Helix secondary structure of a biomimetic polymer: molecular dynamic simulation of thymine polimers

GARAY, ALBERTO S.; ALARCÓN, RAMIRO; RODRIGUES, DANIEL E.

Buzios, Río de Janeiro, Brasil

Congreso; Biophysics 2009, VII Congreso Iberoamericano de Biofísica; 2009

Sociedad de Biofísica de Brasil y Argentina, IUPAB

Synthetic polymers of Thymine that uses the capacity of this nucleotide base to dimmerize when photoactivated by UV light (known from biological processes) are being used as “green chemistry” alternatives to PVC. Despite of their incipient technological applications there are few basic studies about its molecular structure. One of these polymers is based on vinylbenzylthymine (VBT), copolymerized with vinylbenzylamonio (VBA) to make it soluble in water. We performed Molecular Dynamic (MD) simulations in water of the polymer VBT-VBA in 1:1 stechiometric ratio for chains lengths between 20 and 32 monomers. Starting from different ad-hoc configurations and after an annealing and equilibration stage we analyzed the structure of the polymer and the basic interactions that make it stable. From a Ramachandran like graph a backbone / dihedral angle pattern could be identified showing a characteristic helix distribution (-60° , -140°). We found this stable helix conformation (at 300 K) has 4.3 residues per turn and a pitch of 6.95 Å (vertical distance between two points on the helix). The shorter polymers present precursor structures of this helix also. This secondary structure tends to minimize thymine ring solvent exposition to water in favor of the polar VBA residues. We also observe that thymine rings tend to stack among them but also with benzene rings in a parallel or perpendicular conformations. There are scarce thymine i,i+4 interactions favored by Van der Waals contributions. In the loops that joint two helix segments a hydrophobic nucleation of thymine residues is observed. This type of helix are not usual in proteins but has been speculated to be present in the structure of collagen.