Research

Deciphering the Molecular Mechanism of Curvature Controlled Interaction of Proteins with Biological Membrane and Its Relevancy in Cellular Function: A Spectroscopic and Microscopic Study 

Three-dimensional (3D) topography of the plasma membrane of biological cells plays a crucial role in controlling different fields of cellular physiology, even in immunology and cancer biology. Thus, it might be obvious to consider that there is a synergy between the 3D membrane topography and the conformation and function of membrane proteins which in turn controls cellular function. It may be easily realized that if protein molecules accumulate on the concave surface of a membrane, they will experience that the membrane surface is curved toward them which will lead to more crowding around the proteins compared to the situation when the proteins are arranged on the convex surface of a membrane. Thus, the microenvironment sensed by the proteins on the concave surface of a membrane will be significantly different compared to proteins on the convex surface of the membrane which may lead to a change of conformation/ conformational or folding dynamics of the proteins, which in turn affects the function of the protein. However, the role of 3D membrane topography in controlling the conformation and the conformational/folding dynamics of proteins and their effect on cellular function remains unappreciated.

In this project, we want to decipher the molecular mechanism of the interaction of membrane proteins with respect to 3D membrane topography (membrane curvature) using various microscopic and spectroscopic techniques. For that, we will start with commercially available peripheral membrane proteins and gradually move to more complex membrane proteins, such as curvature sensing and generating Bin/amphiphysin/Rvs (BAR) domain proteins and epsin domain proteins, intrinsically disordered proteins, transmembrane proteins. We will covalently label the membrane proteins in-house using fluorescent probes and incorporate the protein molecule either inside small lipid vesicles (concave surface) or let them interact from outside of the small lipid vesicles (convex surface) and will investigate the interaction pattern from different spectroscopic microscopic methods. Using fluorescence spectroscopy, we will measure the change of apparent binding constant of protein while interacting from concave vs convex membrane surface. From circular dichroism spectroscopy, we will investigate the change in the protein’s conformation due to the curvature of the membrane. From time-correlated single photon counting spectroscopy, we will understand the difference between polarity and water dynamics sensed by protein molecules due to membrane topography. From single molecule spectroscopy, we will decipher the impact of membrane curvature on folding dynamics and domain distance of the proteins. Later the acquired knowledge about the synergy between membrane topography and conformation, folding dynamics, and function of membrane proteins will be used to unravel more complex questions about the role of membrane topography and membrane projections in controlling the function of immune cells. 

Development of low-cost protein-coated copper nano-cluster for drug delivery and ion sensing: A spectroscopic and microscopic study 

Copper nanoclusters owing to their low cost and unique properties are rapidly gaining attention in numerous fields such as electronics, engineering, agriculture, environment, energy, pharmaceutical, and biomedical applications. However, the major challenge for the synthesis of copper nanoclusters is their tendency to undergo oxidation. Coating agents play a crucial role as a stabilizer of nanoclusters. In recent years, proteins, a class of natural biomolecules, becomes an attractive alternative, in place of synthetic polymers, due to their biocompatibility, biodegradability, and comparable mild condition for the preparation of nanoclusters. In this project, we will develop a one-pot bio-compatible synthesis scheme for protein-coated copper nanoclusters. We will start with papain as the coating agent due to its anti-cancer property. We will investigate the probable application of the papain-coated copper nanoclusters such as biocompatibility, drug delivery capability, ion, temperature, pH, and water quality sensing capability using different spectroscopic and microscopic methods. Later we will use molecular dynamics simulation and coarse grain model to decipher the kinetics of the interaction, the physicochemical characteristics of the binding site, and the nanocluster adsorption capacity with respect to the protein.