Protein Biophysics Lab

 

 

2021

 

64. Gloria Gamiz-Arcoa, Valeria A. Rissoa, Eric A. Gaucher, Jose A. Gavira, Athi N. Naganathan, Beatriz Ibarra-Molero, Jose M. Sanchez-Ruiz (2021). Combining ancestral reconstruction with folding-landscape simulations to engineer heterologous protein expression. J. Mol. Biol., (In Press; DOI: https://doi.org/10.1016/j.jmb.2021.167321). 

 

63. Athi N. Naganathan, Adithi Kannan (2021). A Hierarchy of Coupling Free Energies Underlie the Thermodynamic and Functional Architecture of Protein Structures. Curr. Res. Struct. Biol., 3, 257-267. 

 

62. Juan Luis Pacheco-Garcia, Ernesto Anoz-Carbonell, Pavla Vankova, Adithi Kannan, Rogelio Palomino-Morales, Noel Mesa-Torres, Eduardo Salido, Petr Man, Milagros Medina, Athi N. Naganathan, Angel L. Pey (2021). Structural Basis of the Pleiotropic and Specific Phenotypic Consequences of Missense Mutations in the Multifunctional NAD(P)H:Quinone Oxidoreductase 1 and their Pharmacological Rescue. Redox Biology, 102112. 

 

61. Achinta Sannigrahi, Sourav Chowdhury, Bidisha Das, Amrita Banerjee, Animesh Halder, Mohammed Saleem, Athi N Naganathan, Sanat Karmakar & Krishnananda Chattopadhyay (2021). The Metal Cofactor Zinc and Interacting Membranes Modulate SOD1 Conformation-Aggregation Landscape in an In Vitro ALS Model. eLife, 10, e61453. 

 

60. Soundhararajan Gopi, Bincy Lukose & Athi N Naganathan (2021). Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. J. Phys. Chem. B, 125, 3546-3555. 

 

59. Surbhi Garg, Amin Sagar, Gayathri S. Singaraju, Rahul Dani, Naimat Kalim Bari, Athi N Naganathan & Sabyasachi Rakshit (2021). Weakening of Interaction Networks with Aging in Tip-Link Protein Induces Hearing Loss. Biochem. J., 478 (1), 121–134. 

 

2020

 

58. Sandhyaa Subramanian, Hemashree Golla, Kalivarathan Divakar, Adithi Kannan, David De Sancho & Athi N. Naganathan (2020). Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? J. Phys. Chem. B, 124, 8973-8983.  

 

57. Kabita Bhattacharjee, Soundhararajan Gopi & Athi N. Naganathan (2020). A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble. J. Phys. Chem. Lett., 11, 6749-6756. 

 

56. Abhishek Narayan, Soundhararajan Gopi, Bincy Lukose & Athi N. Naganathan (2020). Electrostatic Frustration Shapes Folding Mechanistic Differences in Paralogous Bacterial Stress Response Proteins. J. Mol. Biol., 432, 4830-4839. 

 

55. Soundhararajan Gopi & Athi N. Naganathan (2020). Non-specific DNA-driven quinary interactions promote structural transitions in proteins. Phys. Chem. Chem. Phys., 22, 12671-12677. 

 

54. Athi N. Naganathan (2020). Molecular origins of folding rate differences in the thioredoxin family. Biochem. J., 477, 1083-1087. 

 

53. Athi N. Naganathan (2020). Protein folding: how, why, and beyond. Protein Homeostasis Diseases: Mechanisms and Novel Therapies, 3-22. 

 

52. Soundhararajan Gopi, Devanshu Devanshu, Nandakumar Rajasekaran, Sathvik Anantakrishnan & Athi N. Naganathan (2020). pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations. ACS Omega, 5, 1142-1146. 

 

51. Sneha Munshi, Divya Rajendran, Samyuktha Ramesh, Sandhyaa Subramanian, Kabita Bhattacharjee, Meagha Ramana Kumar & Athi N. Naganathan (2020). Controlling Structure and Dimensions of a Disordered Protein via Mutations. Biochemistry, 59, 171-174.  [Featured in "Future of Biochemistry 2020: The Asia-Pacific Issue"]

 

2019

 

50. Soundhararajan Gopi, Akashnathan Aranganathan & Athi N. Naganathan (2019). Thermodynamics and Folding Landscapes of Large Proteins from a Statistical Mechanical Model. Curr. Res. Struct. Biol., 1, 6-12.

 

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. Nat. Commun., 10, 1995

 

47. Sneha Munshi, Sandhyaa Subramanian, Samyuktha Ramesh, Hemashree Golla, Divakar Kalivarathan, Madhurima Kulkarni, Luis Alberto Campos Prieto, Ashok Sekhar & Athi N. Naganathan (2019). Engineering Order and Cooperativity in a Disordered Protein. Biochemistry, 58, 2389–2397. 

 

46. Athi N. Naganathan (2019). Modulation of Allosteric Coupling by Mutations: from Protein Dynamics and Packing to Altered Native Ensembles and Function. Curr. Opin. Struct. Biol., 54, 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. Hum. Mol. Genet., 281 1-5. 

 

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 & Athi N. Naganathan (2018). Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble. J. Mol. Biol., 430, 2688-2694.    [Recommended by Faculty of 1000 (F1000)]

 

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.    [Recommended by Faculty of 1000 (F1000)]

 

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.   [Highlighted by Biochemistry as one of the top cited articles published in 2017]

 

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. Proc. Natl. Acad. Sci. U.S.A., 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. U.S.A., 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

2019, Maintained by Protein Biophysics Lab, IIT Madras, Chennai-36, India