Relationship between conformation and geometry as evidenced by molecular dynamics simulation of C?,?-dialkylated glycines

Abstract: The relationship between the local backbone conformation and bond angles at C a of symmetrically substituted C a,a -dialkylated glycines (C a,a -dimethylglycine or a -aminoisobutyric acid, Aib; C a,a -diethylglycine, Deg; C a,a -di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the C a bond angles. The MD simulations show that the C a bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-C a -C * ( t ) angle is the most sensitive confor- mational parameter and, in the folded form, is always larger and more flexible than in the extended one.