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Athi N. Naganathan

athi
Assistant Professor
Ph. D., University of Maryland, USA
B. Tech., Anna University, Chennai
Office: BT 101
Tel: +91-44-2257-4140
Email: athi@iitm·ac·in
Lab: BT 216(Website)

Research Interests

  • Experimental Characterization of Protein Conformational Behavior
  • Modeling and Predicting Folding Landscapes using Statistical Models
  • Understanding Protein Folding and Dynamics through Coarse-Grained and All-Atom Molecular Simulations
  • Multi-Scale Exploration of Protein Conformational Ensembles

Publications
Google Scholar Citations

  • Athi N. Naganathan & David De Sancho (2015). Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein. J. Phys. Chem. B, 119, 14925–14933.
  • Soundhararajan Gopi, Nandakumar Rajasekaran, Animesh Singh, Sayan Ranu & Athi N. Naganathan (2015). Energetic and Topological Determinants of a Phosphorylation-Induced Disorder-to-Order Protein Conformational Switch. Phys. Chem. Chem. Phys., 17, 27264-27269.
  • Sneha Munshi & Athi N. Naganathan (2015). Imprints of Function on the Folding Landscape: Functional Role for an Intermediate in a Conserved Eukaryotic Binding Protein. Phys. Chem. Chem. Phys., 17, 11042 – 11052.
  • Priyashree Chaudhary,  Athi N. Naganathan & M. Michael Gromiha (2015). Folding RaCe: A Robust Method for Predicting Changes in Protein Folding Rates upon Point Mutations. Bioinformatics,  pii: btv091. 
  • Athi N. Naganathan, Jose M. Sanchez-Ruiz, Sneha Munshi & Swaathiratna Suresh (2015). Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints? J. Phys. Chem. B, 119, 1323–1333
  • Athi N. Naganathan & Victor Muñoz (2014). Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier.Journal of Physical Chemistry B, 118, 8982-8994.
  • Abhishek Narayan & Athi N. Naganathan (2014). Evidence for the Sequential Folding Mechanism in RNase H from an Ensemble-Based Model. Journal of Physical Chemistry B, 118, 5050-5058.
  • Srinivasan Sivanandan & Athi N. Naganathan (2013). A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IkBa. PLoS Computational Biology, 9(12): e1003403.
  • Athi N. Naganathan & Modesto Orozco (2013). The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator. Journal of Physical Chemistry B, 117, 13842-13850.
  • Athi N. Naganathan (2013). Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Computational Molecular Science, 3, 504-514.
  • Athi N. Naganathan (2013). A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities. Journal of Physical Chemistry B, 117, 4956-4964.
  • Athi N. Naganathan (2012). Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics. Journal of Chemical Theory and Computation, 8, 4646-4656.
  • Athi N. Naganathan, Raul-Perez Jimenez, Victor Muñoz & Jose M. Sanchez-Ruiz (2011). Estimation of Protein Folding Free Energy Barriers from Calorimetric Data by Multi-Model Bayesian Analysis. Physical Chemistry Chemical Physics, 13, 17064-17076.
  • Athi N. Naganathan & Modesto Orozco (2011). The Protein Folding Transition-State Ensemble from a Gō-like Model. Physical Chemistry Chemical Physics, 13, 15166-15174.
  • Athi N. Naganathan & Modesto Orozco (2011). The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding. Journal of the American Chemical Society, 133, 12154-12161.
  • Pierpaolo Bruscolini & Athi N. Naganathan (2011). Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model. Journal of the American Chemical Society, 133, 5372-5379.
  • Athi N. Naganathan, Peng Li, Raul-Perez Jimenez, Jose M. Sanchez-Ruiz & Victor Muñoz (2010). Navigating the Downhill Protein Folding Regime via Structural Homologues. Journal of the American Chemical Society, 132, 11183-11190.
  • Athi N. Naganathan & Victor Muñoz (2010). Insights into Protein Folding Mechanisms from Large-Scale Analysis of Mutational Effects. Proceedings of the National Academy of Sciences USA, 107, 8611-8616.
  • Stephen J. Decamp, Athi N. Naganathan, Steven A. Waldauer, Olgica Bakajin & Lisa J. Lapidus (2009). Direct Observation of Downhill Folding of l-Repressor in a Microfluidic Mixer. Biophysical Journal, 97, 1772-1777.
  • Peng Li, Fabiana Y. Oliva, Athi N. Naganathan & Victor Muñoz (2009). Dynamics of One-State Downhill Protein Folding. Proceedings of the National Academy of Sciences USA, 106, 103-108.
  • Victor Muñoz, Mourad Sadqi, Athi N. Naganathan & David de Sancho (2008). Exploiting the Downhill Folding Regime via Experiment. Human Frontier Science Program Journal, 2, 342-353.
  • Athi N. Naganathan & Victor Muñoz (2008). Determining Denaturation Midpoints in Multiprobe Equilibrium Protein Folding Experiments. Biochemistry, 47, 6752-6761.
  • Athi N. Naganathan, Urmi Doshi & Victor Muñoz (2007). Protein Folding Kinetics: Barrier Effects in Chemical and Thermal Denaturation Experiments. Journal of the American Chemical Society, 129, 5673-5682.
  • Athi N. Naganathan, Urmi Doshi, Adam Fung, Mourad Sadqi & Victor Muñoz (2006). Dynamics, Energetics and Structure in Protein Folding. Biochemistry, 45, 8466-8475.
  • Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Muñoz (2005). Direct Measurement of Barrier Heights in Protein Folding. Journal of the American Chemical Society, 127, 17970-17971.
  • Athi N. Naganathan, Raul Perez-Jimenez, Jose M. Sanchez-Ruiz & Victor Muñoz (2005). Robustness of Downhill Folding: Guidelines for the Analysis of Equilibrium Folding Experiments on Small Proteins. Biochemistry, 44, 7435-7449.
  • Athi N. Naganathan & Victor Muñoz (2005). Scaling of Folding Times with Protein Size. Journal of the American Chemical Society, 127, 480-481.

Book Chapters

  • Modesto Orozco, Laura Orellana, Adam Hospital, Athi N. Naganathan, Agusti Emperador, Oliver Carrillo & Josep L. Gelpí (2011). Coarse Grained Representation of Protein Flexibility: Foundations, Successes and Shortcomings. Advances in Protein Chemistry and Structural Biology, 85, 183-215.

Honours and Awards

  • INSA Medal for Young Scientist. (2015)
  • Wellcome Trust / DBT India Alliance Intermediate Fellowship. (2015)
  • Innovative Young Biotechnologist Award (IYBA), Department of Biotechnology, New Delhi, India. (2012)
  • Juan de la Cierva Fellowship, Spanish Ministry of Science and Innovation. (2009-2011)
  • Dr. Herman Kraybill Biochemistry Fellowship, University of Maryland, USA. (2006-2007)
  • Paul Mazzocchi Fellowship, College of Chemical and Life Sciences, University of Maryland, USA. (2002-2004)