Growing
evidence
supports
the
view
that
enzymatic
activity
results
from
a
subtle
interplay
between chemical
kinetics and
molecular
motions. A
systematic
analysis
is performed here to delineate
the type
and level of
coupling between catalysis
and conformational
mechanics.
The dynamics
of a set of
98 enzymes representative
of different EC classes
are
analyzed
with the Gaussian
network model (GNM)
and compared
with experimental
data.
In more than
70% of the examined
enzymes, the
global hinge
centers predicted by
the GNM are
found to be colocalized
with the catalytic
sites experimentally
identified. Low translational
mobility (<7%) is observed for
the catalytic
residues, consistent with
the
fine-tuned design of enzymes to
achieve
precise mechanochemical
activities.
Ligand
binding sites, while closely neighboring catalytic
sites, enjoy a
moderate
flexibility to accommodate
the ligand
binding. These
findings could serve
as additionalcriteria
for assessing
drug binding residues
and could
lessen the
computational
burden of substrate
docking searches.
See also
Molecular Mastication
Mechanics
by Dmitry A.
Kondrashov;
George N. Phillips Jr. (pp. 836-837).
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