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Combining our findings with our previous observation of ultrafast water motions at the interface of a loose binding polymerase (Dpo4), we conclude that the binding interface is dynamic and the water molecules in various binding clefts, channels, and caves are mobile and even fluid with different levels of mobility for loose or tight binding polymerases.
We recently reported our direct probing of solvent accessibility and mobility at the binding interface of a loose binding polymerase (Dpo4)–DNA complex and observed ultrafast interfacial water dynamics, concluding a fluid binding interface and mobile active site and implying a lower fidelity of the polymerase.
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The loose binding appears to produce a buffering effect on enzyme concentration, effectively eliminating bell-shaped dose response curves.
In most cases the interaction consists of a loose, reversible binding of the drug molecule, although some drugs can form strong chemical bonds with their target sites, resulting in long-lasting effects.
Combining these observed dynamics, our MD simulations, X-ray structures, and our previous studies of the loose binding Dpo4 polymerase, we can paint a general picture of polymerase DNA binding interactions and dynamics.
For Dpo4, we only observed a 15 20% increase in the long relaxation times but also an increase in the solvation speeds, consistent with the loose binding interface and more interfacial water molecules.
The mutator activity of I260Q was first identified by a genetic screen (21), and subsequent kinetic characterization showed that while this mutant possessed parameters of DNA binding similar to that of wild-type, it interestingly showed loose binding discrimination of mismatched dNTP substrates, and thus a low fidelity (22).
In this report, we used a methodology similar to that in our previous study of the loose binding Dpo4 DNA complex to characterize the water dynamics at the binding interface for the binary and ternary complexes of pol β with femtosecond resolution.
I had treated my loose binding to another course of duct tape, shouldered my pack and hoped for the best.
Unlike typical chalcogenides, Sb2Se3 is particularly appealing due to its single stable crystal phase, layered structure with loose binding of no dangling bonds.
Robot planning problem can be solved by representing it as constraint satisfaction problem (CSP) due to it being able to support loose binding of services and variables of wider domain.
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