Athi N. Naganathan, Ph.D. - Publications

Affiliations: 
2007 Biochemistry University of Maryland, College Park, College Park, MD 
Area:
Biochemistry, General Biophysics

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Lukose B, Maruno T, Faidh MA, Uchiyama S, Naganathan AN. Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS. Nucleic Acids Research. PMID 38340344 DOI: 10.1093/nar/gkae090  0.323
2023 Kannan A, Chaurasiya DK, Naganathan AN. Conflicting Interfacial Electrostatic Interactions as a Design Principle to Modulate Long-Range Interdomain Communication. Acs Bio & Med Chem Au. 4: 53-67. PMID 38404745 DOI: 10.1021/acsbiomedchemau.3c00047  0.344
2023 Kumar A, Madhurima K, Naganathan AN, Vallurupalli P, Sekhar A. Probing excited state Hα chemical shifts in intrinsically disordered proteins with a triple resonance-based CEST experiment: Application to a disorder-to-order switch. Methods (San Diego, Calif.). PMID 37607621 DOI: 10.1016/j.ymeth.2023.08.009  0.325
2023 Madhurima K, Nandi B, Munshi S, Naganathan AN, Sekhar A. Functional regulation of an intrinsically disordered protein via a conformationally excited state. Science Advances. 9: eadh4591. PMID 37379390 DOI: 10.1126/sciadv.adh4591  0.359
2023 Anantakrishnan S, Naganathan AN. Thermodynamic architecture and conformational plasticity of GPCRs. Nature Communications. 14: 128. PMID 36624096 DOI: 10.1038/s41467-023-35790-z  0.392
2022 Neira JL, Naganathan AN, Mesa-Torres N, Salido E, Pey AL. Phosphorylation of Thr9 Affects the Folding Landscape of the N-Terminal Segment of Human AGT Enhancing Protein Aggregation of Disease-Causing Mutants. Molecules (Basel, Switzerland). 27. PMID 36557898 DOI: 10.3390/molecules27248762  0.338
2022 Kannan A, Naganathan AN. Ensemble origins and distance-dependence of long-range mutational effects in proteins. Iscience. 25: 105181. PMID 36248733 DOI: 10.1016/j.isci.2022.105181  0.343
2022 Pacheco-García JL, Loginov DS, Naganathan AN, Vankova P, Cano-Muñoz M, Man P, Pey AL. Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core. Scientific Reports. 12: 17200. PMID 36229482 DOI: 10.1038/s41598-022-22088-1  0.35
2022 Mitra S, Oikawa H, Rajendran D, Kowada T, Mizukami S, Naganathan AN, Takahashi S. Flexible Target Recognition of the Intrinsically Disordered DNA-Binding Domain of CytR Monitored by Single-Molecule Fluorescence Spectroscopy. The Journal of Physical Chemistry. B. 126: 6136-6147. PMID 35969476 DOI: 10.1021/acs.jpcb.2c02791  0.328
2022 Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations. Antioxidants (Basel, Switzerland). 11. PMID 35740007 DOI: 10.3390/antiox11061110  0.389
2022 Rajendran D, Mitra S, Oikawa H, Madhurima K, Sekhar A, Takahashi S, Naganathan AN. Quantification of Entropic Excluded Volume Effects Driving Crowding-Induced Collapse and Folding of a Disordered Protein. The Journal of Physical Chemistry Letters. 13: 3112-3120. PMID 35357183 DOI: 10.1021/acs.jpclett.2c00316  0.463
2022 Golla H, Kannan A, Gopi S, Murugan S, Perumalsamy LR, Naganathan AN. Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble. Acs Central Science. 8: 282-293. PMID 35233459 DOI: 10.1021/acscentsci.1c01548  0.314
2022 Naganathan AN. Predicting and Simulating Mutational Effects on Protein Folding Kinetics. Methods in Molecular Biology (Clifton, N.J.). 2376: 373-386. PMID 34845621 DOI: 10.1007/978-1-0716-1716-8_21  0.509
2021 Naganathan AN, Kannan A. A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures. Current Research in Structural Biology. 3: 257-267. PMID 34704074 DOI: 10.1016/j.crstbi.2021.09.003  0.434
2021 Naganathan AN, Dani R, Gopi S, Aranganathan A, Narayan A. Folding Intermediates, Heterogeneous Native Ensembles and Protein Function. Journal of Molecular Biology. 433: 167325. PMID 34695380 DOI: 10.1016/j.jmb.2021.167325  0.547
2021 Gamiz-Arco G, Risso VA, Gaucher EA, Gavira JA, Naganathan AN, Ibarra-Molero B, Sanchez-Ruiz JM. Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression. Journal of Molecular Biology. 433: 167321. PMID 34687715 DOI: 10.1016/j.jmb.2021.167321  0.453
