Conformational free energy maps for globobiose (alpha-D-Galp-(1-->4)-beta-D-Galp) in implicit and explicit aqueous solution

Four Ramachandran maps of the conformational potential of mean force (PMF) for the galactose disaccharide globobiose (alpha-D-Galp-(1-->4)-beta-D-Galp) were calculated in vacuum, explicit water, with a simple high dielectric constant and a distance-dependent dielectric coefficient, respectively. This simple model of the galactan alpha-(1-->4)-linkage is shown to be conformationally restricted, with only a small range of syn-phi/syn-psi conformations predominating at standard temperature and pressure. This has implications for the preferred conformation and chain dynamics of alpha-galactosides. In addition, comparison of the relevant PMF surfaces reveals the substitution of a high dielectric constant for explicit water solution to be a valid approximation for reproducing the minimum energy conformation of this glycosidic linkage.     

Ramachandran free-energy surfaces for disaccharides: trehalose, a case study

We present calculated potential of mean force surfaces for rotation about phi, psi dihedral angles of the alpha(1<-->1)alpha-glycosidic linkage in the disaccharide trehalose (alpha-D-Glc-(1<-->1)-alpha-D-Glc) in both vacuum and aqueous solution. The effects of aqueous solvation upon the alpha(1<-->1)alpha-glycosidic linkage are investigated through comparison of the vacuum and aqueous solution free-energy surfaces. These surfaces reveal that trehalose is restricted to a single minimum-energy conformation in both vacuum and solution. The exceptional rigidity of this disaccharide in solution may provide a molecular rationale for the antidesiccant properties of trehalose glasses.     

Molecular modeling provides insights into the loading of sialic acid‐containing antigens onto CRM197: the role of chain flexibility in conjugation efficiency and glycoconjugate architecture

Vaccination is the most cost-effective way to control disease caused by encapsulated bacteria; the capsular polysaccharide (CPS) is the primary virulence factor and vaccine target. Neisseria meningitidis (Nm) serogroups B, C, Y and W all contain sialic acid, a common surface feature of human pathogens. Two protein-based vaccines against serogroup B infection are available for human use while four tetravalent conjugate vaccines including serogroups C, W and Y have been licensed. The tetravalent Menveo® conjugate vaccine is well-defined: a simple monomeric structure of oligosaccharides terminally conjugated to amino groups of the carrier protein CRM₁₉₇. However, not only is there a surprisingly low limit for antigen chain attachment to CRM₁₉₇, but different serogroup saccharides have consistently different CRM₁₉₇ loading, the reasons for which are unclear. Understanding this phenomenon is important for the long-term goal of controlling conjugation to prepare conjugate vaccines of optimal immunogenicity. Here we use molecular modeling to explore whether antigen flexibility can explain the varying antigen loading of the conjugates. Because flexibility is difficult to separate from other structural factors, we focus on sialic-acid containing CPS present in current glycoconjugate vaccines: serogroups NmC, NmW and NmY. Our simulations reveal a correlation between Nm antigen flexibility (NmW?>?NmC?>?NmY) and the number of chains attached to CRM₁₉₇, suggesting that increased flexibility enables accommodation of additional chains on the protein surface. Further, in silico models of the glycoconjugates confirm the relatively large hydrodynamic size of the saccharide chains and indicate steric constraints to further conjugation.