title: Simulated evolution of emergent chiral structures in polyalanine.
abstract: The relationship between monomer chirality and polymer structure has been studied using both theoretical and experimental methods. Atomistic models, such as the ones employed in computational protein folding and design, can be used to study the relationship between monomer chirality and the properties of polypeptides. Using a simulated evolution approach that combines side-chain epimerization with backbone flexibility, we recapitulate the relationship between basic forces that drive secondary structure formation and sequence homochirality. Additionally, we find heterochiral motifs including a C-terminal helix capping interaction and stable helix-reversals that result in bent helix structures. Our studies show that simulated evolution of chirality with backbone flexibility can be a powerful tool in the design of novel heteropolymers with tuned stereochemical properties.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA. vikas@mail.med.upenn.edu
authors.forename: Vikas
authors.initials: V
authors.lastname: Nanda
authors.forename: William F
authors.initials: WF
authors.lastname: Degrado
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013237:Stereoisomerism; D013816:Thermodynamics
chemical_list: D010455:Peptides; C019529:polyalanine