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Items: 1 to 50 of 232

1.

Local frustration around enzyme active sites.

Freiberger MI, Guzovsky AB, Wolynes PG, Parra RG, Ferreiro DU.

Proc Natl Acad Sci U S A. 2019 Feb 14. pii: 201819859. doi: 10.1073/pnas.1819859116. [Epub ahead of print]

PMID:
30765513
2.

Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer.

Lu W, Schafer NP, Wolynes PG.

Nat Commun. 2018 Nov 23;9(1):4949. doi: 10.1038/s41467-018-07320-9.

3.

Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.

Chen M, Lin X, Lu W, Schafer NP, Onuchic JN, Wolynes PG.

J Chem Theory Comput. 2018 Nov 13;14(11):6102-6116. doi: 10.1021/acs.jctc.8b00683. Epub 2018 Oct 8.

PMID:
30240202
4.

Surveying the Energy Landscapes of Aβ Fibril Polymorphism.

Chen M, Schafer NP, Wolynes PG.

J Phys Chem B. 2018 Oct 1. doi: 10.1021/acs.jpcb.8b07364. [Epub ahead of print]

PMID:
30215519
5.

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

Wu H, Wolynes PG, Papoian GA.

J Phys Chem B. 2018 Aug 9. doi: 10.1021/acs.jpcb.8b05791. [Epub ahead of print]

PMID:
30091924
6.

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes.

Di Pierro M, Potoyan DA, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):7753-7758. doi: 10.1073/pnas.1806297115. Epub 2018 Jul 9.

7.

Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs).

Wang Z, Potoyan DA, Wolynes PG.

BMC Syst Biol. 2018 Jan 30;12(1):4. doi: 10.1186/s12918-018-0525-6.

8.

Stochastic dynamics of genetic broadcasting networks.

Potoyan DA, Wolynes PG.

Phys Rev E. 2017 Nov;96(5-1):052305. doi: 10.1103/PhysRevE.96.052305. Epub 2017 Nov 3.

9.

Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm.

Wang Z, Potoyan DA, Wolynes PG.

J R Soc Interface. 2018 Jan;15(138). pii: 20170809. doi: 10.1098/rsif.2017.0809.

10.

The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)-Amylometer: Predicting Amyloid Propensity and Fibril Topology Using an Optimized Folding Landscape Model.

Chen M, Schafer NP, Zheng W, Wolynes PG.

ACS Chem Neurosci. 2018 May 16;9(5):1027-1039. doi: 10.1021/acschemneuro.7b00436. Epub 2018 Jan 10.

PMID:
29241326
11.

Aging, Jamming, and the Limits of Stability of Amorphous Solids.

Lubchenko V, Wolynes PG.

J Phys Chem B. 2018 Apr 5;122(13):3280-3295. doi: 10.1021/acs.jpcb.7b09553. Epub 2018 Jan 9.

12.

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors.

Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG.

J Am Chem Soc. 2017 Dec 27;139(51):18558-18566. doi: 10.1021/jacs.7b08741. Epub 2017 Dec 15.

13.

Frustration, function and folding.

Ferreiro DU, Komives EA, Wolynes PG.

Curr Opin Struct Biol. 2018 Feb;48:68-73. doi: 10.1016/j.sbi.2017.09.006. Epub 2017 Nov 5. Review.

14.

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12126-12131. doi: 10.1073/pnas.1714980114. Epub 2017 Oct 31.

15.

Theory, simulations, and experiments show that proteins fold by multiple pathways.

Eaton WA, Wolynes PG.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9759-E9760. doi: 10.1073/pnas.1716444114. Epub 2017 Oct 30. No abstract available.

16.

Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40).

Zheng W, Tsai MY, Wolynes PG.

J Am Chem Soc. 2017 Nov 22;139(46):16666-16676. doi: 10.1021/jacs.7b08089. Epub 2017 Nov 7.

17.

Protein structure prediction: making AWSEM AWSEM-ER by adding evolutionary restraints.

Sirovetz BJ, Schafer NP, Wolynes PG.

Proteins. 2017 Nov;85(11):2127-2142. doi: 10.1002/prot.25367. Epub 2017 Aug 27.

18.

Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease.

Chen M, Wolynes PG.

Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4406-4411. doi: 10.1073/pnas.1702237114. Epub 2017 Apr 11.

19.

Dynamical theory of shear bands in structural glasses.

Wisitsorasak A, Wolynes PG.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):1287-1292. doi: 10.1073/pnas.1620399114. Epub 2017 Jan 20.

20.

Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.

Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG.

J Phys Chem B. 2017 Apr 20;121(15):3473-3482. doi: 10.1021/acs.jpcb.6b09347. Epub 2016 Nov 11.

21.

Exploring the aggregation free energy landscape of the amyloid-β protein (1-40).

Zheng W, Tsai MY, Chen M, Wolynes PG.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11835-11840. Epub 2016 Oct 3.

22.

Transferable model for chromosome architecture.

Di Pierro M, Zhang B, Aiden EL, Wolynes PG, Onuchic JN.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12168-12173. Epub 2016 Sep 29.

23.

The Aggregation Free Energy Landscapes of Polyglutamine Repeats.

Chen M, Tsai M, Zheng W, Wolynes PG.

J Am Chem Soc. 2016 Nov 23;138(46):15197-15203. Epub 2016 Nov 10.

24.

Genomic Energy Landscapes.

Zhang B, Wolynes PG.

Biophys J. 2017 Feb 7;112(3):427-433. doi: 10.1016/j.bpj.2016.08.046. Epub 2016 Sep 30. Review.

