Heat-induced structural changes in the Fab fragment of IgG recognized by molecular dynamics stimulation--implications...

Molecular dynamics simulation was used to identify the conformational alterations in the Fab fragment (Kol), driven by heating at 300, 320, and 340 K. Comparison of heat-modified VH,CH1 and VL,CL domain structures with the corresponding crystal conformations revealed specific differences, most definitely expressed in the CH1 domain. These are dislocations of predominantly peripheral peptide loops exposed to the V-C interdomain interface, comprising in particular the 175-185 amino acids of the heavy chain, as well as the 112-123 amino acids of the interdomain hinge fragment. The deviations, limited to peripheral domain regions at 300 and 320 K, spread at 340 K. The resulting relaxation of the tertiary packing in the protein (including the hydrophobic core) initiates global melting of the domain. These theoretical results were supported by experimental findings concerning penetration and binding of dyes (Congo Red, Trypan Blue, ANS) to the protein. Packing relaxation of the CH1 domain is turned on after disruption of the specific peptide arrangement formed at the V-C interdomain interface basically at the hinge portion (117-122) and at fragments of adjacent peptide loops (149-154, 171-179) of CH1 origin, most probably playing the role of a switching mechanism. The dislocations also comprise the 131-141 amino acids of the loops accommodated at the CH1-CH2 interface. However, the lack of crystallographic data concerning the Fab-Fc interface limits discussion of this effect to speculation. It was concluded that the unconcerted movements of the V and C parts of the Fab fragment are an intrinsic driving mechanism, introducing structural alterations into the C domains. It is suggested that the domain relaxation, induced by heating or mechanical constraints, allows for intermolecular interactions, affecting in this way the stability of the immune complex.