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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

 

  1. Soundhararajan Gopi,  Devanshu Devanshu,  Praveen Krishna, and Athi N. Naganathan (2018). pStab: Prediction of Stable Mutants, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration. Bioinformatics. (In press, DOI: 10.1093/bioinformatics/btx697)
  2. Nandakumar Rajasekaran, Ashok Sekhar, and Athi N. Naganathan (2017). A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations. J. Phys. Chem. Lett., 8, 4779–4784. ⇦ [Recommended by Faculty of 1000 (F1000)]

  3. Soundhararajan Gopi, Animesh Singh, Swaathiratna Suresh, Suvadip Paul, Sayan Ranu, and Athi N. Naganathan (2017). Toward a Quantitative Description of Microscopic Pathway Heterogeneity in Protein Folding. Phys. Chem. Chem. Phys., 19, 20891 – 20903.

  4. Nandakumar Rajasekaran, and Athi N. Naganathan (2017). A Self-Consistent Structural Perturbation Approach for Determining the Magnitude and Extent of Allosteric Coupling in Proteins. Biochem. J., 474, 2379–2388.

  5. Abhishek Narayan, and Athi N. Naganathan (2017). Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein. J. Phys. Chem. Lett.,  8, 1683–1687.

  6. Abhishek Narayan, Luis A. Campos, Sandhya Bhatia, David Fushman, and Athi N. Naganathan (2017). Graded Structural Polymorphism in a Bacterial Thermosensor Protein. J. Am. Chem. Soc., 139, 792–802.

  7. Nandakumar Rajasekaran, Swaathiratna Suresh, Soundhararajan Gopi, Karthik Raman, and Athi N. Naganathan (2017). A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry, 56, 294–305.

  8. Athi N. Naganathan (2016). Predictive Modeling of Protein Folding Thermodynamics, Mutational Effects and Free-Energy Landscapes. Proc. Indian Natn Sci Acad, 82, 1211-1228.

  9. Priyashree Chaudhary, Athi N. Naganathan , M. Michael Gromiha (2016). Prediction of change in protein    unfolding rates upon point mutations in two state proteins. Biochimica et Biophysica Acta, 1864, 1104–1109.

  10. Nandakumar Rajasekaran, Soundhararajan Gopi, Abhishek Narayan & Athi N. Naganathan (2016).  Quantifying Protein Disorder through Measures of Excess Conformational Entropy. J. Phys. Chem. B, 120, 4341–4350.

  11. Beatriz Ibarra-Molero, Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Muñoz (2016). Modern Analysis of Protein Folding by Differential Scanning Calorimetry. Methods in Enzymology, 567, 281 – 318.

  12. 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.

  13. 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.

  14. 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.

  15. 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. 

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  21. Athi N. Naganathan (2013). Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Computational Molecular Science, 3, 504-514.

  22. Athi N. Naganathan (2013). A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities. Journal of Physical Chemistry B, 117, 4956-4964.

  23. 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.

  24. 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.

  25. 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.

  26. Athi N. Naganathan & Modesto Orozco (2011). The Protein Folding Transition-State Ensemble from a Gō-like Model. Physical Chemistry Chemical Physics, 13, 15166-15174.

  27. 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.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. Athi N. Naganathan & Victor Muñoz (2008). Determining Denaturation Midpoints in Multiprobe Equilibrium Protein Folding Experiments. Biochemistry, 47, 6752-6761.

  35. 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.

  36. Athi N. Naganathan, Urmi Doshi, Adam Fung, Mourad Sadqi & Victor Muñoz (2006). Dynamics, Energetics and Structure in Protein Folding. Biochemistry, 45, 8466-8475.

  37. 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.

  38. 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.

  39. 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)