Exact(3)
In absence of this H-bond network, GalCer-NFA cannot adopt this active conformation (Figures 4 5).
One cluster is close to the extended conformation observed in the pYEEI-Src SH2 complex (CA-RMSD = 1 2 Å); the other cluster, with CA-RMSD = 4 5 Å is close to a helical conformation (Figures 4 and 5).
When we examined the minichromosomes from M phase cells, we noticed a striking feature: in addition to two adjacent circles representing two replicated minichromosomes, there was a prominent rod-like structure with one end at or near the junction between the minichromosomes, forming a "closed-scissors conformation" (Figures 4, A B).
Similar(57)
This revealed substantial structural deviations for residues 20-22 compared to the dimeric conformation (Figure 4).
It is very intriguing that C12M01 selectively docks to the P-loop extended conformation (Figure 8a, Glide docking score = −9.0), while C12M02 selectively docks to the P-loop folded conformation (Figure 8b, Glide docking score = −9.7).
Six- membered rings of [(H2O 4O2] are also in chair conformation (Figure 6) and the rings are linked as in cis-decalin.
In order to construct a fixed structural configuration, one is required to fix the mandatory base pairing and unpaired region of the molecules, thus creating a partial conformation (Figure 4) of the molecules for each meta-stable state.
Hydrogen bond interactions between the co-crystallized water molecules (O-H···O hydrogen bonds, range from 2.74 - 2.79 Å) led to formation of a six-membered ring water cluster with chair conformation (Figure 4).
In another conformation (Figure 3a, cluster 3, light green) Lys296 is hydrogen bonded to Tyr268.
Molecular dynamics studies of GalCer-NFA remarkably converged to the same type of conformation (Figure 4a).
Additionally, from 5 to 15 ns the H12 is displaced and partially distorted with respect to the original conformation (Figure 7C).
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