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Faculty

Athi N. Naganathan

Athi N. Naganathan

Ph. D.,University of Maryland, USA

B. Tech., Anna University, Chennai

Professor

athi@iitm.ac.in

Office : BT 115 Block -2

+91-44-2257-4140

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

Complete list of publications can be found on Scopus

2022

    1. Adithi Kannan & Athi N. Naganathan (2022). Ensemble Origins and Distance-Dependence of Long-Range Mutational Effects in Proteins. iScience, In Press;.doi
    1. 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.doi
    1. 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.doi
    1. 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.doi
    1. 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.doi
    1. Athi N. Naganathan (2022). Predicting and Simulating Mutational Effects on Protein Folding Kinetics. Methods Mol. Biol., 2376, 373-386.doi

2021

    1. 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.doi
    1. 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. doi
    1. 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. doi
    1. 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.doi
    1. 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. doi
    1. 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.doi
    1. 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.doi

2020

    1. 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. (In press, DOI:10.1021/acs.jpcb.0c05976).doi
    1. 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.doi
    1. 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.doi
    1. Soundhararajan Gopi & Athi N. Naganathan (2020). Non-specific DNA-driven quinary interactions promote structural transitions in proteins. Phys. Chem. Chem. Phys., 22, 12671-12677.doi
    1. Athi N. Naganathan (2020). Molecular origins of folding rate differences in the thioredoxin family.Biochem. J., 477, 1083-1087.doi
    1. Athi N. Naganathan (2020). Protein folding: how, why, and beyond. Protein Homeostasis Diseases: Mechanisms and Novel Therapies, 3-22.doi
    1. 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.doi
    1. 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. doi[Featured in -Future of Biochemistry 2020: The Asia-Pacific Issue-]

2019

    1. 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.doi
    1. Abhishek Narayan, Kabita Bhattacharjee & Athi N. Naganathan (2019). Thermally versus Chemically Denatured Protein States. Biochemistry, 58, 2519-2523.doi
    1. 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.doi
    1. 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.doi
    1. 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.doi
    1. Encarnaci-n Medina-Carmona, Isabel Betancor-Fern-ndez, 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.doi

2018

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

2017

  1. 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)]doi
    1. 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 doi
    1. 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 doi
    1. 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 doi
    1. 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 doi
    1. 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]doi

2016

    1. Athi N. Naganathan (2016). Predictive Modeling of Protein Folding Thermodynamics, Mutational Effects and Free-Energy Landscapes. Proc. Indian Natn. Sci. Acad., 82, 1211-1228_ **doi**
    1. 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_ **doi**
    1. 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)]doi
    1. Beatriz Ibarra-Molero, Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Mu-oz (2016). Modern Analysis of Protein Folding by Differential Scanning Calorimetry. Methods Enzymol., 567, 281 - 318_**doi**

2015

    1. 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_**doi**
    1. 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_ **doi**
    1. 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.doi
    1. 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.doi
    1. 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.doi

2014

    1. Athi N. Naganathan & Victor Mu-oz (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.doi
    1. 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.doi

2013

    1. 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.doi, doi
    1. 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.doi
    1. Athi N. Naganathan (2013). Coarse-Grained Models of Protein Folding as Detailed Tools to Connect with Experiments. WIREs: Comput. Mol. Sci., 3, 504-514.doi
    1. Athi N. Naganathan (2013). A Rapid, Ensemble and Free Energy Based Method for Engineering Protein Stabilities. J. Phys. Chem. B, 117, 4956-4964.doi

2012

    1. 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. doi,doi

2011

    1. Modesto Orozco, Laura Orellana, Adam Hospital, Athi N. Naganathan, Agusti Emperador, Oliver Carrillo & Josep L. Gelp- (2011). Coarse Grained Representation of Protein Flexibility: Foundations, Successes and Shortcomings. Adv. Protein Chem. Struct. Biol., 85, 183-215.doi
  1. Athi N. Naganathan, Raul-Perez Jimenez, Victor Mu-oz & 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.doi
    1. Athi N. Naganathan & Modesto Orozco (2011). The Protein Folding Transition-State Ensemble from a Go-like Model. Phys. Chem. Chem. Phys., 13, 15166-15174.doi
    1. 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. doi
    1. Pierpaolo Bruscolini & Athi N. Naganathan (2011). Quantitative Prediction of Protein Folding Behaviors from a Simple Statistical Model. J. Am. Chem. Soc., 133, 5372-5379. doi

2010

    1. Athi N. Naganathan, Peng Li, Raul-Perez Jimenez, Jose M. Sanchez-Ruiz & Victor Mu-oz (2010). Navigating the Downhill Protein Folding Regime via Structural Homologues. J. Am. Chem. Soc., 132, 11183-11190.doi
    1. Athi N. Naganathan & Victor Mu-oz (2010). Insights into Protein Folding Mechanisms from Large-Scale Analysis of Mutational Effects. Proc. Natl. Acad. Sci. U.S.A., 107, 8611-8616. doi, link

2009

    1. 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.doi,link
    1. Peng Li, Fabiana Y. Oliva, Athi N. Naganathan & Victor Mu-oz (2009). Dynamics of One-State Downhill Protein Folding. Proc. Natl. Acad. Sci. U.S.A., 106, 103-108.doi,link

2008

    1. Victor Mu-oz, Mourad Sadqi, Athi N. Naganathan & David de Sancho (2008). Exploiting the Downhill Folding Regime via Experiment. HFSP J., 2, 342-353.doi,link

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

2007

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

2006

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

2005

    1. Athi N. Naganathan, Jose M. Sanchez-Ruiz & Victor Mu-oz (2005). Direct Measurement of Barrier Heights in Protein Folding. J. Am. Chem. Soc., 127, 17970-17971.doi
    1. Athi N. Naganathan, Raul Perez-Jimenez, Jose M. Sanchez-Ruiz & Victor Mu-oz (2005). Robustness of Downhill Folding: Guidelines for the Analysis of Equilibrium Folding Experiments on Small Proteins. Biochemistry, 44, 7435-7449.doi
    1. Athi N. Naganathan & Victor Mu-oz (2005). Scaling of Folding Times with Protein Size. J. Am. Chem. Soc., 127, 480-481.doi