Conformational Effects of Mutations and Spherical Confinement in Small Peptides through Hybrid Multi-Population Genetic Algorithms

Abstract

In this work the role of spherical confinement combined with single and block mutations in small peptides on the onset of specific conformational states is analyzed. An intramolecular potential for the polypeptide chain, composed by a bending term plus a Lennard-Jones type long range potential is proposed. For the intermolecular interaction with the sphere an integrated Lennard-Jones (LJ) type potential is used between monomers and the sphere surface. To compute the set of minima values for the total intra and intermolecular potential a combination of a multi-population genetic algorithm and an hybridized Nelder—Mead simplex algorithm are used, that yield to a larger degree of precision in the prediction of the set of minima potential energy values. To characterize the conformational states of the peptides the gyration tensor, radius of gyration, the asphericity, and the linear anisotropy are computed, and the influence of single-point and block mutations on the most energetically stable conformations are assed. Results suggest that the spherical confinement does have a significant influence of the polymer conformations; and single-point mutations introduced along the chain also have a prominent role on peptide's folded states. This opens up the possibility to targeted-designed peptides with particular and desired properties upon folding.