The analysis of MD trajectories of 2 ns showed that the open close motion was coupled with inter-domain twisting motion in the ligand-free state, and some loop regions in the small domain contributed primarily to the flexibility of this protein while the main secondary structures maintained the fairly stable conformation.
The ATPase module in TmcA might be required to accommodate C34 in the catalytic centre of the GNAT domain by twisting tRNAMet, and/or for the efficient turnover of the reaction by promoting product release.
Thus, although structural changes driven by movement of the Ct domain may cause twisting and rotational changes to the pore-lining helices similar to those seen in other potassium channel types, changes in the K2P M4 segment should have a major effect only at the selectivity filter.
To reach the R-ES conformation, the apical domains must twist ∼100° clockwise and complete their elevation (see Table S1).
The movements can be followed in Movie S1, which shows the succession of apical domain tilt, elevation and twisting movements, along with smaller rocking and tilting motions of the equatorial domains.
SDS activation of P. imperator hemocyanin oligomer also twisted domain I away from domains II and III, consequently removing F49 about 3.5 Å away from its original position [ 51].
Extrapolating the PFM images to case for uniform fields, we posit that, while reversible switching is essentially a linear motion of the ferroelastic domains, irreversible switching takes place via domain wall twists.
The opening/closing and twisting motions of two domains are closely related to the conformational changes of l-MtAlaDH induced by NADH.
The twisting motions of the apical domains are best appreciated in an end view movie of the whole ring (Movie S2).
Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein.
In this way, keeping the angle between the lever arms roughly intact during stepping and twisting partially about the leading head causes the translocating motor domain to preferentially reach the desired binding site.
