Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences(2001)

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Lattice models, because of their coarse-grained nature, are best suited for studying the “designability problem” [1-2]. The “designabi lity problem” is the phenomenon in which the majority of a known structure’s 16,000 proteins have their native conformations concentrated into a relatively small number of about 500 topological conformation classes. Here it is shown that on a lattice, the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks [3]. A combination of physical, mathematical and biological reasons that cause the phenomenon are given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that though different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology. In this case, the main folding force arises from the differing hydrophobicity of the residues but does not originate, for example, from the steric hindrance effect caused by the differing sizes of the residues [4].