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Items: 34

1.

CuATSM Protects Against the In Vitro Cytotoxicity of Wild-Type-Like Copper-Zinc Superoxide Dismutase Mutants but not Mutants That Disrupt Metal Binding.

Farrawell NE, Yerbury MR, Plotkin SS, McAlary L, Yerbury JJ.

ACS Chem Neurosci. 2019 Mar 20;10(3):1555-1564. doi: 10.1021/acschemneuro.8b00527. Epub 2018 Dec 7.

PMID:
30462490
2.

Prediction of Misfolding-Specific Epitopes in SOD1 Using Collective Coordinates.

Peng X, Cashman NR, Plotkin SS.

J Phys Chem B. 2018 Nov 5. doi: 10.1021/acs.jpcb.8b07680. [Epub ahead of print]

PMID:
30351123
3.

pH dependent membrane binding of the Solanum tuberosum plant specific insert: An in silico study.

Dupuis JH, Yu H, Habibi M, Peng X, Plotkin SS, Wang S, Song C, Yada RY.

Biochim Biophys Acta Biomembr. 2018 Dec;1860(12):2608-2618. doi: 10.1016/j.bbamem.2018.10.001. Epub 2018 Oct 3.

PMID:
30291921
4.

A Rational Structured Epitope Defines a Distinct Subclass of Toxic Amyloid-beta Oligomers.

Silverman JM, Gibbs E, Peng X, Martens KM, Balducci C, Wang J, Yousefi M, Cowan CM, Lamour G, Louadi S, Ban Y, Robert J, Stukas S, Forloni G, Hsiung GR, Plotkin SS, Wellington CL, Cashman NR.

ACS Chem Neurosci. 2018 Jul 18;9(7):1591-1606. doi: 10.1021/acschemneuro.7b00469. Epub 2018 Apr 16.

PMID:
29614860
5.

Soft Vibrational Modes Predict Breaking Events during Force-Induced Protein Unfolding.

Habibi M, Plotkin SS, Rottler J.

Biophys J. 2018 Feb 6;114(3):562-569. doi: 10.1016/j.bpj.2017.11.3781.

6.

The unfolding mechanism of monomeric mutant SOD1 by simulated force spectroscopy.

Habibi M, Rottler J, Plotkin SS.

Biochim Biophys Acta Proteins Proteom. 2017 Nov;1865(11 Pt B):1631-1642. doi: 10.1016/j.bbapap.2017.06.009. Epub 2017 Jun 16.

PMID:
28629863
7.

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.

Habibi M, Rottler J, Plotkin SS.

PLoS Comput Biol. 2016 Nov 29;12(11):e1005211. doi: 10.1371/journal.pcbi.1005211. eCollection 2016 Nov.

8.

Protein Transfer Free Energy Obeys Entropy-Enthalpy Compensation.

Mills EA, Plotkin SS.

J Phys Chem B. 2015 Nov 5;119(44):14130-44. doi: 10.1021/acs.jpcb.5b09219. Epub 2015 Oct 26.

PMID:
26423005
9.

Intercellular propagated misfolding of wild-type Cu/Zn superoxide dismutase occurs via exosome-dependent and -independent mechanisms.

Grad LI, Yerbury JJ, Turner BJ, Guest WC, Pokrishevsky E, O'Neill MA, Yanai A, Silverman JM, Zeineddine R, Corcoran L, Kumita JR, Luheshi LM, Yousefi M, Coleman BM, Hill AF, Plotkin SS, Mackenzie IR, Cashman NR.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3620-5. doi: 10.1073/pnas.1312245111. Epub 2014 Feb 18.

10.

Unfolded protein ensembles, folding trajectories, and refolding rate prediction.

Das A, Sin BK, Mohazab AR, Plotkin SS.

J Chem Phys. 2013 Sep 28;139(12):121925. doi: 10.1063/1.4817215.

PMID:
24089737
11.

Density functional theory for protein transfer free energy.

Mills EA, Plotkin SS.

J Phys Chem B. 2013 Oct 24;117(42):13278-90. doi: 10.1021/jp403600q. Epub 2013 Aug 14.

PMID:
23944753
12.

SOD1 exhibits allosteric frustration to facilitate metal binding affinity.

Das A, Plotkin SS.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3871-6. doi: 10.1073/pnas.1216597110. Epub 2013 Feb 19.

13.

Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways.

Mohazab AR, Plotkin SS.

PLoS One. 2013;8(1):e53642. doi: 10.1371/journal.pone.0053642. Epub 2013 Jan 24.