2021 Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. The Journal of Physical Chemistry. B. PMID 33818099 DOI: 10.1021/acs.jpcb.1c00972  0.313
2020 Gopi S, Aranganathan A, Naganathan AN. Erratum to "Thermodynamics and folding landscapes of large proteins from a statistical mechanical model" [Current Research in Structural Biology 1 (2019) 6-12]. Current Research in Structural Biology. 2: 239. PMID 34236346 DOI: 10.1016/j.crstbi.2020.12.003  0.404
2020 Subramanian S, Golla H, Divakar K, Kannan A, De Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? The Journal of Physical Chemistry. B. PMID 32955882 DOI: 10.1021/Acs.Jpcb.0C05976  0.806
2020 Bhattacharjee K, Gopi S, Naganathan AN. A Disordered Loop Mediates Heterogeneous Unfolding of an Ordered Protein by Altering the Native Ensemble. The Journal of Physical Chemistry Letters. 6749-6756. PMID 32787218 DOI: 10.1021/Acs.Jpclett.0C01848  0.598
2020 Narayan A, Gopi S, Lukose B, Naganathan AN. Electrostatic Frustration Shapes Folding Mechanistic Differences in Paralogous Bacterial Stress Response Proteins. Journal of Molecular Biology. PMID 32628955 DOI: 10.1016/J.Jmb.2020.06.026  0.466
2020 Gopi S, Naganathan AN. Non-specific DNA-driven quinary interactions promote structural transitions in proteins. Physical Chemistry Chemical Physics : Pccp. 22: 12671-12677. PMID 32458879 DOI: 10.1039/D0Cp01758B  0.463
2020 Naganathan AN. Molecular origins of folding rate differences in the thioredoxin family. The Biochemical Journal. 477: 1083-1087. PMID 32187349 DOI: 10.1042/Bcj20190864  0.487
2020 Gopi S, Devanshu D, Rajasekaran N, Anantakrishnan S, Naganathan AN. pPerturb: A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations. Acs Omega. 5: 1142-1146. PMID 31984271 DOI: 10.1021/acsomega.9b03371  0.413
2019 Gopi S, Aranganathan A, Naganathan AN. Thermodynamics and folding landscapes of large proteins from a statistical mechanical model. Current Research in Structural Biology. 1: 6-12. PMID 34235463 DOI: 10.1016/j.crstbi.2019.10.002  0.551
2019 Munshi S, Rajendran D, Ramesh S, Subramanian S, Bhattacharjee K, Kumar MR, Naganathan AN. Controlling Structure and Dimensions of a Disordered Protein via Mutations. Biochemistry. PMID 31557007 DOI: 10.1021/Acs.Biochem.9B00678  0.491
2019 Narayan A, Bhattacharjee K, Naganathan AN. Thermally versus Chemically Denatured Protein States. Biochemistry. PMID 31083972 DOI: 10.1021/Acs.Biochem.9B00089  0.609
2019 Narayan A, Gopi S, Fushman D, Naganathan AN. A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair. Nature Communications. 10: 1995. PMID 31040281 DOI: 10.1038/S41467-019-10002-9  0.487
2019 Munshi S, Subramanian S, Ramesh S, Golla H, Kalivarathan D, Kulkarni M, Campos Prieto LA, Sekhar A, Naganathan AN. Engineering Order and Cooperativity in a Disordered Protein. Biochemistry. PMID 31002232 DOI: 10.1021/Acs.Biochem.9B00182  0.552
2018 Naganathan AN. Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function. Current Opinion in Structural Biology. 54: 1-9. PMID 30268910 DOI: 10.1016/J.Sbi.2018.09.004  0.52
2018 Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Human Molecular Genetics. PMID 30215702 DOI: 10.1093/Hmg/Ddy323  0.401
2018 Munshi S, Gopi S, Asampille G, Subramanian S, Campos LA, Atreya HS, Naganathan AN. Tunable order-disorder continuum in protein-DNA interactions. Nucleic Acids Research. PMID 30107436 DOI: 10.1093/Nar/Gky732  0.385
2018 Narayan A, Naganathan AN. Switching Protein Conformational Substates by Protonation and Mutation. The Journal of Physical Chemistry. B. PMID 30048131 DOI: 10.1021/Acs.Jpcb.8B05108  0.405
2018 Munshi S, Rajendran D, Naganathan AN. Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble. Journal of Molecular Biology. PMID 29885328 DOI: 10.1016/J.Jmb.2018.06.008  0.503
2018 Gopi S, Paul S, Ranu S, Naganathan AN. Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding. The Journal of Physical Chemistry Letters. 1771-1777. PMID 29565127 DOI: 10.1021/Acs.Jpclett.8B00538  0.585
2018 Munshi S, Gopi S, Subramanian S, Campos LA, Naganathan AN. Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA. Nucleic Acids Research. PMID 29538715 DOI: 10.1093/Nar/Gky176  0.448
