Protein Biophysics Lab

 

 

2018

 

41. Soundhararajan Gopi, Suvadip Paul, Sayan Ranu, and 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, and Athi N. Naganathan (2018). Protein Plasticity driven by Disorder and Collapse governs the Heterogeneous Binding of CytR to DNA. Nucleic Acids Res. (In press, DOI: 10.1093/nar/gky176)

 

39. 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., 34, 875-877. 

 

2017

 

38. 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)]

 

37. 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. 

 

36. 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. 

 

35. 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. 

 

34. 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. 

 

33. 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. 

 

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. Biochim. Biophys. 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.    [Recommended by Faculty of 1000 (F1000)]

 

29. Beatriz Ibarra-Molero, Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Muñoz (2016). Modern Analysis of Protein Folding by Differential Scanning Calorimetry. Methods Enzymol., 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. Adv Protein Chem Struct Biol., 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 Gō-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. PNAS 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. PNAS 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 J., 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. 

 

Research Articles

2014, Maintained by Protein Biophysics Lab, IIT Madras, Chennai-36, India