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With the exception of the eukaryotic small ubiquitin-like modifier (SUMO) family of proteins (reviewed in [26]), conserved motifs surrounding modified residues have not been observed for Ub or other Ubls.
However, modified residues have been identified in both the N-terminal gate and the catalytic core.
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(40) The toxicity is dependent more on what role the modified residue has in the proper folding and functioning of the protein.
A number of modified cysteine residues have been identified, all of which are distal to the DNA cleavage religation active site.
Here, we evaluated the application of PEPstrMOD in handling the peptides having modified residues.
We introduced several Förster resonance energy transfer (FRET) donor−acceptor pairs into the TatA and Gurken peptides, modifying residues that had been shown not to be part of the recognition motif of the substrate.
For example, the loop of helix 69 has at least three modified residues, makes intersubunit contacts, and interacts with both A- and P-site tRNAs [2].
In addition to peptides having natural amino acids, ParaPep also consists of peptides having d-amino acids and chemically modified residues.
The "variable face" has a total of 37 modified residues, compared with just 19 such residues seen on the "conserved face" of the protein – an almost two-fold increase.
The ability of these aldehydes to modify cysteine residues has received the most attention because these residues are often involved in structural or functional protein alterations induced by oxidative events.
2. We have restored the residue codes for the majority of the modified residues through "MODRES" records from PDB files.
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