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Predicted Unfolding Order of the 13 α‐Helices in the Catalytic Domain of Glucoamylase from Aspergillus awamori var. X100 by Molecular Dynamics Simulations
Author(s) -
Liu HsuanLiang,
Wang WenChi
Publication year - 2003
Publication title -
biotechnology progress
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 129
eISSN - 1520-6033
pISSN - 8756-7938
DOI - 10.1021/bp034045q
Subject(s) - aspergillus awamori , molecular dynamics , helix (gastropod) , chemistry , crystallography , catalysis , stereochemistry , biophysics , computational chemistry , biochemistry , biology , enzyme , ecology , snail
The unfolding mechanism of the 13 α‐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 α‐helices followed a random ordered mechanism as α8→α1→α11→α7→α10→α3→α12→α13→α4→α5→α9→α6→α2. No significant relationships were found between the unfolding order and the length and the hydrophobicity of the helix. α‐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 α‐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.