IMSc Webinar

Quantifying signal transfer in proteins

Anil Kumar Sahoo

Department of Physics, Freie University of Berlin

In this talk, I will present our work on relating atomic-level protein dynamics to its functions, e.g., biological signaling. Cells and organisms react to external and internal signals by proteins that consist of sensor and effector modules. Sensors detect environmental changes, such as light, pH, hormones, etc., while corresponding effectors trigger a response. First, I will discuss the initial step for signaling, i.e., drug molecules binding to proteins. I will exemplify this with our recent simulation and theoretical modeling efforts in collaboration with experimentalists to understand polyelectrolyte–protein interactions and help design polymers for SARS-CoV-2 virus inhibition. Later, I will introduce basic statistical-mechanics concepts to derive transmit functions that describe how a local time-dependent perturbation, which can be a deformation or a force, propagates in a viscoelastic medium such as a protein. Transmit functions are defined by equilibrium fluctuations fromsimulations or experimental observations. We apply this framework to our molecular dynamics simulation data of a bacterial signaling protein, for quantifying signal transfer efficiency of its principal deformation modes, namely shift, splay, and twist. Finally, I will conclude the talk with a few future research directions.