Simple exact models

Dill K A, Bromberg S, Yue K, Fiebig K M, Yee D P, Thomas P D and Chan H S 1995 Principles of protein folding—a perspective from simple exact models Protein Sci. 561-602... 

KA Dill, S Bromberg, K Yue, KM Fiebig, DP Yee, PD Thomas, HS Chan. Principles of protein folding—A perspective from simple exact models. Protein Sci 4 561-602, 1995. 

Use of Dynamic Monte Carlo to Simulate Protein Dynamics Simple, Exact Models Protein-Like Models... 

Simple, exact models [51] consist of simple lattice polymers or heteropolymers where each amino acid in the hypothetical protein is represented by a bead occupying a single lattice point. Because of their simplicity, these models have generated considerable attention [57,58]. 

Finally, it should be pointed out that simple, exact models could be used to test new sampling methodologies [88-90] or optimization techniques [84,91]. A good example is the work by Hao and Scheraga [92], where pairwise contact energy parameters have been optimized to maximize the stability of the native state with respect to other conformations for a 27-mer chain composed of 10 different residues types [92]. 

It is also possible to design a simple, exact model with side chains [95]. As would be expected, the presence of side chains increases the entropy difference between folded and unfolded states. The possible effects of somewhat more complex and cooperative interactions have also been investigated [96]. 

The simple, exact models described in the previous section employ nearest-neighbor interactions as the only amino acid sequence specific contribution to the conformational energy. Consequently, the dominance of nonpolar... 

Lattice models have proved to be extremely useful in studies of simple, exact models and somewhat more complex models of protein-like systems. Similarly, the conformational space of a real protein could be discretized and explored in a very efficient way by various versions of Monte Carlo sampling techniques. Depending on the assumed level of discretization and model of force field, various levels of accuracy can be achieved. For example, simple lattice models of real proteins were studied by Ueda et al. 

All these studies seem to indicate that the cooperativity of the folding process is due to the specific pattern of tertiary interactions and/or the specific interplay between short- and long-range interactions. This may appear to be a trivial statement, but detailed analysis of the results from the simple, exact model, protein-like models and reduced models of real proteins show several specific requirements for the protein folding cooperativity. It is very encouraging that over the entire spectrum of theoretical model studies of the protein folding process, these requirements essentially overlap [35-37,51,83,92,95]. Naturally, various models place different stress on the specific interactions that may control protein folding and structural uniqueness. 

Of course, we cannot expect the description to reflect all the details of the charge distribution in the butadiene molecule, but one may expect this approach to be able to reflect at least some rough features of the 77 electron distribution. If the results of more advanced calculations contradict the rough particle-in-box results, then we should take a closer look at them and search for an error. This is the strength of the simple exact model systems. They play the role of the beacons - points of reference. 

Protein Sci., 4, 561 (1995). Principles of Protein Folding-a Perspective from Simple Exact Models. 

Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D., Chan, H.S., 1995. Principles of protein folding-a perspective from simple exact models. Protein Science A Publication of the Protein Society 4 (4), 561. 

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