shown that, combined with MHCI-peptide binding predictions, cleavage predictions by the immunoproteasome and proteasome models significantly increase the discovery rate of CD8 T cell epitopes restricted by different MHCI molecules, including A*0201, A*0301, A*2402, B*0702, B*2705.ConclusionsWe have developed models that are specific to predict cleavage by the proteasome and the immunoproteasome. These models ought to be instrumental to identify protective CD8 T cell epitopes and are readily available for free public use at http://imed.med.ucm.es/Tools/PCPS/.

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

“…However, the method can, in principle, also be used for longer epitopes. Both proteasomal cleavage and TAP binding can be predicted, and integrated prediction systems have been developed (for more information, see [15,58,80]). However, even though the improvement of prediction accuracy regarding verified MHC ligands has been statistically significant, the impact seems to be marginal compared with MHC binding predictions alone [79].…”

“…Thus, under normal circumstances, this process is performed by the constitutive proteasome that has strong stochastic elements in cleavage preferences [13,14]. However, careful mapping of cleavage sites has led to a general description of the cleavage specificity [15]. In immune-alert cells, certain subunits in the proteasome complex that are responsible for the actual cleavage are replaced, and the cleavage becomes more specific, but still with stochastic elements.…”

HIV Protease Inhibitor–Induced Cathepsin Modulation Alters Antigen Processing and Cross-Presentation

“…HIV PIs block the HIV aspartyl protease preventing the cleavage of HIV Gag-Pol polyproteins and the conversion of HIV particles into mature infectious virions (2). The ability of proteasomes to cleave similar bonds as HIV-1 protease (3) raised questions about interactions between HIV PIs and proteasomal catalytic sites.…”

Sequence-Specific Alterations of Epitope Production by HIV Protease Inhibitors

“…The design of the first generation HIV PIs is based on the transition state mimetic of the Phe-Pro bond, the major substrate of HIV-I protease (10). Evidence showing the ability of the 20S proteasome to cleave similar bonds (11) raised questions about possible interactions between HIV PI and the proteasome catalytic sites.…”