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The structure, stability and bonding pattern of the Fe(NHE 2 complexes (where E = B, Al and Ga) have been studied using density functional theory.
This crystal structure also confirms the predicted disulphide bonding pattern of the receptor and the existence of a cysteine-rich finger domain.
The amino-furazane heterocycle, a constant scaffold in the whole series, mimics the donor/acceptor hydrogen bonding pattern of the bicarbonate with the Val 167 backbone.
Strikingly, the hydrogen bonding pattern of the β-strand β5 to both β3 and β1 is entirely different (Fig 4B, compare middle and right).
It is interesting to note that there is no room for a water molecule near G568 in the ternary complex, but there are two ordered water molecules that interrupt the backbone hydrogen bonding pattern of the P helix near G568 in the apo structure, causing a significant kink in the α-helix (see below).
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The hydrogen bonding pattern of this loop (residues 153 160) in the open and closed conformations suggested that the loop is open in the absence of bound ligand, which enables the substrate (or inhibitor) to enter the active site.
The hydrogen bonding pattern of this lowest energy conformer, calculated between Irigenin-EDA complex over time at 300 K was found to be above the average (1.8 hydrogen bonds), (Fig. 7, ESI†).
Hydrogen bonding patterns of the dimer, catemer and expanded dimer types have been found, as well as supramolecular architectures such as chains, rows, sheets and networks.
Although rough structures were obtained for the PI3K inhibitor complexes before the MD simulations, the refinement of the structures by these simulations clarified the hydrogen bonding patterns of the complexes.
The ligand-induced changes in interhelical hydrogen bonding patterns of the 5-HT1A receptor were followed by rigid body movements of TMH2, 4 and 6 relative to each other and to the other TMHs, which may reflect the structural conversion into an active receptor structure.
After considerable thought about what else might be different about these two seemingly very similar proteins, we have analyzed the hydrogen bonding patterns of the two proteins as one possible way in which they might differ.
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