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Superoxide dismutase: Fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation
Author(s) -
Shen Jian,
Subramaniam Shankar,
Wong Chung F.,
Mccammon J. Andrew
Publication year - 1989
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360281205
Subject(s) - chemistry , solvation , superoxide dismutase , molecular dynamics , active site , dynamics (music) , channel (broadcasting) , biophysics , chemical physics , computational chemistry , molecule , biochemistry , enzyme , organic chemistry , physics , acoustics , electrical engineering , biology , engineering
The molecular dynamics (MD) simulation of superoxide dismutase (SOD) in water is carried out for a total of 23 ps. The simulation system is a 26 Å sphere centered at the active site of SOD, including 1602 atoms from SOD and 1761 water molecules. There is no gross deviation from the x‐ray structure for the average MD structure. The structure and potential fluctuations around the active site are examined. The results provide new insight to the interactions between SOD and its substrate superoxide.