Molecular Dynamics Simulation of an ι-Carrageenan Hexamer as Single and Double Helices

• Main Authors: dela Cerna, Mark Vincent C, Garcia, Renz Marion G, Guidote, Armando M, Jr, Claudio, Gil C
• Format: text
• Published: Archīum Ateneo 2022
• Subjects: carageenan; Chemistry
• Online Access: https://archium.ateneo.edu/chemistry-faculty-pubs/184; https://bioone.org/journals/journal-of-the-kentucky-academy-of-science/volume-82/issue-1/1098-7096-82.1.32/Molecular-Dynamics-Simulation-of-an-%ce%b9-Carrageenan-Hexamer-as-Single/10.3101/1098-7096-82.1.32.short
• Institution: Ateneo De Manila University

Carrageenan gelation is characterized by a coil-to-helix transition. The conformation the polymer adopts in solution, however, is not yet fully understood at the molecular level. Here, molecular dynamics (MD) simulations were carried out on two possible conformations of ι-carrageenan hexamers – a single helix and a double helix. All-atom simulations were carried out using the Carbohydrate Solution Force Field (CSFF) in explicit water (SPC). Dihedral angle distributions from simulations of the single helix and the individual chains of the double helix were compared revealing similarity between these conformations. In the case of the double helix, an overall attractive interaction has been calculated between the two chains, possibly due to contribution from sulfate groups and hydroxyl groups, preventing it from unravelling. Simulation calculations revealed no significant difference in the total energy of the single helical and double helical carrageenan in equivalent systems indicating no strong preference by the polymer to adopt one configuration over the other. It is suggested that the double helix can form in solution due to the dihedral angle conformation within the single helices and is stabilized by attractive interactions identified. An increased understanding of gelation process, including the coil-to-helix transition, in carrageenans can allow for the development of processing methods to control their properties for specific applications.