Assessment of local hydrophobicity and its effect in mediating protein related associations
Date
2015
Authors
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Publisher
University of Delaware
Abstract
Hydrophobic effects play a key important role in mediating the biological association and self-assembly processes. Among them, a prime example where hydrophobic effects have profound implications is from the protein related associations. In the context of protein related interactions, such as protein-ion interaction, protein-ligand interaction and protein-protein interaction, a prior knowledge of relevant binding interfaces, which are defined as clusters of residues involved directly with binding interactions, is difficult. In the binding events that mainly driving by hydrophobic effects, a routinely and widely used approach to predict the binding residues is simply based on the hydropathy value of single residue. However, recent studies suggest that consideration of hydrophobicity for single residues on a protein surface require accounting of the local environment dictated by neighboring residues and local water. Therefore, in the case of hydrophobic mediated association, it is the effective hydrophobicity with the consideration of neighboring effect and context dependency that determines whether the residue would involve in the binding patch. In this dissertation, I first use a method derived from percolation theory to evaluate spanning water networks in the first hydration shells of a series of small proteins in order to locate a critical hydration level to best distinguish the effective hydrophobic and hydrophilic region around protein surface. Further, residue based water density could be applied to scale the effective hydrophobicity at such a critical hydration level. Finally, single-linkage clustering methods were applied to cluster the effective hydrophobic residues in a well defined patch that are putatively involved in binding interactions. This simple method is able to predict with sufficient accuracy and coverage the binding interface residues of a series of proteins. The approach is competitive with automated servers. The results of this study highlight the importance of accounting of local environment in determining the hydrophobic nature of individual residues on protein surfaces. With the identified effective hydrophobic patch that is extensively involved in the protein binding, it is possible to further explore the ion specificity around the region. Umbrella sampling molecular dynamics simulation approach was applied to study the potentials of mean force along an order parameter bridging the state where the ion is fully solvated and one where it is biased via harmonic restraints close around the protein-water interface. Specifically, the protein hydrophobin-II (HFBII) with 71 amino acid residues expressed by filamentous fungi was the target protein. Such a choice is due to the fact that HFBII has an amphiphilic structure character with a well defined hydrophobic patch and several hydrophilic patches. Therefore, it is possible to compare the ion-specific effect around the hydrophobic and hydrophilic region of the protein. Two representative ions, Cl anion and I anion, which have been shown previously by simulations as displaying specific-ion behaviors at aqueous liquid-vapor interfaces, were considered in the study. We further explore anion-induced interface fluctuations near protein-water interfaces using coarse-grained representations of interfaces. As in the case of a pure liquid-vapor interface, at the hydrophobic protein-water interface, the larger, less charge-dense iodide anion displays a marginal interfacial stability compared with the smaller, more charge-dense chloride anion. Furthermore, consistent with the results at aqueous liquid-vapor interfaces, iodide induces larger fluctuations of the protein-water interface compared to chloride, which is an indication of the possible connection between the surface stability of the ion and the induced fluctuation of protein-water interfacial height of the ion. The correlation is further confirmed in the case of denaturant guanidinium cation and urea with different configurations as they approach the hydrophobic protein patch. Finally, hydrophobic effective was discussed in the context of protein-protein interaction. Using a rigid body model, the thermodynamic signatures of the association between ubiquitin and ubiquitin interaction motif was explored. Much like in the case of a purely hydrophobic solute, association is favored by entropic contributions from release of water from the interprotein regions and association is disfavored by loss of enthalpic interactions. This is a further demonstration of the signature of the hydrophobic effect mediated association from the computational approach.