Unraveling universal thermodynamic and structural behavior of HP model protein adsorption
Li, Ying Wai
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The hydrophobic-polar (HP) model is a simplified lattice model for simulating protein folding. With a minor modification, it can be used to study general categories of surface adsorption of protein from a coarse-grained perspective. In this work, the thermodynamic behavior and structural properties are studied by means of Wang-Landau sampling complemented by multicanonical sampling. A number of benchmark HP sequences have been considered with different types of surfaces, each of which attracts either: all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. For some structural "transition" processes, the specific heat only shows obscure or missing signals, and thus a comprehensive analysis is vital in distinguishing structural "transitions" between "phases" for polymeric systems. From the analysis of the combined patterns of various structural observables, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, fundamental, general categories of folding and transition hierarchies have been identified. A connection between the transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the intra-chain attraction among H monomers, has also been inferred. As the classification of transition categories is founded on multiple benchmark sequences, it is believed that the folding hierarchies and identification scheme are generic for different HP chains interacting with attractive surfaces, regardless of the chain length, sequence, or type of surface attraction.