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 varyin g length [polyalanine (3-23 residues), polyglutamine (2-8 residues), polyis oleucine (2-6 residues), polyleucine (2-9 residues), polyphenylalanine (2-7 residues), polythreonine (8-14 residues), polytryptophan (2-9 residues), a nd polyvaline (2-7 residues)] have been studied by ion mobility methods and molecular modeling simulations. The average amino acid contributions to cr oss section for 4-9 residue homopolymers agree with intrinsic size paramete rs for these residues derived from data for tryptic digest peptides [J. Phy s. Chem. B 1999, 103, 1203]. Some variations in residue sizes with changes in oligomer length are apparent for small oligomers and those with polar an d aromatic ring side chains. Molecular modeling simulations reveal thar all of these homopolymers have roughly spherical (globular) structures. Confor mations 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 effi cient ring stacking), a prominent factor for the polyphenylalanine and poly tryptophan systems; and (3) hydrogen bonding involving side chains, backbon e carbonyls, and the charged residue, apparent in the polyglutamine and pol ythreonine systems.