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An Analytical
Approach to Protein Design.
Skorobogatiy
Maksim, Hong Guo & Martin Zuckermann.
Department of
Physics McGill University 3600 Rue
University Montreal, Quebec H3A--2T8 Canada
We have considered the problem of protein design
analytically based on
a model where the contact energy between amino acid residues is
fitted
phenomenologically using the Miyazawa--Jernigan matrix. Due to
the simple
form of the contact energy function, an analytical prescription
is found
which allows us to design energetically stable sequences for
fixed amino
acid residues compositions and target structures.
The theoretically obtained sequences are compared with real
proteins and
good correspondence is obtained. Our calculation also allows us
to
comment on the kinetics of protein folding. In particular we
examine the
problem of the existence of a funnel-like energy landscape for
the folding
kinetics. The existance of hedgehog like landscape was also found
for
systems in which dynamics is implemented with a set of local
moves.
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