Protein Biophysics Lab

Rahul Dani, Iladeiti Kurbah, Dhruv Kumar Chaurasiya, Rohan Nath, Arunkumar Krishnan, David Fushman & Athi N. Naganathan (2026). Selective Control of Ligand Binding through a Distal Mutation that Alters the Protein Native Ensemble. Proc. Natl. Acad. Sci. U.S.A., 123, e2519658123.

Dhruv Kumar Chaurasiya & Athi N. Naganathan (2026). Diverse Conformational Ensembles Define the Shared Folding-allosteric Landscapes of Protein Kinases. Biophys. J., 125, 557–571.

Lawanya Natarajan, Dmitry Loginov, Alan Kadek, Petr Man & Athi N. Naganathan (2025). Local and Global Breathing Motions Prime the Access to Buried Binding Site in an Antibiotic-Sequestering Protein. ACS Bio Med Chem Au., 5, 840–851.

Adithi Kannan & Athi N. Naganathan (2025). Mapping the Conformational Heterogeneity Intrinsic to the Protein Native Ensemble. Biochemistry, 64, 2939–2957.

Rommie E. Amaro, Johan Åqvist, ... Modesto Orozco (2025). The Need to Implement FAIR Principles in Biomolecular Simulations. Nat. Methods., 22, 641–645.

Saloni Goyal, Divya Rajendran, Anup Kumar Mani & Athi N. Naganathan (2025). Polyphosphate Discriminates Protein Conformational Ensembles More Efficiently than DNA Promoting Diverse Assembly and Maturation Behaviors. eLife, 14:RP105461.

Bincy Lukose, Saloni Goyal & Athi N. Naganathan (2025). Oligomerization-mediated Phase Separation in the Nucleoid-associated Sensory Protein H-NS is Controlled by Ambient Cues. Protein Sci., 34, e5250.

Atanasio Gómez-Mulas, Athi N. Naganathan & Angel L. Pey (2025). The Lack of Trade-off Between Conformational Stability and Binding Affinity in a Nanobody with Therapeutic Potential for a Misfolding Disease. Int. J. Biol. Macromol., 284, 138046.

Adithi Kannan & Athi N. Naganathan (2024). Engineering the Native Ensemble to Tune Protein Function: Diverse Mutational Strategies and Interlinked Molecular Mechanisms. Curr. Opin. Struct. Biol. , 89, 102940.

Divya Rajendran, Saloni Goyal, Dhruv Kumar Chaurasiya & Athi N. Naganathan (2024). Determinants of Unfolding Cooperativity and Binding Are Decoupled in a DNA Binding Domain. J. Phys. Chem. B., 128, 9341–9352.

Lawanya Natarajan, Maria Laura De Sciscio, Alessandro Nicola Nardi, Ashok Sekhar, Alessandra Del Giudice, Marco D’Abramo & Athi N. Naganathan (2024). A Finely Balanced Order–Disorder Equilibrium Sculpts the Folding–Binding Landscape of an Antibiotic Sequestering Protein. Proc. Natl. Acad. Sci. U.S.A. , 121, e2318855121.

Bincy Lukose, Takahiro Maruno, Mohammed A. Faidh, Susumu Uchiyama & Athi N. Naganathan (2024). Molecular and Thermodynamic Determinants of Self-Assembly and Hetero-Oligomerization in the Enterobacterial Thermo-Osmo-Regulatory Protein H-NS. Nucleic Acids Res., gkae090.

Adithi Kannan, Dhruv Kumar Chaurasiya & Athi N. Naganathan (2024). Conflicting Interfacial Electrostatic Interactions as a Design Principle to Modulate Long-Range Interdomain Communication. ACS Bio Med Chem Au., 4, 53–67.

Rahul Dani, Westley Pawlosky, Dhruv Kumar Chaurasiya, Nonavinakere Seetharam Srilatha, Sonal Agarwal, David Fushman & Athi N. Naganathan (2023). Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry , 62, 2982–2996.

Ajith Kumar, Kulkarni Madhurima, Athi N. Naganathan, Pramodh Vallurupalli & Ashok Sekhar (2023). Probing Excited State 1Hα Chemical Shifts in Intrinsically Disordered Proteins with a Triple Resonance-Based CEST Experiment. Methods, 218, 198–209.

