Useful information on the relationship between structure, structural fluctuations, and functionality was provided in recent studies of Klinman that suggest the following model for proton-coupled enzyme catalysis.
Taken together, one may use this framework to establish principles to describe how macromolecular structure and structural fluctuations influence ET reactions.
Hatcher, E; Balaeff, A; Keinan, S; Venkatramani, R Beratann, DN, PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms., Journal of the American Chemical Society, vol. 130 no.
On accumulation of 1 µs for each of the structures, the protein exercised structural fluctuations, but basically retained its shape without any deviations that should be accounted for (data not shown).
Root mean square deviation (RMSD) of the G-quadruplex reveals the entire structural fluctuations of a nucleotide structure throughout the MD simulation.
When accounting for structural fluctuations or measurement errors, a single rigid structure may not be sufficient to represent a protein.
The major structural changes in the subunit structure caused by the S228P mutation was obtained by tracing the structural fluctuations during the 20 ns simulations (Fig. S11A).
Kumar, R. & Grubmüller, H. do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
Egami, T. & Srolovitz, D. Local structural fluctuations in amorphous and liquid metals: a simple theory of the glass transition.
Hence, our simulations indicate that LacY has evolved a capability of displaying large structural fluctuations in particular from Phe 27 towards the periplasm to enable substrate uptake.
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations.
