Comparative modeling and protein‐like features of hydrophobic–polar models on a two‐dimensional lattice

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Abstract
Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic–polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness‐favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein‐like features: (1) Shapes are compact in both models, especially when a compactness‐favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein‐like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our study supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models. Proteins 2012;
Funding Information
  • The National Institutes of Health Award (GM041455)
  • National Science Foundation award (CNS-0619926)
  • Stanford Bio-X Fellowship

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