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Items: 40

1.

Entropic Control of an Excited Folded-Like Conformation in a Disordered Protein Ensemble.

Munshi S, Rajendran D, Naganathan AN.

J Mol Biol. 2018 Jun 7. pii: S0022-2836(18)30584-9. doi: 10.1016/j.jmb.2018.06.008. [Epub ahead of print]

2.

Extracting the Hidden Distributions Underlying the Mean Transition State Structures in Protein Folding.

Gopi S, Paul S, Ranu S, Naganathan AN.

J Phys Chem Lett. 2018 Apr 5;9(7):1771-1777. doi: 10.1021/acs.jpclett.8b00538. Epub 2018 Mar 23.

PMID:
29565127
3.

Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA.

Munshi S, Gopi S, Subramanian S, Campos LA, Naganathan AN.

Nucleic Acids Res. 2018 May 4;46(8):4044-4053. doi: 10.1093/nar/gky176.

4.

pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration.

Gopi S, Devanshu D, Krishna P, Naganathan AN.

Bioinformatics. 2018 Mar 1;34(5):875-877. doi: 10.1093/bioinformatics/btx697.

PMID:
29092002
5.

A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations.

Rajasekaran N, Sekhar A, Naganathan AN.

J Phys Chem Lett. 2017 Oct 5;8(19):4779-4784. doi: 10.1021/acs.jpclett.7b02021. Epub 2017 Sep 20.

PMID:
28910120
6.

Toward a quantitative description of microscopic pathway heterogeneity in protein folding.

Gopi S, Singh A, Suresh S, Paul S, Ranu S, Naganathan AN.

Phys Chem Chem Phys. 2017 Aug 9;19(31):20891-20903. doi: 10.1039/c7cp03011h.

PMID:
28745340
7.

A self-consistent structural perturbation approach for determining the magnitude and extent of allosteric coupling in proteins.

Rajasekaran N, Naganathan AN.

Biochem J. 2017 Jul 6;474(14):2379-2388. doi: 10.1042/BCJ20170304.

PMID:
28522638
8.

Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein.

Narayan A, Naganathan AN.

J Phys Chem Lett. 2017 Apr 6;8(7):1683-1687. doi: 10.1021/acs.jpclett.7b00475. Epub 2017 Mar 30.

9.

Graded Structural Polymorphism in a Bacterial Thermosensor Protein.

Narayan A, Campos LA, Bhatia S, Fushman D, Naganathan AN.

J Am Chem Soc. 2017 Jan 18;139(2):792-802. doi: 10.1021/jacs.6b10608. Epub 2017 Jan 6.

PMID:
27991780
10.

A General Mechanism for the Propagation of Mutational Effects in Proteins.

Rajasekaran N, Suresh S, Gopi S, Raman K, Naganathan AN.

Biochemistry. 2017 Jan 10;56(1):294-305. doi: 10.1021/acs.biochem.6b00798. Epub 2016 Dec 27.

PMID:
27958720
11.

Prediction of change in protein unfolding rates upon point mutations in two state proteins.

Chaudhary P, Naganathan AN, Gromiha MM.

Biochim Biophys Acta. 2016 Sep;1864(9):1104-1109. doi: 10.1016/j.bbapap.2016.06.001. Epub 2016 Jun 2.

PMID:
27264959
12.

Quantifying Protein Disorder through Measures of Excess Conformational Entropy.

Rajasekaran N, Gopi S, Narayan A, Naganathan AN.

J Phys Chem B. 2016 May 19;120(19):4341-50. doi: 10.1021/acs.jpcb.6b00658. Epub 2016 May 4.

PMID:
27111521
13.

Modern Analysis of Protein Folding by Differential Scanning Calorimetry.

Ibarra-Molero B, Naganathan AN, Sanchez-Ruiz JM, Muñoz V.

Methods Enzymol. 2016;567:281-318. doi: 10.1016/bs.mie.2015.08.027. Epub 2015 Nov 6.

PMID:
26794359
14.

Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein.

Naganathan AN, De Sancho D.

J Phys Chem B. 2015 Nov 25;119(47):14925-33. doi: 10.1021/acs.jpcb.5b09568. Epub 2015 Nov 16.

PMID:
26524123
15.

Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch.

Gopi S, Rajasekaran N, Singh A, Ranu S, Naganathan AN.

Phys Chem Chem Phys. 2015 Nov 7;17(41):27264-9. doi: 10.1039/c5cp04765j.

PMID:
26421497
16.

Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein.

Munshi S, Naganathan AN.

Phys Chem Chem Phys. 2015 Apr 28;17(16):11042-52. doi: 10.1039/c4cp06102k.

PMID:
25824585
17.

Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations.

Chaudhary P, Naganathan AN, Gromiha MM.

Bioinformatics. 2015 Jul 1;31(13):2091-7. doi: 10.1093/bioinformatics/btv091. Epub 2015 Feb 16.

PMID:
25686635
18.

Are protein folding intermediates the evolutionary consequence of functional constraints?

Naganathan AN, Sanchez-Ruiz JM, Munshi S, Suresh S.

J Phys Chem B. 2015 Jan 29;119(4):1323-33. doi: 10.1021/jp510342m. Epub 2015 Jan 7.

PMID:
25525671
19.

Thermodynamics of downhill folding: multi-probe analysis of PDD, a protein that folds over a marginal free energy barrier.

