Pursuing the structural basis for carbohydrates biological functions

Carbohydrates constitute the most abundant and diverse group of biological macromolecules on the planet, playing a critical role in a plethora of biological and biotechnological processes, from immunity and cancer to fermentation and vaccines development. A major characteristic that contributes for this role is the broad spectrum of structures and conformations that carbohydrates may exhibit. In fact, carbohydrates possess some unique conformational features, such as the exo-anomeric effect, the gauche effect and the puckering on their rings, and our research group has been dedicated for about 20 years to contribute in the elucidation of the structural basis for the wide range of biological activities this class of biomolecules possess, including the development of force field parameters, methodologies and applications to multiple molecular systems. For instance, in spite of the fact that the main conformation in solution for most hexopyranoses is known to be a chair for about 60 years, we recently demonstrated that up to 20% of carbohydrate residues on PDB are distorted in experimental conditions. While this value is influenced by the type of residue, the structures’ resolution and by the small number of residue counts on the database. In this context, we initiated a series of efforts to try to elucidate the origin of such unusual conformations, if of biological relevance (and consequently, to be used as templates for drug design) of experimental artifacts based on local structural problems. One example of crystallographic structures in which unusual hexopyranose conformations appear is the carbohydrate-binding module 21 (CBM21) from Rhizopus oryzae glucoamylase (RoGA) (PDB entry code 4BFN) showing an unusual 1S3 Glc conformation. Through a combination of molecular dynamics and metadynamics simulations, at both MM and QM/MM levels, we were able to evidence that, on the RogA case, the skewed conformation is likely an experimental artifact. Additionally, CBM21 binding to carbohydrates was observed to be highly dynamic, dependent mainly on the polysaccharide size, and able to move along the polysaccharide chain. These observations are being expanded to other CBMs and carbohydrate binding proteins in order to evaluate if this is a general behavior for X-ray derived structures for non-enzymatic proteins complexed to carbohydrates and, consequently, offer a solid support for the design of carbomimetics targeting such proteins.