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Items: 1 to 50 of 64

1.

Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners.

Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y.

Proc Natl Acad Sci U S A. 2019 Nov 11. pii: 201911880. doi: 10.1073/pnas.1911880116. [Epub ahead of print]

2.

Turnover versus treadmilling in actin network assembly and remodeling.

Ni Q, Papoian GA.

Cytoskeleton (Hoboken). 2019 Sep 16. doi: 10.1002/cm.21564. [Epub ahead of print]

PMID:
31525282
3.

Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling.

Chandrasekaran A, Upadhyaya A, Papoian GA.

PLoS Comput Biol. 2019 Jul 9;15(7):e1007156. doi: 10.1371/journal.pcbi.1007156. eCollection 2019 Jul.

4.

Quantifying dissipation in actomyosin networks.

Floyd C, Papoian GA, Jarzynski C.

Interface Focus. 2019 Jun 6;9(3):20180078. doi: 10.1098/rsfs.2018.0078. Epub 2019 Apr 19.

5.

The Oligomerization Landscape of Histones.

Zhao H, Winogradoff D, Dalal Y, Papoian GA.

Biophys J. 2019 May 21;116(10):1845-1855. doi: 10.1016/j.bpj.2019.03.021. Epub 2019 Apr 17.

PMID:
31005236
6.

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.

Wu H, Wolynes PG, Papoian GA.

J Phys Chem B. 2018 Dec 13;122(49):11115-11125. doi: 10.1021/acs.jpcb.8b05791. Epub 2018 Aug 9.

7.

Internal modifications in the CENP-A nucleosome modulate centromeric dynamics.

Bui M, Pitman M, Nuccio A, Roque S, Donlin-Asp PG, Nita-Lazar A, Papoian GA, Dalal Y.

Epigenetics Chromatin. 2017 Apr 4;10:17. doi: 10.1186/s13072-017-0124-6. eCollection 2017.

8.

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.

Avdoshenko SM, Das A, Satija R, Papoian GA, Makarov DE.

Sci Rep. 2017 Mar 21;7(1):269. doi: 10.1038/s41598-017-00287-5.

9.

Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.

Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian GA.

J Am Chem Soc. 2016 Oct 12;138(40):13207-13218. Epub 2016 Aug 12.

PMID:
27454815
10.

Exploring the Free Energy Landscape of Nucleosomes.

Zhang B, Zheng W, Papoian GA, Wolynes PG.

J Am Chem Soc. 2016 Jul 6;138(26):8126-33. doi: 10.1021/jacs.6b02893. Epub 2016 Jun 27.

PMID:
27300314
11.

Steric Effects Induce Geometric Remodeling of Actin Bundles in Filopodia.

Dobramysl U, Papoian GA, Erban R.

Biophys J. 2016 May 10;110(9):2066-75. doi: 10.1016/j.bpj.2016.03.013.

12.

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks.

Popov K, Komianos J, Papoian GA.

PLoS Comput Biol. 2016 Apr 27;12(4):e1004877. doi: 10.1371/journal.pcbi.1004877. eCollection 2016 Apr.

13.

Stochastic Resonance in Protein Folding Dynamics.

Davtyan A, Platkov M, Gruebele M, Papoian GA.

Chemphyschem. 2016 May 4;17(9):1305-13. doi: 10.1002/cphc.201501125. Epub 2016 Apr 28.

PMID:
26992148
14.

Environmental Fluctuations and Stochastic Resonance in Protein Folding.

Dave K, Davtyan A, Papoian GA, Gruebele M, Platkov M.

Chemphyschem. 2016 May 4;17(9):1341-8. doi: 10.1002/cphc.201501041. Epub 2016 Jan 20.

15.

Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome.

Winogradoff D, Zhao H, Dalal Y, Papoian GA.

Sci Rep. 2015 Nov 25;5:17038. doi: 10.1038/srep17038.

16.

The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects.

Winogradoff D, Echeverria I, Potoyan DA, Papoian GA.

J Am Chem Soc. 2015 May 20;137(19):6245-53. doi: 10.1021/jacs.5b00235. Epub 2015 May 8.

