We explore the question of whether local effects (originating from the amino acids intrinsic secondary structure propensities) or nonlocal effects (reflecting the sequence of amino acids as a whole) play a larger role in determining the fold of small globular proteins. We present a coarse grained computational model that allows us to quantitatively explore the degree of frustration a given polar, non polar pattern can tolerate when the secondary structure intrinsic propensities are in opposition to it. We observe that the fold of small, globular proteins is determined by the pattern of polar, non polar amino acids regardless of their intrinsic secondary structure propensities. In addition, we use our model to investigate the relative stability of two different sets of de novo designed proteins. Our work suggests that simple computational models can be used as a complementary tool in protein design.

Sequence periodicity and secondary structure propensity in model proteins

243rd National Meeting (2012)

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