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Items: 26

1.

Oleuropein derivatives from olive fruit extracts reduce α-synuclein fibrillation and oligomer toxicity.

Mohammad-Beigi H, Aliakbari F, Sahin C, Lomax C, Tawfike A, Schafer NP, Amiri-Nowdijeh A, Eskandari H, Møller IM, Hosseini-Mazinani M, Christiansen G, Ward JL, Morshedi D, Otzen DE.

J Biol Chem. 2019 Jan 17. pii: jbc.RA118.005723. doi: 10.1074/jbc.RA118.005723. [Epub ahead of print]

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.

Uncovering the molecular mechanisms behind disease-associated leptin variants.

Haglund E, Nguyen L, Schafer NP, Lammert H, Jennings PA, Onuchic JN.

J Biol Chem. 2018 Aug 17;293(33):12919-12933. doi: 10.1074/jbc.RA118.003957. Epub 2018 Jun 27.

PMID:
29950524
6.

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer.

Lin X, Roy S, Jolly MK, Bocci F, Schafer NP, Tsai MY, Chen Y, He Y, Grishaev A, Weninger K, Orban J, Kulkarni P, Rangarajan G, Levine H, Onuchic JN.

J Mol Biol. 2018 Aug 3;430(16):2422-2438. doi: 10.1016/j.jmb.2018.05.011. Epub 2018 Jun 5.

PMID:
29758263
7.

Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain.

Stenvang M, Schafer NP, Malmos KG, Pérez AW, Niembro O, Sormanni P, Basaiawmoit RV, Christiansen G, Andreasen M, Otzen DE.

J Mol Biol. 2018 Apr 13;430(8):1116-1140. doi: 10.1016/j.jmb.2018.03.001. Epub 2018 Mar 7.

PMID:
29524512
8.

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
9.

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.

10.

The transcriptional regulator GalR self-assembles to form highly regular tubular structures.

Agerschou ED, Christiansen G, Schafer NP, Madsen DJ, Brodersen DE, Semsey S, Otzen DE.

Sci Rep. 2016 Jun 9;6:27672. doi: 10.1038/srep27672.

11.

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.

12.

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.

13.

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.

14.

Biophysical characterization and modeling of human Ecdysoneless (ECD) protein supports a scaffolding function.

Mir RA, Lovelace J, Schafer NP, Simone PD, Kellezi A, Kolar C, Spagnol G, Sorgen PL, Band H, Band V, Borgstahl GEO.

AIMS Biophys. 2016;3(1):195-208. doi: 10.3934/biophy.2016.1.195. Epub 2016 Mar 9.

15.

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.

16.

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
17.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops.

Paslawski W, Lillelund OK, Kristensen JV, Schafer NP, Baker RP, Urban S, Otzen DE.

Proc Natl Acad Sci U S A. 2015 Jun 30;112(26):7978-83. doi: 10.1073/pnas.1424751112. Epub 2015 Jun 8.

18.

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.

19.

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.

20.

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.

21.

Free energy landscapes for initiation and branching of protein aggregation.

Zheng W, Schafer NP, Wolynes PG.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20515-20. doi: 10.1073/pnas.1320483110. Epub 2013 Nov 27.

22.

Funneling and frustration in the energy landscapes of some designed and simplified proteins.

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

J Chem Phys. 2013 Sep 28;139(12):121908. doi: 10.1063/1.4813504.

23.

Frustration in the energy landscapes of multidomain protein misfolding.

Zheng W, Schafer NP, Wolynes PG.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1680-5. doi: 10.1073/pnas.1222130110. Epub 2013 Jan 14.

24.

Discrete kinetic models from funneled energy landscape simulations.

Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG.

PLoS One. 2012;7(12):e50635. doi: 10.1371/journal.pone.0050635. Epub 2012 Dec 12. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/16c11a12-4245-403c-80ab-e6662baf16cd.

25.

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.

26.

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.

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