This unwinding includes a change of the backbone conformation of Lys117, the abrogation of the electrostatic contact of Asp115 with the calcium ion and also with other auxiliary electrostatic contacts and the hydrophobic interactions involving Pro113.
In all the five WT trajectories which exhibited complete unfolding, step 2 occurred within 0.5 ns after step 1, with step 3 following within 1.5 ns after step 2; the RMSD increased through the three steps, showing that the conformational change of the backbone of the middle region of the peptide increased as the process advanced (Table 3).
In contrast, only minor adjustments of side chains involved in the interaction surface are observed, without significant changes of the backbone, within hPD-L1.
The conformational changes of the backbone as well as the side chains of poly(di-n-hexylsilane) during the isothermal crystallization from the disordered phase was investigated.
However, a close inspection of their models revealed that such binding mode of P1-His requires structural changes of the backbone atoms of the P1 residue.
Regular structures, which are most likely to be adopted in the lipid bilayer than in the aqueous solution as suggested by MD simulations and experimental data show that conformational changes of the backbone of PG1 when immersed in a lipid bilayer are relatively small due to its structural stabilization by the two disulfide bridges in the rigid part of the peptide (residues 4 16) [34], [34].
Most importantly, this results in changes in ion affinities and/or conformational changes of the backbone (e.g., helical tilts), that are required for ion transport and photosensory transduction (see the respective subsections below for a detailed description of these events).
Herein, we describe the rational design of 100 temperature-adapted adenylate kinase enzymes using a multistate design strategy that incorporates the impact of conformational changes to backbone structure and stability, in addition to experimental analysis of thermostability and function.
Moreover, any change of the polymer backbone related to a change of its polarity and glass transition temperature (Tg) will lead to a strong effect on the thermo-rheological properties.
As mentioned above, we can see here one of the main interests of MetaViz: it is possible to change the backbone of the drawing to center it on specific metabolic pathways.
