Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles.
Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.
Suzuki
Teppei
T
Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan. teppei_suzuki@moegi.waseda.jp
Kawashima
Hirotaka
H
Kotoku
Hiromi
H
Sota
Takayuki
T
D003198:Computer Simulation; D008956:Models, Chemical; D010429:Pentoses / Q000737:chemistry*; D012996:Solutions; D014867:Water / Q000737:chemistry*
D010429:Pentoses; D012996:Solutions; D014867:Water