The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions.
The hydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the hydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue hydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the hydration of flexible biomolecules such as carbohydrates.
Andersson
C
C
Department of Dairy and Food Science, Royal Veterinary and Agricultural University, Frederiksberg, Denmark.
Engelsen
S B
SB
D000465:Algorithms; D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D008958:Models, Molecular; D008962:Models, Theoretical; D013395:Sucrose / Q000737:chemistry*; D014867:Water
D002241:Carbohydrates; D014867:Water; D013395:Sucrose