2017 Gopi S, Devanshu D, Krishna P, Naganathan AN. pStab: Prediction of Stable Mutants, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration. Bioinformatics (Oxford, England). PMID 29092002 DOI: 10.1093/Bioinformatics/Btx697  0.448
2017 Rajasekaran N, Sekhar A, Naganathan AN. A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations. The Journal of Physical Chemistry Letters. PMID 28910120 DOI: 10.1021/Acs.Jpclett.7B02021  0.58
2017 Gopi S, Singh A, Suresh S, Paul S, Ranu S, Naganathan AN. Toward a quantitative description of microscopic pathway heterogeneity in protein folding. Physical Chemistry Chemical Physics : Pccp. PMID 28745340 DOI: 10.1039/C7Cp03011H  0.661
2017 Rajasekaran N, Naganathan AN. A Self-Consistent Structural Perturbation Approach for Determining the Magnitude and Extent of Allosteric Coupling in Proteins. The Biochemical Journal. PMID 28522638 DOI: 10.1042/Bcj20170304  0.588
2017 Narayan A, Naganathan AN. Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein. The Journal of Physical Chemistry Letters. PMID 28345920 DOI: 10.1021/Acs.Jpclett.7B00475  0.58
2016 Narayan A, Campos LA, Bhatia S, Fushman D, Naganathan AN. Graded Structural Polymorphism in a Bacterial Thermosensor Protein. Journal of the American Chemical Society. PMID 27991780 DOI: 10.1021/Jacs.6B10608  0.516
2016 Rajasekaran N, Suresh S, Gopi S, Raman K, Naganathan AN. A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry. PMID 27958720 DOI: 10.1021/Acs.Biochem.6B00798  0.491
2016 Chaudhary P, Naganathan AN, Gromiha MM. Prediction of change in protein unfolding rates upon point mutations in two state proteins. Biochimica Et Biophysica Acta. PMID 27264959 DOI: 10.1016/J.Bbapap.2016.06.001  0.53
2016 Rajasekaran N, Gopi S, Narayan A, Naganathan AN. Quantifying Protein Disorder through Measures of Excess Conformational Entropy. The Journal of Physical Chemistry. B. PMID 27111521 DOI: 10.1021/Acs.Jpcb.6B00658  0.515
2016 Ibarra-Molero B, Naganathan AN, Sanchez-Ruiz JM, Muñoz V. Modern Analysis of Protein Folding by Differential Scanning Calorimetry. Methods in Enzymology. 567: 281-318. PMID 26794359 DOI: 10.1016/Bs.Mie.2015.08.027  0.771
2015 Naganathan AN, De Sancho D. Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein. The Journal of Physical Chemistry. B. 119: 14925-33. PMID 26524123 DOI: 10.1021/Acs.Jpcb.5B09568  0.788
2015 Gopi S, Rajasekaran N, Singh A, Ranu S, Naganathan AN. Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch. Physical Chemistry Chemical Physics : Pccp. 17: 27264-9. PMID 26421497 DOI: 10.1039/C5Cp04765J  0.46
2015 Munshi S, Naganathan AN. Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein. Physical Chemistry Chemical Physics : Pccp. 17: 11042-52. PMID 25824585 DOI: 10.1039/C4Cp06102K  0.592
2015 Chaudhary P, Naganathan AN, Gromiha MM. Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations. Bioinformatics (Oxford, England). 31: 2091-7. PMID 25686635 DOI: 10.1093/Bioinformatics/Btv091  0.513
2015 Naganathan AN, Sanchez-Ruiz JM, Munshi S, Suresh S. Are protein folding intermediates the evolutionary consequence of functional constraints? The Journal of Physical Chemistry. B. 119: 1323-33. PMID 25525671 DOI: 10.1021/Jp510342M  0.568
2014 Naganathan AN, Muñoz V. Thermodynamics of downhill folding: multi-probe analysis of PDD, a protein that folds over a marginal free energy barrier. The Journal of Physical Chemistry. B. 118: 8982-94. PMID 24988372 DOI: 10.1021/Jp504261G  0.757
2014 Narayan A, Naganathan AN. Evidence for the sequential folding mechanism in RNase H from an ensemble-based model. The Journal of Physical Chemistry. B. 118: 5050-8. PMID 24762044 DOI: 10.1021/Jp500934F  0.591
2013 Sivanandan S, Naganathan AN. A disorder-induced domino-like destabilization mechanism governs the folding and functional dynamics of the repeat protein IκBα. Plos Computational Biology. 9: e1003403. PMID 24367251 DOI: 10.1371/Journal.Pcbi.1003403  0.522
