Representatives of the conformations and changes in conformation observed are presented in Figure 2A and the conformations found for all the peptides at the different pHs are summarized in Figure 2B.
We chose the model with the lowest Discrete Optimized Protein Energy (DOPE: −0.84) as representative of the active conformation of Btk.
Therefore, interpreting the regions that have a RMSD lower than a certain threshold (e.g. 0.2 Hz), as representative of the cycle's conformation seems more reasonable than taking the optimal fit for granted, especially when comparing different compounds.
Thus, none of the previously determined structures of eukaryotic P5CDHs are truly representative of the aldehyde-free conformation.
In our application of this technique, we cast the problem of conformational search to identify optimal (low energy) conformations as one of experimental design, and use MOLS to identify a small sample as representative of the vast conformational space.
The conformation in Figure 6e is representative of the extended structure similar to the conformation shown in Figure 6a, which supports the experimental CCS alignment for both 4,4′-MDA and the larger 2,4′-MDA conformation.
In this study, the solvated carbohydrate determinants remained relatively inflexible or rigid during extensive MD simulations, confirming earlier observations that the free conformation is representative of the biologically active state for Lewis system antigens (reviewed in [26]).
We propose that the surface properties of the WT nsp4C dimer are representative of an "open" conformation given that its positive, negative and hydrophobic areas are all exposed (Fig. 1).
Therefore, N-myristylation may help to lock the enzyme in conformations that are more representative of the active state of enzyme, because the ternary complex is more likely to adopt conformations suitable for catalysis.
41, 57, 58 To improve the recognition of active compounds in the PI3Kα model (2RD0), we used induced fit docking with Glide 5.6 and Prime 2.2 to construct multiple receptor conformations 59, 60 representative of the response of the binding site residues to the template ligand AS-605240.
