Delineating the role of emerging hydrogen-bonded waters and water-clusters in protein-protein recognition mechanism

Dhananjay Joshi^1*, Jung-Hsin Lin^1,2,3,4

¹Research Center for Applied Science, Academia Sinica, Taipei, Taiwan
²Institute for Biomedical Sciences, Academia Sinica, Taipei, Taiwan
³School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
⁴College of Engineering, Chang Gung University, Taoyuan, Taiwan

* Presenter:Dhananjay Joshi, email:joshid@gate.sinica.edu.tw

The role of water molecules in the formation of stable protein-protein complex is often elusive, especially when the interface is hydrophilic. Protein-protein recognition through the hydrogen-bonded interactions of interfacial waters is a highly discussed topic. The molecular dynamics (MD) simulation is, thus far, mainly used to analyze localized water-protein interactions through the residence time of waters in the binding pocket, their occupancy, number of neighborhood waters, hydrogen-bonding of waters with the protein surface, etc. However, how the interfacial waters contribute to molecular recognition is still unclear. In this work, a novel method is developed to analyze non-localized water interface. First, several conformations along the physical trajectories of molecular association and dissociation are chosen such that the interacting proteins are on the way to encounter and form a complex but are still significantly separated. These starting conformations are subjected to protein-position restraint MD simulations so that the dynamics of waters can be rigorously studied. The simulation data is extensively analyzed using our newly developed python codes for hydrogen-bond analysis. Unlike revealing the localized protein-water interactions, all the interfacial hydrogen-bonded waters are extracted from the simulation trajectories. These waters are subjected to the clustering analysis, and for the first time, several crucial water-clusters in the interface that are far from the protein surface, are revealed along with the clusters that close to the surface and involved in localized interactions. The conserved position of waters in the interface suggests that they must have a crucial role of bridging the interacting proteins before forming stabilized complex. Thus, a highly generalized way of analyzing interfacial waters provides an insight into the water-mediated protein-protein recognition mechanism.

Keywords: Protein-protein Interaction, Molecular Dynamics Simulation, Water clusters, Interfacial water interactions, hydrogen-bond analysis