Influence of substrate pattern on the adsorption of HP lattice proteins

• Published in: Molecular simulation Vol. 44; no. 12; pp. 1025 - 1030
• Main Authors: Wilson, Matthew S., Shi, Guangjie, Wüst, Thomas, Li, Ying Wai, Landau, David P.
• Format: Journal Article
• Language: English
• Published: Abingdon Taylor & Francis Ltd 13.08.2018; Taylor & Francis
• Subjects: Adsorption; CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; Computer simulation; HP model; Hydrophobicity; Monte Carlo simulation; Mutation; protein adsorption; Proteins; Substrates; Surface chemistry; Wang-Landau sampling
• ISSN: 0892-7022; 1029-0435
• DOI: 10.1080/08927022.2018.1471691

With the highly simplified hydrophobic-polar model representation of a protein, we can study essential qualitative physics without an unnecessarily large computational overhead. Using Wang-Landau sampling in conjunction with a set of efficient Monte Carlo trial moves, we studied the adsorption of short HP lattice proteins on various simple patterned substrates and in particular for checkered patterned surfaces. A set of single-site mutated HP proteins is used to investigate the role of hydrophobicity of a protein chain and surface pattern for substrates with various pattern cell sizes relative to the protein's native configuration. For most cases, we found that the adsorption transition occurs at a lower temperature, while the hydrophobic core formation is less affected. The flattening procedure after the HP protein is adsorbed is more sensitive to the change in surface patterns and single-site mutations. These observations stay valid for both strongly and weakly attractive surfaces.