With the advances in genomic technologies and structural tools, we are increasingly learning about the identity and structural organizations of individual proteins that play a critical role in cellular signal transduction. These proteins usually work in an organized, interdependent macromolecular network. The next set of challenges are to: (1) understand the proteins in this network in terms of their composition, post-translational modifications (PTMs) and stoichiometry with spatiotemporal resolution, (2) understand the regulatory role of kinases and phosphatases within these networks, (3) understand the role of lipid microenvironment in dictating the assembly and function of proteins, (4) determine how physico-chemical perturbations, such as oxidative/chemotoxic stress and aging, affect proteins in this network, and (5) probe how proteins in this molecular network are altered in disease states. The Bhattacharyya Lab aims to answer some of these outstanding molecular questions in the context of learning and memory, and cognitive impairments in Down Syndrome.

I. Kinase signaling in the brain

How we learn, how our memories form, and how under certain neuropathological conditions such faculties are compromised? Protein kinases orchestrate the regulation of signaling pathways that are pivotal to cellular development and function. We aim to achieve a molecular understanding of the regulation and activation of kinases that are critical for learning, memory and synaptic plasticity. This includes (a) CaMKII, one of the most abundant protein kinases in neurons, (b) Dyrk1a, whose overexpression in trisomy 21 (Down Syndrome) leads to severe cognitive impairments, and (c) Dyrk3, a key regulator of cellular phase separation. We plan to address these questions using a multidisciplinary approach, combining structural biology and biophysics, single-molecule microscopy, and native mass spectrometry with computational techniques (Fig. 1). Our work will uncover how these kinases are moderated by layers of regulatory mechanisms and will help elucidate what goes awry under pathological conditions.

II. Lipids matter in kinase signaling

How do endogenous lipid microenvironments affect the assembly and signalling of receptor kinases? Lipids are known to modulate the activity of protein kinases. Alterations in the global membrane-lipid composition have been reported for neurological disorders, cancer, metabolic diseases and aging, where protein kinases play a critical role in disease development, perpetuation and prognosis. The goal of our lab is to obtain a high-resolution understanding of how such disease-associated changes in the global lipidome affect the lipid distribution in the immediate vicinity of receptor kinases, thereby affecting their ability to propagate signals. Using a novel spatial lipidomics technique, along with microscopy and biochemical approaches, our work will reveal how modifications in the lipid microenvironment around kinases (using Trk receptor tyrosine kinases as an example) potentially alter their signaling properties under physiological and pathological conditions.