Monte Carlo study of substrate-induced folding and refolding of lattice proteins.
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 prefolded 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.
Coluzza
Ivan
I
Department of Chemistry, Cambridge University Centre for Computational Chemistry, Cambridge, United Kingdom. ic247@cam.ac.uk
Frenkel
Daan
D
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins