Publications and Presentations

2019

49. Abhishek Narayan, Kabita Bhattacharjee & Athi N. Naganathan (2019). Thermally versus Chemically Denatured Protein States. Biochemistry, 58, 2519-2523. 

48. Abhishek Narayan, Soundhararajan Gopi, David Fushman & Athi N. Naganathan (2019). A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair. Nature Communications10, 1995.

47. Sneha Munshi, Sandhyaa Subramanian, Samyuktha Ramesh, Hemashree Golla, Divakar Kalivarathan, Madhurima Kulkarni, Luis Alberto Campos Prieto, Ashok Sekhar, and Athi N. Naganathan (2019). Engineering Order and Cooperativity in a Disordered ProteinBiochemistry58, 2389-2397. 

46. Athi N. Naganathan (2019). Modulation of Allosteric Coupling by Mutations: from Protein Dynamics and Packing to Altered Native Ensembles and Function. Current Opinion in Structural Biology54, 1-9.

45. Encarnación Medina-Carmona, Isabel Betancor-Fernández, Jaime Santos, Noel Mesa-Torres, Silvia Grottelli, Cristina Batlle, Athi N. Naganathan, Elisa Oppici, Barbara Cellini, Salvador Ventura, Eduardo Salido & Angel L. Pey (2019). Insight into the Specificity and Severity of Pathogenic Mechanisms Associated with Missense Mutations through Experimental and Structural Perturbation Analyses. Human Molecular Genetics28, 1-15.

2018

44. Sneha Munshi, Soundhararajan Gopi, Gitanjali Asampille, Sandhyaa Subramanian, Luis Campos, Hanudatta Atreya & Athi N. Naganathan (2018). Tunable Order-Disorder Continuum in Protein-DNA Interactions. Nucleic Acids Res.46, 8700–8709.

43. Abhishek Narayan & Athi N. Naganathan (2018). Switching Protein Conformational Substates by Protonation and Mutation. J. Phys. Chem. B. 122, 11039-11047.

42. Sneha Munshi, Divya Rajendran, and Athi N. Naganathan (2018). Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble. J. Mol. Biol., 430, 2688-2694.

41. Soundhararajan Gopi, Suvadip Paul, Sayan Ranu & Athi N. Naganathan (2018). Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding. J. Phys. Chem. Lett., 9, 1771-1777.

40. Sneha Munshi, Soundhararajan Gopi,  Sandhyaa Subramanian,  Luis Campos & Athi N. Naganathan (2018). Protein Plasticity driven by Disorder and Collapse governs the Heterogeneous Binding of CytR to DNA. Nucleic Acids Res., 46, 4044-4053.

39. Soundhararajan Gopi,  Devanshu Devanshu,  Praveen Krishna & Athi N. Naganathan (2018). pStab: Prediction of Stable Mutants, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration. Bioinformatics.34, 875-877.

2017

38. Nandakumar Rajasekaran, Ashok Sekhar & Athi N. Naganathan (2017). A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations. J. Phys. Chem. Lett., 8, 4779–4784.

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

36. Nandakumar Rajasekaran & 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.

35. Abhishek Narayan & 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. 

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

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

2016

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

31. 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.

30. 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.

29. 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.

2015

28. 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.

27. 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.

26. 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.

25. 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.

24. 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.

2014

23. 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. J. Phys. Chem. B, 118, 8982-8994.

22. Abhishek Narayan & Athi N. Naganathan (2014). Evidence for the Sequential Folding Mechanism in RNase H from an Ensemble-Based Model. J. Phys. Chem. B, 118, 5050-5058.

2013

21. 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 Comput Biol., 9(12): e1003403.  

20. Athi N. Naganathan & Modesto Orozco (2013). The Conformational Landscape of an Intrinsically Disordered DNA-Binding Domain of a Transcription Regulator. J. Phys. Chem. B, 117, 13842-13850.

19. Athi N. Naganathan (2013). Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Comput Mol. Sci., 3, 504-514.

18. Athi N. Naganathan (2013). A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities. J. Phys. Chem. B, 117, 4956-4964.

2012

17. Athi N. Naganathan (2012). Predictions from an Ising-Like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics. J. Chem. Theory Comput., 8, 4646-4656.

2011

16. 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.

15. 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. Phys. Chem. Chem. Phys., 13, 17064-17076.

14. Athi N. Naganathan & Modesto Orozco (2011). The Protein Folding Transition-State Ensemble from a Go-like Model. Phys. Chem. Chem. Phys., 13, 15166-15174.

13. Athi N. Naganathan & Modesto Orozco (2011). The Native Ensemble and Folding of a Protein Molten-Globule: Functional Consequence of Downhill Folding. J. Am. Chem. Soc., 133, 12154-12161.

12. Pierpaolo Bruscolini & Athi N. Naganathan (2011). Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model. J. Am. Chem. Soc., 133, 5372-5379.

2010

11. Athi N. Naganathan, Peng Li, Raul-Perez Jimenez, Jose M. Sanchez-Ruiz & Victor Muñoz (2010). Navigating the Downhill Protein Folding Regime via Structural Homologues. J. Am. Chem. Soc., 132, 11183-11190.

10. Athi N. Naganathan & Victor Muñoz (2010). Insights into Protein Folding Mechanisms from Large-Scale Analysis of Mutational Effects. Proc. Natl. Acad. Sci. USA, 107, 8611-8616.  

2009

9. 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. Biophys J., 97, 1772-1777.  

8. Peng Li, Fabiana Y. Oliva, Athi N. Naganathan & Victor Muñoz (2009). Dynamics of One-State Downhill Protein Folding. Proc Natl Acad Sci USA, 106, 103-108.

2008

7. Victor Muñoz, Mourad Sadqi, Athi N. Naganathan & David de Sancho (2008). Exploiting the Downhill Folding Regime via Experiment. HFSP Journal, 2, 342-353.

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

2007

5. Athi N. Naganathan, Urmi Doshi & Victor Muñoz (2007). Protein Folding Kinetics: Barrier Effects in Chemical and Thermal Denaturation Experiments. J. Am. Chem. Soc., 129, 5673-5682.

2006

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

2005

3. Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Muñoz (2005). Direct Measurement of Barrier Heights in Protein Folding. J. Am. Chem. Soc., 127, 17970-17971.

2. 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.  

1. Athi N. Naganathan & Victor Muñoz (2005). Scaling of Folding Times with Protein Size. J. Am. Chem. Soc., 127, 480-481.