PMID:
25905561
17.

DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.

Echeverria I, Papoian GA.

PLoS Comput Biol. 2015 Feb 12;11(2):e1003980. doi: 10.1371/journal.pcbi.1003980. eCollection 2015 Feb.

18.

Concerted dihedral rotations give rise to internal friction in unfolded proteins.

Echeverria I, Makarov DE, Papoian GA.

J Am Chem Soc. 2014 Jun 18;136(24):8708-13. doi: 10.1021/ja503069k. Epub 2014 Jun 4.

PMID:
24844314
19.

Capsid deformations reveal complex mechano-chemistry.

Popov KI, Papoian GA.

Biophys J. 2013 Nov 19;105(10):2233-4. doi: 10.1016/j.bpj.2013.09.055. No abstract available.

20.

Molecular transport modulates the adaptive response of branched actin networks to an external force.

Hu L, Papoian GA.

J Phys Chem B. 2013 Oct 24;117(42):13388-96. doi: 10.1021/jp405179e. Epub 2013 Sep 5.

PMID:
23962335
21.

Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia.

Erban R, Flegg MB, Papoian GA.

Bull Math Biol. 2014 Apr;76(4):799-818. doi: 10.1007/s11538-013-9844-3. Epub 2013 May 3.

PMID:
23640574
22.

Interfacial energy conversion in Ru(II) polypyridyl-derivatized oligoproline assemblies on TiO2.

Ma D, Bettis SE, Hanson K, Minakova M, Alibabaei L, Fondrie W, Ryan DM, Papoian GA, Meyer TJ, Waters ML, Papanikolas JM.

J Am Chem Soc. 2013 Apr 10;135(14):5250-3. doi: 10.1021/ja312143h. Epub 2013 Mar 26.

PMID:
23514453
23.

Predictive energy landscapes for protein-protein association.

Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19244-9. doi: 10.1073/pnas.1216215109. Epub 2012 Nov 5.

24.

Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation.

Potoyan DA, Papoian GA.

Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17857-62. doi: 10.1073/pnas.1201805109. Epub 2012 Sep 17.

25.

Theory of active transport in filopodia and stereocilia.

Zhuravlev PI, Lan Y, Minakova MS, Papoian GA.

Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10849-54. doi: 10.1073/pnas.1200160109. Epub 2012 Jun 18.

26.

Tunable energy transfer rates via control of primary, secondary, and tertiary structure of a coiled coil peptide scaffold.

Wilger DJ, Bettis SE, Materese CK, Minakova M, Papoian GA, Papanikolas JM, Waters ML.

Inorg Chem. 2012 Nov 5;51(21):11324-38. doi: 10.1021/ic300669t. Epub 2012 Jun 8.

PMID:
22679929
27.

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing.

Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA.

J Phys Chem B. 2012 Jul 26;116(29):8494-503. doi: 10.1021/jp212541y. Epub 2012 May 10.

28.

Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations.

Potoyan DA, Zhuravlev PI, Papoian GA.

J Phys Chem B. 2012 Feb 9;116(5):1709-15. doi: 10.1021/jp209980b. Epub 2012 Jan 26.

PMID:
22212071
29.

Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?

Savelyev A, Materese CK, Papoian GA.

J Am Chem Soc. 2011 Dec 7;133(48):19290-3. doi: 10.1021/ja207984z. Epub 2011 Nov 11.

PMID:
22039974
30.
31.

How does the antagonism between capping and anti-capping proteins affect actin network dynamics?

Hu L, Papoian GA.

J Phys Condens Matter. 2011 Sep 21;23(37):374101. doi: 10.1088/0953-8984/23/37/374101. Epub 2011 Aug 23.

PMID:
21862844
32.

Nonequilibrium water transport in a nonionic microemulsion system.

Minakova M, Savelyev A, Papoian GA.

J Phys Chem B. 2011 May 26;115(20):6503-8. doi: 10.1021/jp201431u. Epub 2011 Apr 29.

PMID:
21528855
33.

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics.

Potoyan DA, Papoian GA.

