When Sugars Get Wet. A Comprehensive Study of the Behavior of Water on the Surface of Oligosaccharides

Abstract

In this article, we characterize the behavior of water on the surface of a diverse group of carbohydrates and attempt to determine the role of saccharide size, linkage, and branching as well as secondary structure on the dynamics and structure of water at the surface. In order to better understand the similarities and differences in the behavior of the solvent on the carbohydrate surface, we explore residence times, rotational correlation functions, local solvent occupancy numbers, and diffusivities. We find that due to the differences in secondary structure water residence times are longer and translational and rotational dynamics are retarded when in contact with wide helices and branched sugars. In the case of extended helices and smaller oligosaccharides, water dynamics is faster and less hindered. This indicates that branching, the type of linkage between monomers, and the anomeric configuration all play a major role in determining the structure and dynamics of water on the surface of carbohydrates.

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

“…However, despite being a phenomenon common to many saccharides, above a definite concentration trehalose appears to reduce the water diffusion [38] and increase the water residence time to a larger extent than its homologues [41,42]. Furthermore, water around trehalose has the longest residence times and is more structured than in the proximity of maltose and sucrose [43].…”

Toward structure prediction of cyclic peptides

“…[24][25][26][27][28][29][30][31][32][33][34][35] Among these, replica-exchange molecular dynamics (REMD), 24, 36 also known as parallel tempering, is probably the most commonly used method. [24][25][26][27][28][29][30][31][32][33][34][35] Among these, replica-exchange molecular dynamics (REMD), 24, 36 also known as parallel tempering, is probably the most commonly used method.…”

A combined nuclear magnetic resonance and molecular dynamics study of the two structural motifs for mixed-linkage β-glucans: methyl β-cellobioside and methyl β-laminarabioside

“…20 These studies all included explicit treatment of solvent. Explicit solvent was also included in recent work 21 by Ramadugu et al where the surface behavior of water on different carbohydrates including b-(1?3) and b-(1?4) linked nonamers of glucose was studied with 5 ns AMBER/GLYCAM MD simulations.…”