14.

Mechanical probes of SOD1 predict systematic trends in metal and dimer affinity of ALS-associated mutants.

Das A, Plotkin SS.

J Mol Biol. 2013 Mar 11;425(5):850-74. doi: 10.1016/j.jmb.2012.12.022. Epub 2013 Jan 3.

PMID:
23291526
15.

Intermolecular transmission of superoxide dismutase 1 misfolding in living cells.

Grad LI, Guest WC, Yanai A, Pokrishevsky E, O'Neill MA, Gibbs E, Semenchenko V, Yousefi M, Wishart DS, Plotkin SS, Cashman NR.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16398-403. doi: 10.1073/pnas.1102645108. Epub 2011 Sep 19.

16.

A theory for the anisotropic and inhomogeneous dielectric properties of proteins.

Guest WC, Cashman NR, Plotkin SS.

Phys Chem Chem Phys. 2011 Apr 7;13(13):6286-95. doi: 10.1039/c0cp02061c. Epub 2011 Feb 28.

PMID:
21359369
17.

An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability.

Linhananta A, Hadizadeh S, Plotkin SS.

Biophys J. 2011 Jan 19;100(2):459-68. doi: 10.1016/j.bpj.2010.11.087.

18.

Toward a mechanism of prion misfolding and structural models of PrP(Sc): current knowledge and future directions.

Guest WC, Plotkin SS, Cashman NR.

J Toxicol Environ Health A. 2011;74(2-4):154-60. doi: 10.1080/15287394.2011.529065. Review.

PMID:
21218344
19.

Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvation.

Guest WC, Cashman NR, Plotkin SS.

Biochem Cell Biol. 2010 Apr;88(2):371-81. doi: 10.1139/o09-180.

PMID:
20453937
20.

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality.

Morriss-Andrews A, Rottler J, Plotkin SS.

J Chem Phys. 2010 Jan 21;132(3):035105. doi: 10.1063/1.3269994.

PMID:
20095755
21.

Immunological mimicry of PrPC-PrPSc interactions: antibody-induced PrP misfolding.

Li L, Guest W, Huang A, Plotkin SS, Cashman NR.

Protein Eng Des Sel. 2009 Aug;22(8):523-9. doi: 10.1093/protein/gzp038. Epub 2009 Jul 14.

PMID:
19602568
22.

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

Abrahamsson E, Plotkin SS.

J Mol Graph Model. 2009 Sep;28(2):140-5. doi: 10.1016/j.jmgm.2009.05.001. Epub 2009 May 18.

PMID:
19515592
23.

Minimal folding pathways for coarse-grained biopolymer fragments.

Mohazab AR, Plotkin SS.

Biophys J. 2008 Dec 15;95(12):5496-507. doi: 10.1529/biophysj.108.135046. Epub 2008 Sep 26.

24.

Generalization of distance to higher dimensional objects.

Plotkin SS.

Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14899-904. Epub 2007 Sep 11.

25.

Determination of barrier heights and prefactors from protein folding rate data.

Plotkin SS.

Biophys J. 2005 Jun;88(6):3762-9. Epub 2005 Mar 11.

26.

Protein folding rates correlate with heterogeneity of folding mechanism.

Oztop B, Ejtehadi MR, Plotkin SS.

Phys Rev Lett. 2004 Nov 12;93(20):208105. Epub 2004 Nov 12.

PMID:
15600977
27.

Three-body interactions improve the prediction of rate and mechanism in protein folding models.

Ejtehadi MR, Avall SP, Plotkin SS.

Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15088-93. Epub 2004 Oct 6.

28.
29.

Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding.

Plotkin SS, Wolynes PG.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4417-22. Epub 2003 Apr 3.

30.

Understanding protein folding with energy landscape theory. Part II: Quantitative aspects.

Plotkin SS, Onuchic JN.

Q Rev Biophys. 2002 Aug;35(3):205-86. Review. No abstract available.

PMID:
12599750
31.

Understanding protein folding with energy landscape theory. Part I: Basic concepts.

Plotkin SS, Onuchic JN.

Q Rev Biophys. 2002 May;35(2):111-67. Review. No abstract available.

PMID:
12197302
32.
33.

Investigation of routes and funnels in protein folding by free energy functional methods.

Plotkin SS, Onuchic JN.

Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6509-14.

34.

Correlated energy landscape model for finite, random heteropolymers.

Plotkin SS, Wang J, Wolynes PG.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Jun;53(6):6271-6296. No abstract available.

PMID:
9964988

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