Influence of substrate pattern on the adsorption of HP lattice proteins |
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Authors: | Matthew S. Wilson Guangjie Shi Thomas Wüst Ying Wai Li David P. Landau |
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Affiliation: | 1. Centre for Simulational Physics, The University of Georgia, Athens, GA, USA.;2. Scientific IT Services, ETH Zürich IT Services, Zürich, Switzerland.;3. National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA. |
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Abstract: | 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. |
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Keywords: | HP model Wang-Landau sampling Monte Carlo simulation protein adsorption |
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