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Items: 37

1.

pStab: Prediction of Stable Mutants, Unfolding Curves, Stability Maps and Protein Electrostatic Frustration.

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

Bioinformatics. 2017 Oct 28. doi: 10.1093/bioinformatics/btx697. [Epub ahead of print]

PMID:
29092002
2.

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
3.

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
4.

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
5.

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.

6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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
14.

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
15.

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
16.

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
17.

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
18.

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.

19.

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
20.

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
21.

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
22.

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
23.

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
24.

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
25.

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
26.

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
27.

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
28.

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.

29.

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.

30.

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.

31.

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.

32.

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
33.

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.

34.

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.

35.

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
36.

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
37.

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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