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Since it is the 5'-end of a miRNA that determines its target specificity, incorrect cleavage may result in an accumulation of aberrant miRNA molecules.
These mutations result in incorrect cleavage of the protein, producing a deposited protein of amyloid-β (Aβ) that is more likely to form plaques [ 1, 5].
The breakpoint sequences observed share the structural features of palindrome formation triggered by double-strand breaks near short inverted segments or by incorrect cleavage by a Holliday junction resolvase at an inverted repeat-mediated cruciform structure, and subsequent ligation of hairpins [ 32].
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RAId_DbS has internal counters, C c and C inc, totaling respectively the number of scored peptides with correct and incorrect N-terminal cleavage.
However, the E-value of a peptide with incorrect N-terminal cleavage will be obtained by multiplying the peptide's P-value by C c + C inc [ 13].
Not only do we lift this constraint, we even allow for non-canonical N-terminal cleavages (NNTC), also referred to as "incorrect N-terminal cleavages" by [ 17].
Specifically, we further divide the qualified peptides into ones with correct and incorrect N-terminal cleavages [11] and have separate counters for them.
As a specific example, when trypsin is used as the digesting enzyme, RAId_DbS allows for incorrect N-terminal cleavages.
What was wrong with cleavage?
The increase in the KSV value for the mutant precursor proteins from the wild-type value and the increase in accessibility of the quencher acrylamide to the core of the proteins indicated that the precursor state formed by the mutant NS2-3 proteins was in the incorrect conformation in which cleavage was unable to occur.
Interestingly, the most N-terminal peptide for OEC-23-like (AT2G39470) and an isomerase (AT1G18170) were upstream of the predicted lTP cleavage site (Table 2), indicating either incorrect lTP cleavage site prediction or identification of an intermediate processing step.
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CEO of Professional Science Editing for Scientists @ prosciediting.com