Kulkarni Madhurima, Bodhisatwa Nandi, Sneha Munshi, Athi N. Naganathan & Ashok Sekhar (2023). Functional Regulation of an Intrinsically Disordered Protein via a Conformationally Excited State. Sci. Adv. , 9, eadh4591.

Sathvik Anantakrishnan & Athi N. Naganathan (2023). Thermodynamic Architecture and Conformational Plasticity of GPCRs. Nat. Commun. , 14, 128.

Jose L. Neira, Athi N. Naganathan, Noel Mesa-Torres, Eduardo Salido & Angel L. Pey (2022). Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT. Molecules, 27, 8762.

Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Pavla Vankova, Petr Man, Athi N. Naganathan & Angel L. Pey (2022). Loss of Stability and Unfolding Cooperativity in hPGK1 upon Gradual Structural Perturbation of its N-Terminal Domain Hydrophobic Core. Sci. Rep., 12, 17200.

Adithi Kannan & Athi N. Naganathan (2022). Ensemble Origins and Distance-Dependence of Long-Range Mutational Effects in Proteins. iScience , 25, 105181.

Shrutarshi Mitra, Hiroyuki Oikawa, Divya Rajendran, Toshiyuki Kowada, Shin Mizukami, Athi N. Naganathan & Satoshi Takahashi (2022). Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy. J. Phys. Chem. B , 126, 6136–6147.

Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Ernesto Anoz-Carbonell, Pavla Vankova, Rogelio Palomino-Morales, Eduardo Salido, Petr Man, Milagros Medina, Athi N. Naganathan & Angel L. Pey (2022). Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations. Antioxidants, 11, 1110.

Divya Rajendran, Shrutarshi Mitra, Hiroyuki Oikawa, Kulkarni Madhurima, Ashok Sekhar, Satoshi Takahashi & Athi N. Naganathan (2022). Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein. J. Phys. Chem. Lett., 13, 3112–3120.

Hemashree Golla, Adithi Kannan, Soundhararajan Gopi, Sowmiya Murugan, Lakshmi R. Perumalsamy & Athi N. Naganathan (2022). Structural–Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble. ACS Cent. Sci. , 8, 282–293.

Athi N. Naganathan (2022). Predicting and Simulating Mutational Effects on Protein Folding Kinetics. Methods Mol. Biol., 2376, 373–386.

Athi N. Naganathan, Rahul Dani, Soundhararajan Gopi, Akashnathan Aranganathan & Abhishek Narayan (2021). Folding Intermediates, Heterogeneous Native Ensembles and Protein Function. J. Mol. Biol., 433, 167325.

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., 433, 167321.

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.

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.

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.

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.

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, 121–134. .

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. .

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.

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.

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

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

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

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.

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"]

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.

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

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.

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.

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.

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. , 28, 1–15.

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

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

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)]

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.

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.

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.

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)]

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.

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.

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.

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.

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]

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

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.

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)]

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.

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. J. Phys. Chem. B, 118, 8982–8994.

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.

Srinivasan Sivanandan & Athi N. Naganathan (2013). A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα. PLoS Comput. Biol., 9(12): e1003403.

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.

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

Athi N. Naganathan (2013). A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities. J. Phys. Chem. 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. J. Chem. Theory Comput., 8, 4646–4656.

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.

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.

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

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.

Pierpaolo Bruscolini & Athi N. Naganathan (2011). Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model. J. Am. Chem. Soc., 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. J. Am. Chem. Soc., 132, 11183–11190.

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.

Stephen J. Decamp, Athi N. Naganathan, Steven A. Waldauer, Olgica Bakajin & Lisa J. Lapidus (2009). Direct Observation of Downhill Folding of λ-Repressor in a Microfluidic Mixer. Biophys. J., 97, 1772–1777.

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.

Victor Muñoz, Mourad Sadqi, Athi N. Naganathan & David de Sancho (2008). Exploiting the Downhill Folding Regime via Experiment. HFSP J., 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. J. Am. Chem. Soc., 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. J. Am. Chem. Soc. , 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. J. Am. Chem. Soc., 127, 480–481.