Srirupa Chakraborty

HIV, Ebola, Corona, and other similar viruses are at constant warfare with the human immune system. While the viruses evolve to come up with unique strategies to overcome the immune system, our body must keep up and counteract the threat. One critical battlefront in this war is the glycan (sugar) coating on the viral envelope proteins that act as a shield from antibodies. Understanding the conformational topology of this sugar layer is of particular importance in order to guide vaccine design. However, experimental studies of the glycan barrier remain extremely challenging due to their structurally heterogeneous and dynamic nature. We have designed a set of computational tools to characterize this glycan shield and identify regions of vulnerability and resilience that can be harnessed towards vaccine design. There are four parts to this toolset: (i) high-throughput modeling pipeline to build a physiological ensemble of the glycoprotein in atomistic detail; (ii) describe global and local properties of the shield topology using graph theory; and (iii) quantify the shielding effect towards pinpointing regions which can act as antibody epitope; (iv) develop coarse-grained parameters for glycans in order to capture long temporal dynamics. In my talk, I will briefly go over these tools, describe how such methodology has been extensively validated using experimental cryo-electron microscopy, and how these can be used to guide immunogen design efforts. In the end, I will discuss the extension of these methods to other densely glycosylated systems, aiding in better understanding of the role of glycans in biological processes, as well as utilizing them for bio-inspired material design.

Dr. Srirupa Chakraborty is currently an Assistant Professor of Chemical Engineering and Chemistry at Northeastern University, with an affiliation in Physics. Dr. Chakraborty received her PhD in Biophysics right here at the University at Buffalo, where her graduate work focused on computational modeling of protein dynamics and energetics. After postdoctoral research at IBM Watson Research Center and Los Alamos National Laboratory, she established the SimBioSys Lab at Northeastern. Her group develops computational and machine learning approaches to study viral glycoproteins, mucins, and antibody interactions, bridging molecular modeling with biomedical applications. Dr. Chakraborty has received several recognitions for her work, including the NIH Maximizing Investigators’ Research Award, the CHAVD Early Career Research Award, the ACS Outstanding Postdoctoral Award, and Northeastern’s Sioui Award for Excellence in Teaching. She is also active in scientific service, holding leadership roles in the Biophysical Society and AIChE.

• Time: 11:00 AM
• Location: 206 Furnas Hall