Foldamer

In chemistry, a foldamer is a discrete chain molecule or oligomer that folds into a conformationally ordered state in solution. They are artificial molecules that mimic the ability of proteins, nucleic acids, and polysaccharides to fold into well-defined conformations, such as helices and β-sheets. The structure of a foldamer is stabilized by noncovalent interactions between nonadjacent monomers. Foldamers are studied with the main goal of designing large molecules with predictable structures. The study of foldamers is related to the themes of molecular self-assembly, molecular recognition, and host-guest chemistry.

Foldamers can vary in size, but they are defined by the presence of noncovalent, nonadjacent interactions. This definition excludes molecules like poly(isocyanates) (commonly known as (polyurethane)) and poly(prolines) as they fold into helicies reliably due to adjacent covalent interactions., Foldamers have a dynamic folding reaction [unfolded → folded], in which large macroscopic folding is caused by solvophobic effects (hydrophobic collapse), while the final energy state of the folded foldamer is due to the noncovalent interactions. These interactions work cooperatively to form the most stable tertiary structure, as the completely folded and unfolded states are more stable than any partially folded state.

The structure of a foldamer can often be predicted from its primary sequence. This process involves dynamic simulations of the folding equilibria at the atomic level under various conditions. This type of analysis may be applied to small proteins as well, however computational technology is unable to simulate all but the shortest of sequences.

The folding pathway of a foldamer can be determined by measuring the variation from the experimentally determined favored structure under different thermodynamic and kinetic conditions. The change in structure is measured by calculating the root mean square deviation from the backbone atomal position of the favored structure. The structure of the foldamer under different conditions can be determined computationally and then verified experimentally. Changes in the temperature, solvent viscosity, pressure, pH, and salt concentration can all yield valuable information about the structure of the foldamer. Measuring the kinetics of folding as well as folding equilibria allow one to observe the effects of these different conditions on the foldamer structure.

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