Ching-Hsing Yu, Lothar Schäfer, and Michael Ramek, Local Geometry Trends and Torsional Sensitivity in N-Formyl-L-alanyl-L-alanine Amide and the Limitations of the Dipeptide Approximation J. Phys. Chem. A, 103, 8337-8345 (1999).

Publication abstract:

Based on a database of 11 664 RHF/4-21G ab initio gradient-optimized structures of N-formyl-L-alanyl-L-alanine amide (ALA-ALA), the local geometries and torsional sensitivity of this compound were analyzed to test the dipeptide approximation frequently used in peptide conformational analyses. This database was generated by optimizing the geometries of this compound at grid points in its four-dimensional (, , , ) conformational space defined by 40° increments for the outer torsions and and by 30° increments along the inner torsions and . Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces of the structural parameters of ALA-ALA, and of their gradients, in (, , , ) space. Analysis of the structural surfaces shows not only that the structure of a given residue in a peptide chain depends acutely on the conformational state of a neighboring residue but also that the interresidue effects differ, depending on whether they are transmitted from right to left or from left to right in the peptide chain. Structural gradients are a qualitative measure of the torsional sensitivity, and therefore of the density of states and contributions to vibrational entropy. Analyses of the gradient surfaces show that the density of states in a residue is significantly affected by the dynamics of a neighboring residue. This opens the possibility of dynamic entropic conformational steering in extended peptide chains, i.e., the generation of free energy contributions from dynamic effects of one part of a molecule on another, possibly stabilizing a conformational region of a potential energy surface whose static energy profile is less favorable compared to other regions. The gradient trands illustrate how the overall stability of a complex molecule is not only a function of how the static energy minima of its isolated subunits combine but also of how the dynamics of the subunits interact with one other. These interactions between individual residues represent a hidden cooperative effect that is not apparent at all in the dynamics of isolated dipeptide units.

Related links:

• Ab Initio Study of the Conformational Dependence of the Nonplanarity of the Peptide Group.
• Grid point data.
• Interactive viewing of all conformers (4-21G optimized).
• Lothar Schäfer.
• Michael Ramek.

• Quantum Chemistry Group, TU Graz.