Assistant Professor of Biological Science and Chemistry
Ph.D., Indian Institute of Science
Kalyan Chakrabarti has research interests in the interface between biology and chemistry. He held researcher positions in the Max Planck Institute for Biophysical Chemistry (Göttingen, Germany), the National Cancer Institute (in the National Institute of Health, USA) and the Howard Hughes Medical Institute in the Brandeis University, USA.
His work primarily focuses on protein dynamics and he is the coordinator of an international collaboration to develop a comprehensive framework for investigating protein dynamics involving the Max Planck Institutes in Göttingen and Potsdam, FreieUniversität, Berlin in Germany, and the University of Louisville, USA.
He obtained his B.Sc. Chemistry (Hons.) degree from the Presidency University, Kolkata. He went on to receive his master’s and doctorate degrees from the Indian Institute of Science, in biophysics with specialisation in Nuclear Magnetic Resonance spectroscopy of proteins. He has several contributions in the area of functional role of protein dynamics. In 2016, he along with an international collaboration published one of the most comprehensive examples of conformational selection in protein-protein interaction.
Molecular recognition plays a central role in biology, and protein dynamics has been shown to be important in this process. Solution NMR has an arsenal of experimental techniques for recording dynamics of biomolecules in different timescales at atomic resolution. The focus of my research has been on the role of dynamics in the functioning of biomolecules, specifically, the role played by dynamics in protein-protein/ligand interactions. It is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). In case of the neuronal calcium sensor protein recoverin, which has a favorable rate of binding of ~ 30 s-1, we could show comprehensively that the binding follows a conformational selection mechanism (Chakrabarti et al 2016). The slow rate of binding allowed us to employ stopped-flow kinetics for direct measurement of rates. However, this investigation becomes more difficult in other systems as the rates in question become faster and beyond the detection limit of many biophysical techniques. Therefore, in case of the ubiquitin-conjugating system we had to resort to molecular dynamics simulation, along with NMR relaxation dispersion experiments, to show dynamic origin of allostery of binding to its partner protein, the ubiquitin-ligase (Chakrabarti et al 2017). Currently we are extending the investigation to the model protein ubiquitin, which involves development of both NMR methodology and computational algorithms for data clustering.
Kalyan S. Chakrabarti, Roman Agafonov, Francesco Pontiggia, Renee Otten, Matthew K. Higgins, Gebhard F. X. Schertler, Daniel D. Oprian and Dorothee Kern, “Conformational selection in a protein-protein interaction by dynamic pathway analysis” Cell Reports (2016) 14: 32-42.
Karuna Dixit, N. Megha Karanth, Smita Nair, Khushboo Kumari, Kalyan S. Chakrabarti, H.S. Savithri, and Siddhartha P Sarma “Aromatic interactions drive the coupled folding and binding of the intrinsically disordered Sesbania mosaic virus VPg protein.”, Biochemistry (2020), in press.
Anupam Raina, Kristian Leite, Sofia Guerin, Sameehan U. Mahajani, Kalyan S. Chakrabarti, Diana Voll, Stefan Becker, Christian Griesinger, Mathias Bahr and Sebastian Kugler, “Dopamine promotes the neurodegenerative potential of beta-synuclein” Journal of Neurochemistry (2020) DOI:10.1111/jnc.15134.
Kalyan S. Chakrabarti, Jess Li, Ranabir Das and R. Andrew Byrd, “Conformational dynamics and allostery in E2:E3 interactions driving ubiquitination: gp78 and Ube2g2” Structure (2017) 25 : 794-805.
Kalyan S. Chakrabarti, David Ban, Supriya Pratihar, Jithender G. Reddy, Stefan Becker, Christian Griesinger, Donghan Lee, “High-power 1H composite pulse decoupling provides artifact free exchange-mediated saturation transfer (EST) experiments” Journal of Magnetic Resonance (2016) 269 : 65-69.
Kalyan S. Chakrabarti*, Roman Agafonov*, Francesco Pontiggia, Renee Otten, Matthew K. Higgins, Gebhard F. X. Schertler, Daniel D. Oprian and Dorothee Kern, “Conformational selection in a protein-protein interaction by dynamic pathway analysis” Cell Reports (2016) 14: 32-42. (* contributed equally)
Matthew J. Ranaghan, Prem K. Ramasamy, Kalyan S. Chakrabarti, Vanessa Buosi, Dorothee Kern and Daniel D. Oprian, “A highly conserved cysteine of neuronal calcium sensing proteins controls cooperative binding of Ca+2 to recoverin” Journal of Biological Chemistry (2013) 288: 36160-36167.
Rikard Frederiksen, Nicholas P. Boyer, Benjamin Nickle, Kalyan S. Chakrabarti, Yiannis Koutalos, Rosalie K. Crouch, Daniel Oprian and M. Carter Cornwall, “Low aqueous solubility of 11-cis retinal limits rate of pigment formation and dark adaptation in salamander rods” Journal of General Physiology (2012) 139: 493-505.
Kalyan S. Chakrabarti, Krishan Gopal Thakur, B. Gopal and Siddhartha P. Sarma, “X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate” FEBS Journal (2010) 277: 697-712.
Kalyan S. Chakrabarti and Siddhartha P. Sarma, “NMR assignment of 2H, 13C, 15N labeled amino-terminal domain of apo-pantothenate synthetase from E. coli.” Journal of Biomolecular NMR (2006) 36: 38.
Ashima Mitra*, Kalyan S. Chakrabarti*, M.S. Shahul Hameed, Kalyan V. Srinivas, Ganesan Senthil Kumar and Siddhartha P. Sarma, “High level expression of peptides and proteins using cytochrome b5 as a fusion host” Protein Expression and Purification (2005) 41: 84-97. (*contributed equally)
Kalyan S. Chakrabarti, B. S. Sanjeev and Saraswathi Vishveshwara, “Stability and dynamics of domain-swapped bovine-seminal ribonuclease” Chemistry and Biodiversity (2004) 1: 802-818.
R. Padmashree, K. S. Chakrabarti, D. Sahal, R. Mahalakshmi, S. P. Sarma and S. K. Sikdar, “Functional characterization of the pentapeptide QYNAD on rNaυ1.2 channels and its NMR structure” European Journal of Physiology (2004) 447: 895-907.