Native Structural and Functional Proteoform Characterization of the Prolyl-Alanyl-Specific Endoprotease EndoPro from
Aspergillus niger.
J Proteome Res 2021;
20:4875-4885. [PMID:
34515489 PMCID:
PMC8491274 DOI:
10.1021/acs.jproteome.1c00663]
[Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The prolyl-alanyl-specific
endoprotease (EndoPro) is an industrial
enzyme produced in Aspergillus niger. EndoPro is
mainly used for food applications but also as a protease in proteomics.
In-depth characterization of this enzyme is essential to understand
its structural features and functionality. However, there is a lack
of analytical methods capable of maintaining both the structural and
functional integrity of separated proteoforms. In this study, we developed
an anion exchange (AEX) method coupled to native mass spectrometry
(MS) for profiling EndoPro proteoforms. Moreover, we investigated
purified EndoPro proteoforms with complementary MS-based approaches,
including released N-glycan and glycopeptide analysis, to obtain a
comprehensive overview of the structural heterogeneity. We showed
that EndoPro has at least three sequence variants and seven N-glycosylation
sites occupied by high-mannose glycans that can be phosphorylated.
Each glycosylation site showed high microheterogeneity with ∼20
glycans per site. The functional characterization of fractionated
proteoforms revealed that EndoPro proteoforms remained active after
AEX-separation and the specificity of these proteoforms did not depend
on N-glycan phosphorylation. Nevertheless, our data confirmed a strong
pH dependence of EndoPro cleavage activity. Altogether, our study
demonstrates that AEX-MS is an excellent tool to characterize complex
industrial enzymes under native conditions.
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