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Two distinct binding modes are observed, one of which resembles the hydrogen bonding pattern of bound ATP.
Multiple modifications in the hydrogen bonding pattern to P resulted in systematic changes of the free energy gap.
The best bonding pattern was English bond, in which all the bricks in each course overlapped the ones below and vertical joints were entirely eliminated.
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†).
And in fact, if you look in the sequence here, you find a particular amino acid, a proline, that disrupts the hydrogen bonding pattern at that position of this helix.
Superposition of the two binding modes shows a remarkable similarity in the side chain orientations and hydrogen bonding pattern despite the reversed peptide orientation.
Similar(24)
Inspection of the Pikp-HMA/AVR-PikD complex, with the His-to-Asn mutated in silico, confirms a very different predicted hydrogen-bonding pattern between the proteins.
The hydrogen-bonding pattern remains the same as in the uncomplexed structure, with the bonds being slightly longer to account for the motion.
Because of this conformational change, some of the hydrogen bonds are lost and others converted to a 310 pattern before D6.43, with a π-helix hydrogen-bonding pattern after it (Supplementary Table 2).
We specifically analyzed the hydrogen-bonding pattern in the wild type and mutant simulations.
Protein sequence and structural analysis suggests that Dkks and colipases have the same disulfide-bonding pattern and a similar fold.
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