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In agreement with crystallographic studies, the results suggest that catalysis requires a closed trigger loop and that translocation requires an open trigger loop.
In water, histidine has a p Ka of about 6.46, and a similar p Ka might be expected for His1085 on an open trigger loop.
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Potentially, a single mutant could be analyzed in a closed-trigger-loop catalytic TEC and an open-trigger-loop product TEC (with PPi bound).
The images to the right of Figure 1B show the pore with a closed or open trigger loop conformation.
The open trigger loop conformation may facilitate translocation of nucleic acids.
Because some noncognate NTPs appear to be rejected before trigger loop closing, MD may also be done in open trigger loop conformations.
Open trigger surgery is the standard technique, and traditionally consists of A1 pulley release in which the pulley is completely dissected.
For multisubunit RNAPs, it would be of great interest to simulate the p Ka of Sc RNAP II His1085 in closed and open trigger loop conformations.
All-atom MD simulations of RNAP II and Thermus thermophilus RNAP with closed and open trigger loop conformations focus on the active site and two crucial neighboring structural elements, the trigger loop and the bridge helix.
We infer that Sal interacts with an open (unfolded) trigger-loop conformational state, and likely would prevent the formation of the closed (folded) trigger-loop conformational state.
Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation.
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