title: Relation between calculated amide frequencies and solution structure in Ala-X peptides.
abstract: Computational techniques have been used to aid interpretation of observed systematic shifts in the amide III frequencies of Ala-X peptides. Optimized structures and frequencies have been calculated for Ala-X peptides using GAUSSIAN86/88 with the 4-31G basis, MOPAC, and normal mode methods based on empirical force fields. We observe the following: (1) Frequencies calculated using scaled GAUSSIAN86 force constants correlate well with the experimental results. (2) Structures of the Ala-X peptides optimized by GAUSSIAN show a clear trend toward lower values of the dihedral angle phi as the X side chain becomes larger, while structures optimized here using semiempirical and empirical force fields do not show trends. (3) Computational changes in peptide conformations from beta-sheet to alpha-helix produce large changes in both amide I and amide III frequencies that are inconsistent with the experimental results. (4) Computational changes in the dihedral angle phi of Ala-Ala produce a change in the amide III frequency consistent with the experimental results. (5) The experimental frequency shifts cannot be attributed directly to the effects of changing mass.
authors: Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799.
authors: R W
authors: RW
authors: Williams
authors: J L
authors: JL
authors: Weaver
authors: A H
authors: AH
authors: Lowrey
mesh_terms: D000409:Alanine / Q000737:chemistry; D000577:Amides / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry*; D012996:Solutions
chemical_list: D000577:Amides; D000596:Amino Acids; D010455:Peptides; D012996:Solutions; D000409:Alanine