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 |
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 |
0.807 |
|
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 |
0.61 |
|
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 |
0.662 |
|
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 |
0.581 |
|
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 |
0.79 |
|
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 |
0.621 |
|
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 |
0.447 |
|
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 |
0.636 |
|
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 |
0.809 |
|
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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