New Strategy for the Conformational Analysis of Carbohydrates Based on NOE and ¹³C NMR Coupling Constants. Application to the Flexible Polysaccharide of Streptococcus mitis J22

Abstract

For complex oligosaccharides, which are relatively rigid with modest excursions from a single minimum energy conformation, it is straightforward to build conformational models from NOE data. Other oligosaccharides are more flexible with transitions between distinct minima separated by substantial energy barriers. We show that modeling based on scalar coupling data is superior to NOE-based modeling for the latter case. Long range 13 C-13 C and 13 C-1 H coupling constants measured for the heptasaccharide repeating subunit of the cell wall polysaccharide from Streptococcus mitis J22 are correlated with individual glycosidic dihedral angles, effectively uncoupling the degrees of freedom of the oligosaccharide and allowing a search for combinations of dihedral angles which are energetically reasonable, i.e., with no bad van der Waals contacts, and which can be combined to satisfy all the measured J values. Allowed values of the individual angles can then be combined to search for overall oligosaccharide conformations which contribute to the ensemble. We show that while the polysaccharide from S. mitis J22 is flexible, requiring multiple conformations, most of the flexibility is localized to a few bonds and only a rather small number of conformations is required to reproduce the experimental NOE and scalar coupling data.A central question in the conformation and dynamics of complex oligosaccharides and polysaccharides is whether a given structure is "flexible" (1-3). In fact, no oligosaccharide is likely to be truly rigid since puckering of the pyranoside ring and fluctuations of the glycosidic dihedral angles must occur to some extent in all cases. But the currently available data allows for classification of the types of internal motion in oligosaccharides into two distinct types. We will identify internal motion of the first kind as rapid motion on a picosecond time scale of the internal degrees of freedom within a local minimum with limited excursions of the dihedral angles. Oligosaccharides exhibiting this type of internal motion are sometimes called "rigid" in the sense that experimental NOE 1 data may agree with that calculated for a model having a single conformation. The blood group oligosaccharides, especially the Lewis type, are probably the best example of a relatively rigid conformation exhibiting primarily internal motion of the first kind (4-9).In addition to this first kind of motion, more flexible oligosaccharides can also present a second kind of internal motion which is characterized by larger excursions of glycosidic dihedral angles crossing high-energy barriers from one well-defined minimum to another. The existence of this second kind of flexibility may be inferred when the experimental data are not compatible with a single conformation. The time scale of such motions depends on the height of the barrier separating the energy minima and could range from nanoseconds to microseconds. At this point, we have available limited information, either experimental or theoretical, regarding the ki...

Solution structure of a pentasaccharide representing the repeating unit of the O‐antigen polysaccharide from Escherichia coli O142: NMR spectroscopy and molecular simulation studies

“…However, this was not due to puckering motions of the furanose ring. 40 In addition, further flexibility was provided by the presence of the phosphodiester linkages, which seems very reasonable in the light of recent molecular dynamics simulations on the repeating units of the capsular polysaccharides from Haemophilus influenzae types c and f. 41 Also in the case of S. mitis J22, the 1 H and 13 C NMR chemical shifts of the two materials were highly similar, suggesting the oligomer to be a good model for the study of the polymer.…”

A New Way to Produce Cellobiose Carbonates Using Green Chemistry

“…Several methods can be utilized to elucidate the structure of carbohydrates, such as XRD, [36] NMR, [37] and MALDI-TOF MS. [38] NMR has been widely used to attain conformational and dynamicali nformationa bout sugars dissolved in water. [39] Therefore, in this paper, 1 Ha nd 13 CNMR were investigated to assist the analysiso ft he new cellobiose derivative formed from the reactionofc ellobiosew ith DMC.…”

Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

“…Dynamical information on flexibility or conformation changes in solution also provides information of relevance to enzymatic activity and molecular recognition. The flexibility of carbohydrates in solution has been studied for a long time1–3 and categorized by Bush and Martin‐Pastor as flexibility because of single free‐energy minima and changes due to the transitions among different minima 4–8…”