Theoretical Description of the Puckering States of Cyclic Groups in Carotenoids

Carotenoids belong to one of the most common classes of biological pigments. They are observed in either free form (dissolved in hydrophobic media) or as stoichiometric complexes with protein (carotenoproteins). An interaction between a carotenoid and a protein environment is determined mainly by the molecular conformation and dynamic behavior of a cofactor pigment. In this study, using molecular modeling methods, we have analyzed the whole set of alternative conformational states of cyclic side groups of carotenoids and evaluated the energy effects of their interaction with the conjugated backbone chain. The performed theoretical study resulted in the energy-sorted catalogue of alternative conformational states for biogenic cyclic carotenoids and their optical isomers. Conformational states described in this study can be used for a correct selection of initial conditions for the molecular modeling of carotenoproteins.