Geometrical analysis of structural changes in immunoglobulin domains' transition from native to molten state

Abstract

Molecular dynamics simulation (300, 320, 340 K) performed on the Fab (Kol) fragment of immunoglobulin G revealed that the structural changes associated with relaxation of peptides after their release from the stabilized by the tertiary interaction native conformation may be considered characteristic of the transition from native to molten state. The configuration of peptide chains at temperatures close to melting, liberated from the constraints associated with tertiary packing, was found to deviate toward helical rather than extended forms. The direction of the shift is diagonal on the Φ-Ψ map. The torsional angles tend to concentrate in the C 7 eq region, and some leak to the α R area. The geometrical parameters designed to describe the configuration of the peptide chain in Fab fragment also confirmed that during melting the peptides generally moved toward helical form.