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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