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Protein folding is the process by which a protein structure assumes its functional shape or conformation. All protein molecules are heterogeneous unbranched chains of amino acids. By coiling and folding into a specific three-dimensional shape they are able to perform their biological function.
The simplified model for protein folding introduced by Levitt and Warshel [1] is now emerging as the method of choice for studying protein folding. Our subsequent studies in this direction focus on the development of effective ways for using the simplified model in rigorous evaluation of the free energies of the corresponding all-atom model [2]. More recently we started to focus on the electrostatic energetics of the simplified model, starting to generate a general electrostatically enhanced coarse grained (CG) model [3] [4]. The electrostatic features allowed us to obtain very reasonable results for the absolute folding energy of wide class of proteins.
Elucidating the relationship between the folding landscape of enzymes and their catalytic power has been one of the challenges of modern enzymology. Our work [5] explores this issue by using a simplified folding model to generate the free-energy landscape of an enzyme and then to evaluate the activation barriers for the chemical step in different regions of the landscape. This approach is used to investigate the recent finding that an engineered monomeric chorismate mutase exhibits catalytic efficiency similar to the naturally occurring dimer even though it exhibits the properties of an intrinsically disordered molten globule. It is found that the monomer becomes more confined than its native-like counterpart upon ligand binding but still retains a wider catalytic region. Although the overall rate acceleration is still determined by reduction of the reorganization energy, the detailed contribution of different barriers yields a more complex picture for the chemical process than that of a single path. We are also conducting major studies of the ability of CG models to find the pathways between different folding states.
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