25.

Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA.

Tsai MY, Zhang B, Zheng W, Wolynes PG.

J Am Chem Soc. 2016 Oct 5. [Epub ahead of print]

26.

Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network.

Wang Z, Potoyan DA, Wolynes PG.

J R Soc Interface. 2016 Sep;13(122). pii: 20160606. Epub 2016 Sep 28.

27.

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome.

Zhang B, Wolynes PG.

Phys Rev Lett. 2016 Jun 17;116(24):248101. doi: 10.1103/PhysRevLett.116.248101. Epub 2016 Jun 14.

PMID:
27367409
28.

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
29.

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

Chen M, Lin X, Zheng W, Onuchic JN, Wolynes PG.

J Phys Chem B. 2016 Aug 25;120(33):8557-65. doi: 10.1021/acs.jpcb.6b02451. Epub 2016 May 13.

30.

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Parra RG, Schafer NP, Radusky LG, Tsai MY, Guzovsky AB, Wolynes PG, Ferreiro DU.

Nucleic Acids Res. 2016 Jul 8;44(W1):W356-60. doi: 10.1093/nar/gkw304. Epub 2016 Apr 29.

31.

PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites.

Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA.

J Phys Chem B. 2016 Aug 25;120(33):8532-8. doi: 10.1021/acs.jpcb.6b02359. Epub 2016 May 3.

32.

Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory.

Chen M, Zheng W, Wolynes PG.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):5006-11. doi: 10.1073/pnas.1602702113. Epub 2016 Apr 18.

33.

Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα.

Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA.

Biophys J. 2016 Feb 23;110(4):887-95. doi: 10.1016/j.bpj.2016.01.001.

34.

Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease.

Schafer NP, Truong HH, Otzen DE, Lindorff-Larsen K, Wolynes PG.

Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2098-103. doi: 10.1073/pnas.1524027113. Epub 2016 Feb 8.

35.

Predictive energy landscapes for folding membrane protein assemblies.

Truong HH, Kim BL, Schafer NP, Wolynes PG.

J Chem Phys. 2015 Dec 28;143(24):243101. doi: 10.1063/1.4929598.

36.

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network.

Potoyan DA, Zheng W, Komives EA, Wolynes PG.

Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):110-5. doi: 10.1073/pnas.1520483112. Epub 2015 Dec 23.

37.

Dichotomous noise models of gene switches.

Potoyan DA, Wolynes PG.

J Chem Phys. 2015 Nov 21;143(19):195101. doi: 10.1063/1.4935572.

38.

On the hydrodynamics of swimming enzymes.

Bai X, Wolynes PG.

J Chem Phys. 2015 Oct 28;143(16):165101. doi: 10.1063/1.4933424.

PMID:
26520553
39.

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

Tsai MY, Zheng W, Balamurugan D, Schafer NP, Kim BL, Cheung MS, Wolynes PG.

Protein Sci. 2016 Jan;25(1):255-69. doi: 10.1002/pro.2751. Epub 2015 Aug 8.

40.

Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature-Pressure Plane.

Sirovetz BJ, Schafer NP, Wolynes PG.

J Phys Chem B. 2015 Aug 27;119(34):11416-27. doi: 10.1021/acs.jpcb.5b03828. Epub 2015 Jul 9.

PMID:
26102155
41.

Topology, structures, and energy landscapes of human chromosomes.

Zhang B, Wolynes PG.

Proc Natl Acad Sci U S A. 2015 May 12;112(19):6062-7. doi: 10.1073/pnas.1506257112. Epub 2015 Apr 27.

42.

Evolution, energy landscapes and the paradoxes of protein folding.

Wolynes PG.

Biochimie. 2015 Dec;119:218-30. doi: 10.1016/j.biochi.2014.12.007. Epub 2014 Dec 18. Review.

43.

Learning To Fold Proteins Using Energy Landscape Theory.

Schafer NP, Kim BL, Zheng W, Wolynes PG.

Isr J Chem. 2014 Aug;54(8-9):1311-1337.

44.

Frustration in biomolecules.

Ferreiro DU, Komives EA, Wolynes PG.

Q Rev Biophys. 2014 Nov;47(4):285-363. doi: 10.1017/S0033583514000092. Epub 2014 Sep 16. Review.

45.

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection.

Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12408-13. doi: 10.1073/pnas.1413575111. Epub 2014 Aug 11.

46.

Predictive energy landscapes for folding α-helical transmembrane proteins.

Kim BL, Schafer NP, Wolynes PG.

Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11031-6. doi: 10.1073/pnas.1410529111. Epub 2014 Jul 16.

47.

Stem cell differentiation as a many-body problem.

Zhang B, Wolynes PG.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10185-90. doi: 10.1073/pnas.1408561111. Epub 2014 Jun 19.

48.

Dynamical heterogeneity of the glassy state.

Wisitsorasak A, Wolynes PG.

J Phys Chem B. 2014 Jul 17;118(28):7835-47. doi: 10.1021/jp4125777. Epub 2014 Jun 2.

PMID:
24811573
49.

A second molecular biology revolution? The energy landscapes of biomolecular function.

Nussinov R, Wolynes PG.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6321-2. doi: 10.1039/c4cp90027h. Epub 2014 Mar 10. No abstract available.

PMID:
24608340
50.

On the dephasing of genetic oscillators.

Potoyan DA, Wolynes PG.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2391-6. doi: 10.1073/pnas.1323433111. Epub 2014 Jan 27.

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