Foldable Polymer Research Articles

Alternating DNA and pi-conjugated sequences. Thermophilic foldable polymers.

Foldable polymers with alternating single-strand deoxyribonucleic acid and planar conjugated organic perylene tetracarboxylic diimide units were found to self-organize into loosely folded nanostructures. Upon heating, the loosely folded structures become more ordered as evidenced by pi-stacking in the perylene segments. The folding and unfolding processes driven by the molecular interactions of adjacent perylenes were monitored in both aqueous and organic solutions. Heat-promoted folding, or inverse temperature behavior, which originates from positive enthalpy changes, was only observed in water. Therefore, we attributed this inverse temperature dependence to hydrophobic effects rather than pi-pi molecular orbital overlap between the perylene planes. These findings shed light on the design of new thermophiles in protein engineering as well as the construction of macromolecular-based nanodevices with actuator and sensory properties.

On foldable protein-like models; a statistical-mechanical study with Monte Carlo simulations

This is study of a class of lattice polymer models which have a singular lowest-energy conformation and undergo a phase transition from the statistically random state to the unique ground state. Such foldable lattice polymers can be considered as a crude model for protein molecules. The procedure for constructing a foldable polymer model, including selection of the monomer sequence and optimization of the force field, is described. A solvation term for individual monomers was added to the pairwise contact-based potential commonly used for the lattice polymer model. It is shown that the solvation interactions of individual residues make an important contribution to the folding of protein-like models. The statistical-mechanical characteristics of the models were analyzed with the help of Monte Carlo simulations. The model provides many insights to the protein-folding problem.

Designing amino acid sequences to fold with good hydrophobic cores.

We present two methods for designing amino acid sequences of proteins that will fold to have good hydrophobic cores. Given the coordinates of the desired target protein or polymer structure, the methods generate sequences of hydrophobic (H) and polar (P) monomers that are intended to fold to these structures. One method designs hydrophobic inside, polar outside; the other minimizes an energy function in a sequence evolution process. The sequences generated by these methods agree at the level of 60-80% of the sequence positions in 20 proteins in the Protein Data Bank. A major challenge in protein design is to create sequences that can fold uniquely, i.e. to a single conformation rather than to many. While an earlier lattice-based sequence evolution method was shown not to design unique folders, our method generates unique folders in lattice model tests. These methods may also be useful in designing other types of foldable polymer not based on amino acids.