Molecular dynamics simulations of the unfolding of the starch binding domain from Aspergillus niger glucoamylase.
The 600 ps molecular dynamics simulations to investigate the unfolding of the starch binding domain from Aspergillus niger glucoamylase were conducted in vacuum as well as in an external field with the dielectric constant of 80 with temperature jump technique. Electrostatic interactions play an important role in determining the stability of the beta-strands in this domain. The starch binding site 1 is less stable than site 2 since it is more exposed to the surface. The disulfide bond between C509 and C604 is unstable since these two residues are located near the flexible linker domain and in the mobile loop region between beta-strands 6 and 7, respectively. The melting temperature, at which the total residual beta-strand content is 50% that of the solution structure, is about 544K for the simulations with dielectric constant of 80, leading to the estimated unfolding timescale of 0.48 ms in vitro. In addition, the unfolding of the starch binding domain is proposed to initiate from the interior region by the lost of the integrity of the secondary structure.
Liu
Hsuan-Liang
HL
Department of Chemical Engineering, National Taipei University of Technology, No. 1 Sec. 3 Chung-Hsiao E. Rd., Taipei 106, Taiwan. f10894@ntut.edu.tw
Wang
Wen-Chi
WC
D000818:Animals; D001234:Aspergillus niger / Q000201:enzymology*; D001665:Binding Sites; D020134:Catalytic Domain; D003198:Computer Simulation; D003505:Cyclodextrins / Q000737:chemistry; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013213:Starch / Q000378:metabolism*
D003505:Cyclodextrins; D013213:Starch; D005087:Glucan 1,4-alpha-Glucosidase