Carbohydrate-Dedicated Force Fields and Their Contribution to the Understanding of the Relation between Conformational Degrees of Freedom in Carbohydrate Molecules

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Mini symposium: Glycobiology at the LUMC and beyond

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Carbohydrate-Dedicated Force Fields and Their Contribution to the Understanding of the Relation between Conformational Degrees of Freedom in Carbohydrate Molecules

Wojciech Plazinski 1 , Karina Nester 1 , Karolina Gaweda 1

1 Institute of Catalysis and Surface Chemistry, Krakow, Poland

The understanding of the mechanisms governing the carbohydrate structural and conformational properties is still far behind those concerning other biologically-relevant polymers (e.g. proteins or nucleic acids). The problem partially lies in the lack of the appropriate tools, including validated computational techniques tailored to study carbohydrate-containing systems. This presentation describes our systematic study oriented at development of carbohydrate-dedicated molecular mechanics force fields that can be apply in order to investigate the conformational properties of wide class of carbohydrate mono-, di-, oligo- and polymers in the presence of aqueous solvent as well as of other species of interest (e.g. metal ions). In particular, we are going to present the capabilities of the newly developed extensions of the GROMOS force field in the context of molecular dynamics simulation-based studies on oligo/polymer chains: (i) composed of building blocks of unfunctionalized pyranoses; (ii) composed of building blocks of uronates (protonated, anionic or esterified); (iii) composed of building blocks of unfunctionalized furanoses (fructans); (iv) composed of heterogeneous building blocks belonging to any of the above groups; (v) of uronates (e.g. alginate or pectin) interacting with bivalent metal ions. The results of our study provide an insight into the structural features of carbohydrate-based polymers and carbohydrates-bivalent ions complexes. This includes the description of the refined, dynamic structure of the pectin-Ca2+ and alginate-Ca2+ complexes. Furthermore, we show how the ‘local’ degrees of freedom considered at the level of monomers (e.g. ring shape) can influence the ‘global’ structural features exhibited at the level of polymer chain. Our research show how these ‘local’ properties can be rationally altered (e.g. by the change of environment or chemical modification of the monomer substituents) in order to obtain the desired structure of longer chains. This finding creates new directions in rational design of solution-characteristic properties of carbohydrate-based polymers.

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