J Am Chem Soc. 2011 May 18;133(19):7405-15. doi: 10.1021/ja1111964. Epub 2011 Apr 25.

PMID:
21517079
34.

Chemically accurate coarse graining of double-stranded DNA.

Savelyev A, Papoian GA.

Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20340-5. doi: 10.1073/pnas.1001163107. Epub 2010 Nov 8.

35.

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

Zhuravlev PI, Papoian GA.

Q Rev Biophys. 2010 Aug;43(3):295-332. doi: 10.1017/S0033583510000119. Epub 2010 Sep 7. Review.

PMID:
20819242
36.

Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice?

Oklejas V, Zong C, Papoian GA, Wolynes PG.

Methods. 2010 Sep;52(1):84-90. doi: 10.1016/j.ymeth.2010.05.006. Epub 2010 May 26.

37.

Computing free energies of protein conformations from explicit solvent simulations.

Zhuravlev PI, Wu S, Potoyan DA, Rubinstein M, Papoian GA.

Methods. 2010 Sep;52(1):115-21. doi: 10.1016/j.ymeth.2010.05.003. Epub 2010 May 20.

38.

Design of active transport must be highly intricate: a possible role of myosin and Ena/VASP for G-actin transport in filopodia.

Zhuravlev PI, Der BS, Papoian GA.

Biophys J. 2010 Apr 21;98(8):1439-48. doi: 10.1016/j.bpj.2009.12.4325.

39.

Mechano-chemical feedbacks regulate actin mesh growth in lamellipodial protrusions.

Hu L, Papoian GA.

Biophys J. 2010 Apr 21;98(8):1375-84. doi: 10.1016/j.bpj.2009.11.054.

40.

Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations.

Tanaka N, Papoian GA.

J Theor Biol. 2010 May 21;264(2):490-500. doi: 10.1016/j.jtbi.2010.02.022. Epub 2010 Feb 18.

PMID:
20171230
41.

Functional versus folding landscapes: the same yet different.

Zhuravlev PI, Papoian GA.

Curr Opin Struct Biol. 2010 Feb;20(1):16-22. doi: 10.1016/j.sbi.2009.12.010. Epub 2010 Jan 25. Review.

PMID:
20102791
42.

Counterion atmosphere and hydration patterns near a nucleosome core particle.

Materese CK, Savelyev A, Papoian GA.

J Am Chem Soc. 2009 Oct 21;131(41):15005-13. doi: 10.1021/ja905376q.

PMID:
19778017
43.

Molecular noise of capping protein binding induces macroscopic instability in filopodial dynamics.

Zhuravlev PI, Papoian GA.

Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11570-5. doi: 10.1073/pnas.0812746106. Epub 2009 Jun 25.

44.

Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins.

Zhuravlev PI, Materese CK, Papoian GA.

J Phys Chem B. 2009 Jul 2;113(26):8800-12. doi: 10.1021/jp810659u.

PMID:
19453123
45.

Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

Savelyev A, Papoian GA.

Biophys J. 2009 May 20;96(10):4044-52. doi: 10.1016/j.bpj.2009.02.067.

46.

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

Savelyev A, Papoian GA.

J Phys Chem B. 2009 Jun 4;113(22):7785-93. doi: 10.1021/jp9005058.

PMID:
19425537
47.

Elimination of fast variables in chemical Langevin equations.

Lan Y, Elston TC, Papoian GA.

J Chem Phys. 2008 Dec 7;129(21):214115. doi: 10.1063/1.3027499.

48.

High resolution approach to the native state ensemble kinetics and thermodynamics.

Wu S, Zhuravlev PI, Papoian GA.

Biophys J. 2008 Dec 15;95(12):5524-32. doi: 10.1529/biophysj.108.136697. Epub 2008 Sep 19.

49.

Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm.

Papoian GA.

Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14237-8. doi: 10.1073/pnas.0807977105. Epub 2008 Sep 17. No abstract available.

50.

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

Materese CK, Goldmon CC, Papoian GA.

Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10659-64. doi: 10.1073/pnas.0801850105. Epub 2008 Jul 29.

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