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Biophys J, August 2001, p. 715-724, Vol. 81, No. 2
*Department of Chemistry and Biochemistry, Department
of Physics, and Howard Hughes Medical Institute and
Departments of Chemistry and Biochemistry and of Pharmacology,
University of California, San Diego, La Jolla, California 92093 USA
A 10-ns molecular dynamics simulation of mouse
acetylcholinesterase was analyzed, with special attention paid to the
fluctuation in the width of the gorge and opening events of the back
door. The trajectory was first verified to ensure its stability. We defined the gorge proper radius as the measure for the extent of gorge
opening. We developed an expression of an inter-atom distance
representative of the gorge proper radius in terms of projections on
the principal components. This revealed the fact that collective
motions of many scales contribute to the opening behavior of the gorge.
Covariance and correlation results identified the motions of the
protein backbone as the gorge opens. In the back-door region,
side-chain dihedral angles that define the opening were identified.
Biophys J, August 2001, p. 715-724, Vol. 81, No. 2
© 2001 by the Biophysical Society 0006-3495/01/08/715/10 $2.00
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