Overview

Water plays a key role in almost every biological process. Processes such as protein folding and protein-ligand binding involve complex protein-water interactions that disrupt water’s local structure. A major challenge in understanding the mechanisms behind these processes and predicting how they will occur is quantifying the role of water.

At the Patel group, I use molecular simulations to study the effect of hydration on protein structure and interactions. My aim is to use the understanding we gain from these studies to help inform the design of future drugs and therapeutics.

Researchers often turn to simple model systems to gain insights that will help them understand how complex systems behave. Small hydrophobic polymers are simple systems that can help inform the design of computational experiments to study proteins. By studying the behavior of polymers in collaboration with experts in the field, I plan to translate the key insights we learn from polymers and the methods we develop for them to my work on proteins.

Fig 1: Ubiquitin in water
Fig: Snapshot of C45 in water in a transition state between its extended and collapsed basins. The transition state is characterized by the formation of a locally dewetted cluster of beads. Dewetted beads are colored red. Waters in the hydration shell of C45 are highlighted in cyan, and the hydrogen bonds between them are represented by dotted lines. To learn more, read our J Phys Chem B paper.