Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Biophysics

Background:

• Beta-ribofuranose puckering is fundamental to nucleic acid structure and function.
• Understanding its dynamics in aqueous solution is crucial for biochemical processes.
• Previous studies have explored puckering modes, but detailed molecular origins remain elusive.

Purpose of the Study:

• To investigate the structural fluctuations and low-frequency dynamics of beta-ribofuranose puckering in aqueous solution.
• To identify key geometrical parameters that correlate with puckering dynamics.
• To elucidate the role of hydration in influencing these dynamics.

Main Methods:

• Ab initio molecular dynamics simulations were employed to capture electronic and nuclear motions.
• Analysis of geometrical parameters, including the anomeric-hydroxymethyl oxygen distance.
• Time-frequency analysis using the Hilbert-Huang transform for spectral characterization.

Main Results:

• A strong dynamic correlation was found between the anomeric-hydroxymethyl oxygen distance and the phase angle of puckering.
• Low-frequency dynamics (below 100 cm(-1)) of puckering are dominated by this correlated motion.
• Local hydration interactions involving these oxygen atoms are identified as the primary drivers of hydration effects.

Conclusions:

• The anomeric-hydroxymethyl oxygen distance serves as a critical geometric descriptor for beta-ribofuranose puckering.
• Local solvent interactions, not bulk effects, significantly influence the low-frequency dynamics of puckering.
• Differences in low-frequency dynamics were observed between distinct hydroxymethyl rotamers of beta-ribofuranose.