Predicted unfolding order of the 13 alpha-helices in the catalytic domain of glucoamylase from Aspergillus awamori var. X100 by molecular dynamics simulations.
The unfolding mechanism of the 13 alpha-helices in the catalytic domain of Aspergillus awamori var. X100 glucoamylase was investigated by 200 ps molecular dynamics simulations in explicit water with temperature jump technique. Rather than a simultaneous event, the unfolding of these 13 alpha-helices followed a random ordered mechanism as alpha8-->alpha1-->alpha11-->alpha7-->alpha10-->alpha3-->alpha12-->alpha13-->alpha4-->alpha5-->alpha9-->alpha6-->alpha2. No significant relationships were found between the unfolding order and the length and the hydrophobicity of the helix. alpha-Helix 8 located in the inner region of the catalytic domain was predicted to be the first helix to unfold, indicating that the destruction of the secondary structure motif was initiated from the inner region of the catalytic domain. The dynamic behavior of these alpha-helices induced by increased kinetic energy during the unfolding process is considered to be similar to the expansion and compression of a series of springs under the influence of mechanical stress.
Liu
Hsuan-Liang
HL
Department of Chemical Engineering, National Taipei University of Technology, No. 1 s. 3 Chung-Hsiao E. Rd., Taipei, Taiwan. f10894@ntut.edu.tw
Wang
Wen-Chi
WC
D000595:Amino Acid Sequence; D001230:Aspergillus / Q000201:enzymology*; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D004789:Enzyme Activation; D004795:Enzyme Stability; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D011485:Protein Binding; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature; D014867:Water / Q000737:chemistry*
D014867:Water; D005087:Glucan 1,4-alpha-Glucosidase