Molecular Dynamics Simulations of the Unfolding Mechanism of the Catalytic Domain from Aspergillus awamori var. X100 Glucoamylase

Abstract

In this study, 200 ps molecular dynamics simulations were conducted to investigate the unfolding mechanism of the catalytic domain of glucoamylase from Aspergillus awamori var. X100. The unfolding of this domain was suggested to follow a putative hierarchical manner, in which the heavily O-glycosylated belt region from residues T440 to A471 acted as the initiation site, followed by the a-helix secondary structure destruction, and then the collapse of the catalytic center pocket. The O-glycosylated belt region surrounded the surface of the catalytic domain in its native state at low temperature, whereas it was extended and is more suitable to be classified as part of the subsequent linker domain at high temperatures due to its high flexibility. The inner set helices of the (α/α)₆-barrel seemed to exhibit higher helical content than the outer set ones at all temperatures examined. The distances between the C_α of the three Cys residue pairs fluctuated rapidly at higher temperatures, indicating that these disulfide bonds have little effect on the structural stabilization. The melting temperature, at which the residual total helicity of the catalytic domain is 50%, is much lower than the critical temperature, at which the catalytic center pocket has lost its structural integrity.

Key words:

• molecular dynamics
• unfolding
• glucoamylase
• melting temperature
• helicity
• critical temperature