BIOPHYSICAL THEORY AND MODELING |
Monte Carlo study of substrate-induced folding and refolding of lattice proteins
Ivan Coluzza 1* and Daan Frenkel 2
1 Cambridge University Centre for Computational Chemistry
2 FOM Institute for Atomic and Molecular Physics [AMOLF]
* To whom correspondence should be addressed. E-mail: ic247{at}cam.ac.uk.
Submitted on March 1, 2006
Revised on May 19, 2006
Accepted on 26 October 2006
 |
Abstract |
|---|
Many proteins can switch from one conformation to another under the influence of an external driving force, such as the binding to a specific substrate. Using a simple lattice model we show that it is feasible to design protein-like lattice proteins that can have two different conformations, depending on whether or not they are bound to a substrate. We give three different examples of such substrate-induced refolding. In addition, we have explored substrate-induced folding of lattice proteins that do not fold when free in solution. We show that such proteins can bind with the same high specificity as pre-folded protein, but have a considerably lower binding free energy. In this way proteins can bind to a substrate in a way that is highly specific, yet reversible.
Key Words:
Allostery, Lattice Heteropolymer, Protein Folding, Random Domains
