posted on 2024-01-29, 08:29authored bySayyed
Jalil Mahdizadeh, Michael Stier, Antonio Carlesso, Aurore Lamy, Melissa Thomas, Leif A. Eriksson
Inositol-requiring
enzyme 1 (IRE1) is a transmembrane sensor that
is part of a trio of sensors responsible for controlling the unfolded
protein response within the endoplasmic reticulum (ER). Upon the accumulation
of unfolded or misfolded proteins in the ER, IRE1 becomes activated
and initiates the cleavage of a 26-nucleotide intron from human X-box-containing
protein 1 (XBP1). The cleavage is mediated by the RtcB ligase enzyme,
which splices together two exons, resulting in the formation of the
spliced isoform XBP1s. The XBP1s isoform activates the transcription
of genes involved in ER-associated degradation to maintain cellular
homeostasis. The catalytic activity of RtcB is controlled by the phosphorylation
and dephosphorylation of three tyrosine residues (Y306, Y316, and
Y475), which are regulated by the ABL1 tyrosine kinase and PTP1B phosphatase,
respectively. This study focuses on investigating the mechanism by
which the PTP1B phosphatase activates the RtcB ligase using a range
of advanced in silico methods. Protein–protein docking identified
key interacting residues between RtcB and PTP1B. Notably, the phosphorylated
Tyr306 formed hydrogen bonds and salt bridge interactions with the
“gatekeeper” residues Arg47 and Lys120 of the inactive
PTP1B. Classical molecular dynamics simulation emphasized the crucial
role of Asp181 in the activation of PTP1B, driving the conformational
change from an open to a closed state of the WPD-loop. Furthermore,
QM/MM-MD simulations provided insights into the free energy landscape
of the dephosphorylation reaction mechanism of RtcB, which is mediated
by the PTP1B phosphatase.