Intrinsic size parameters for Val, Ile, Leu, Gln, Thr, Phe, and Trp residues from ion mobility measurements of polyamino acid ions

The conformations of singly charged ions of eight polyamino acids of varying length [polyalanine (3-23 residues), polyglutamine (2-8 residues), polyisoleucine (2-6 residues), polyleucine (2-9 residues), polyphenylalanine (2-7 residues), polythreonine (8-14 residues), polytryptophan (2-9 residues), and polyvaline (2-7 residues)] have been studied by ion mobility methods and molecular modeling simulations. The average amino acid contributions to cross section for 4-9 residue homopolymers agree with intrinsic size parameters for these residues derived from data for tryptic digest peptides [J. Phys. Chem. B 1999, 103, 1203]. Some variations in residue sizes with changes in oligomer length are apparent for small oligomers and those with polar and aromatic ring side chains. Molecular modeling simulations reveal thar all of these homopolymers have roughly spherical (globular) structures. Conformations appear to be influenced by three primary types of interactions: (1) self-solvation of the charge site by backbone carbonyls, a characteristic of all oligomer types; (2) steric hindrance of side chains (leading to efficient ring stacking), a prominent factor for the polyphenylalanine and polytryptophan systems; and (3) hydrogen bonding involving side chains, backbone carbonyls, and the charged residue, apparent in the polyglutamine and polythreonine systems.