Naganathan AN, Muñoz V.

J Phys Chem B. 2014 Jul 31;118(30):8982-94. doi: 10.1021/jp504261g. Epub 2014 Jul 21.

PMID:
24988372
20.

Evidence for the sequential folding mechanism in RNase H from an ensemble-based model.

Narayan A, Naganathan AN.

J Phys Chem B. 2014 May 15;118(19):5050-8. doi: 10.1021/jp500934f. Epub 2014 May 6.

PMID:
24762044
21.

A disorder-induced domino-like destabilization mechanism governs the folding and functional dynamics of the repeat protein IκBα.

Sivanandan S, Naganathan AN.

PLoS Comput Biol. 2013;9(12):e1003403. doi: 10.1371/journal.pcbi.1003403. Epub 2013 Dec 19.

22.

The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator.

Naganathan AN, Orozco M.

J Phys Chem B. 2013 Nov 7;117(44):13842-50. doi: 10.1021/jp408350v. Epub 2013 Oct 28.

PMID:
24127726
23.

A rapid, ensemble and free energy based method for engineering protein stabilities.

Naganathan AN.

J Phys Chem B. 2013 May 2;117(17):4956-64. doi: 10.1021/jp401588x. Epub 2013 Apr 11.

PMID:
23541220
24.

Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics.

Naganathan AN.

J Chem Theory Comput. 2012 Nov 13;8(11):4646-56. doi: 10.1021/ct300676w. Epub 2012 Oct 22.

PMID:
26605620
25.

Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.

Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL.

Adv Protein Chem Struct Biol. 2011;85:183-215. doi: 10.1016/B978-0-12-386485-7.00005-3. Review.

PMID:
21920324
26.

The protein folding transition-state ensemble from a Gō-like model.

Naganathan AN, Orozco M.

Phys Chem Chem Phys. 2011 Sep 7;13(33):15166-74. doi: 10.1039/c1cp20964g. Epub 2011 Jul 21.

PMID:
21776506
27.

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis.

Naganathan AN, Perez-Jimenez R, Muñoz V, Sanchez-Ruiz JM.

Phys Chem Chem Phys. 2011 Oct 14;13(38):17064-76. doi: 10.1039/c1cp20156e. Epub 2011 Jul 19.

PMID:
21769353
28.

The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding.

Naganathan AN, Orozco M.

J Am Chem Soc. 2011 Aug 10;133(31):12154-61. doi: 10.1021/ja204053n. Epub 2011 Jul 15.

PMID:
21732676
29.

Quantitative prediction of protein folding behaviors from a simple statistical model.

Bruscolini P, Naganathan AN.

J Am Chem Soc. 2011 Apr 13;133(14):5372-9. doi: 10.1021/ja110884m. Epub 2011 Mar 18.

PMID:
21417380
30.

Navigating the downhill protein folding regime via structural homologues.

Naganathan AN, Li P, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V.

J Am Chem Soc. 2010 Aug 18;132(32):11183-90. doi: 10.1021/ja103612q.

PMID:
20698685
31.

Insights into protein folding mechanisms from large scale analysis of mutational effects.

Naganathan AN, Muñoz V.

Proc Natl Acad Sci U S A. 2010 May 11;107(19):8611-6. doi: 10.1073/pnas.1000988107. Epub 2010 Apr 23.

32.

Direct observation of downhill folding of lambda-repressor in a microfluidic mixer.

DeCamp SJ, Naganathan AN, Waldauer SA, Bakajin O, Lapidus LJ.

Biophys J. 2009 Sep 16;97(6):1772-7. doi: 10.1016/j.bpj.2009.07.003.

33.

Exploiting the downhill folding regime via experiment.

Muñoz V, Sadqi M, Naganathan AN, de Sancho D.

HFSP J. 2008 Dec;2(6):342-53. doi: 10.2976/1.2988030. Epub 2008 Oct 13.

34.

Dynamics of one-state downhill protein folding.

Li P, Oliva FY, Naganathan AN, Muñoz V.

Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):103-8. doi: 10.1073/pnas.0802986106. Epub 2008 Dec 31.

35.

Determining denaturation midpoints in multiprobe equilibrium protein folding experiments.

Naganathan AN, Muñoz V.

Biochemistry. 2008 Jul 1;47(26):6752-61. doi: 10.1021/bi800336x. Epub 2008 Jun 10.

PMID:
18540681
36.

Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.

Naganathan AN, Doshi U, Muñoz V.

J Am Chem Soc. 2007 May 2;129(17):5673-82. Epub 2007 Apr 10.

37.

Dynamics, energetics, and structure in protein folding.

Naganathan AN, Doshi U, Fung A, Sadqi M, Muñoz V.

Biochemistry. 2006 Jul 18;45(28):8466-75. Review.

38.

Direct measurement of barrier heights in protein folding.

Naganathan AN, Sanchez-Ruiz JM, Muñoz V.

J Am Chem Soc. 2005 Dec 28;127(51):17970-1.

PMID:
16366525
39.

Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins.

Naganathan AN, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V.

Biochemistry. 2005 May 24;44(20):7435-49.

PMID:
15895987
40.

Scaling of folding times with protein size.

Naganathan AN, Muñoz V.

J Am Chem Soc. 2005 Jan 19;127(2):480-1.

PMID:
15643845

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