2013 Naganathan AN, Orozco M. The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator. The Journal of Physical Chemistry. B. 117: 13842-50. PMID 24127726 DOI: 10.1021/Jp408350V  0.466
2013 Naganathan AN. A rapid, ensemble and free energy based method for engineering protein stabilities. The Journal of Physical Chemistry. B. 117: 4956-64. PMID 23541220 DOI: 10.1021/Jp401588X  0.483
2013 Naganathan AN. Coarse‐grained models of protein folding as detailed tools to connect with experiments Wiley Interdisciplinary Reviews: Computational Molecular Science. 3: 504-514. DOI: 10.1002/Wcms.1133  0.62
2012 Naganathan AN. Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics. Journal of Chemical Theory and Computation. 8: 4646-56. PMID 26605620 DOI: 10.1021/Ct300676W  0.58
2011 Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Advances in Protein Chemistry and Structural Biology. 85: 183-215. PMID 21920324 DOI: 10.1016/B978-0-12-386485-7.00005-3  0.446
2011 Naganathan AN, Orozco M. The protein folding transition-state ensemble from a Gō-like model. Physical Chemistry Chemical Physics : Pccp. 13: 15166-74. PMID 21776506 DOI: 10.1039/C1Cp20964G  0.609
2011 Naganathan AN, Perez-Jimenez R, Muñoz V, Sanchez-Ruiz JM. Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis. Physical Chemistry Chemical Physics : Pccp. 13: 17064-76. PMID 21769353 DOI: 10.1039/C1Cp20156E  0.736
2011 Naganathan AN, Orozco M. The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. Journal of the American Chemical Society. 133: 12154-61. PMID 21732676 DOI: 10.1021/Ja204053N  0.633
2011 Bruscolini P, Naganathan AN. Quantitative prediction of protein folding behaviors from a simple statistical model. Journal of the American Chemical Society. 133: 5372-9. PMID 21417380 DOI: 10.1021/Ja110884M  0.635
2010 Naganathan AN, Li P, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V. Navigating the downhill protein folding regime via structural homologues. Journal of the American Chemical Society. 132: 11183-90. PMID 20698685 DOI: 10.1021/Ja103612Q  0.793
2010 Naganathan AN, Muñoz V. Insights into protein folding mechanisms from large scale analysis of mutational effects. Proceedings of the National Academy of Sciences of the United States of America. 107: 8611-6. PMID 20418505 DOI: 10.1073/Pnas.1000988107  0.712
2009 DeCamp SJ, Naganathan AN, Waldauer SA, Bakajin O, Lapidus LJ. Direct observation of downhill folding of lambda-repressor in a microfluidic mixer. Biophysical Journal. 97: 1772-7. PMID 19751683 DOI: 10.1016/J.Bpj.2009.07.003  0.538
2009 Li P, Oliva FY, Naganathan AN, Muñoz V. Dynamics of one-state downhill protein folding. Proceedings of the National Academy of Sciences of the United States of America. 106: 103-8. PMID 19118204 DOI: 10.1073/Pnas.0802986106  0.742
2008 Muñoz V, Sadqi M, Naganathan AN, de Sancho D. Exploiting the downhill folding regime via experiment. Hfsp Journal. 2: 342-53. PMID 19436488 DOI: 10.2976/1.2988030  0.82
2008 Naganathan AN, Muñoz V. Determining denaturation midpoints in multiprobe equilibrium protein folding experiments. Biochemistry. 47: 6752-61. PMID 18540681 DOI: 10.1021/Bi800336X  0.667
2007 Naganathan AN, Doshi U, Muñoz V. Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments. Journal of the American Chemical Society. 129: 5673-82. PMID 17419630 DOI: 10.1021/Ja0689740  0.808
2006 Naganathan AN, Doshi U, Fung A, Sadqi M, Muñoz V. Dynamics, energetics, and structure in protein folding. Biochemistry. 45: 8466-75. PMID 16834320 DOI: 10.1021/Bi060643C  0.805
2005 Naganathan AN, Sanchez-Ruiz JM, Muñoz V. Direct measurement of barrier heights in protein folding. Journal of the American Chemical Society. 127: 17970-1. PMID 16366525 DOI: 10.1021/Ja055996Y  0.744
2005 Naganathan AN, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V. Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins. Biochemistry. 44: 7435-49. PMID 15895987 DOI: 10.1021/Bi050118Y  0.717
2005 Naganathan AN, Muñoz V. Scaling of folding times with protein size. Journal of the American Chemical Society. 127: 480-1. PMID 15643845 DOI: 10.1021/Ja044449U  0.741
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