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UBC Logo Steven Samuel Plotkin, Associate Professor at UBC
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We do research at the interface of physics and biology. Our interests range from the study of dynamics and disorder in the theory of protein folding, misfolding, and aggregation, to DNA function and dynamics, to studies of pattern formation and symmetry breaking in morphogenesis.
Silverman JM, Gibbs E, Martens KM, Balducci C, Peng X, Wang J, Yousefi M, Cowan CM, Lamour G, Louadi A, Ban Y, Robert J, Stukas S, Forloni G, Hsiung GR, Plotkin SS, Wellington CL and Cashman NR "A Synaptotoxic Aβ Oligomer Subclass Epitope Defined by Differential Orientation of a Single Amino Acid Side Chain," Submitted August 2017  
Habibi M, Plotkin SS, and Rottler J "Soft Vibrational Modes Predict Force-induced Protein Unfolding Mechanisms" Accepted, Biophysical Journal (2017)  

Peng X, Gibbs, E, Silverman JM, Cashman NR, and Plotkin SS, "A Method for Systematically Screening Drug Candidates Using Multiple Criteria with Unknown Predictive Importance" Submitted (2017)

 

Habibi M, Rottler J, and Plotkin SS "The Unfolding Mechanism of Monomeric Mutant SOD1 by Simulated Force Spectroscopy", Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, https://doi.org/10.1016/j.bbapap.2017.06.009 (2017)

 

Habibi M, Rottler J, and Plotkin SS "As Simple as Possible but not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy", PLoS Comput Biol 12(11): e1005211. doi:10.1371/journal. pcbi.1005211 (2016)

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"Epitopes in amyloid beta and conformationally-selective antibodies thereto" Inventors: Steven S Plotkin and Neil R Cashman, Provisional Patent 62/393,615 Filed Sept 14, 2016.

 

"Epitopes in Amyloid beta and conformationally-selective antibodies thereto" Inventors: Steven S Plotkin and Neil R Cashman, Provisional Patent 62/365,634. Filed July 22, 2016.

 

"C-terminal epitopes in Amyloid beta and conformationally-selective antibodies thereto" Inventors: Steven S Plotkin and Neil R Cashman, Provisional Patent 62/352,346. Filed June 20, 2016.

 
"N-terminal epitopes in Amyloid beta and conformationally-selective antibodies thereto" Inventors: Steven S Plotkin and Neil R Cashman, Provisional Patent # 62/331,925, Filed May 11, 2016.  
"Epitopes in Amyloid beta and antibodies thereto" Inventors: Steven S Plotkin and Neil R Cashman, .Provisional Patent # 62/309,765, Filed March 17, 2016  
"Amyloid beta epitopes and antibodies thereto" Inventors: Steven S. Plotkin and Neil Cashman, Provisional Patent # 62/289893, Filing date: Filed February 1, 2016  
"Systems and Methods for Predicting Misfolded Protein Epitopes by Collective Coordinate Biasing" Inventor: Steven S. Plotkin, Provisional Patent Application # 62/253044, Filed November 9, 2015  
Mills EA, Plotkin SS "Protein Transfer Free Energy Obeys Entropy-Enthalpy Compensation"  J. Phys. Chem. B.119 (44), pp14130–14144 (2015). http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b09219  PDF

Grad LI, et al "Intercellular propagated misfolding of wild-type Cu/Zn superoxide dismutase occurs via exosome-dependent and -independent mechanisms" Proc. Natl. Acad. Sci. USA 111, 3620-3625 (2014) http://www.pnas.org/content/111/9/3620.full.pdf+html?with-ds=yes

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Chen S, Witt DM, Plotkin SS "Quantizing models of (2+1)-dimensional gravity on non-orientable manifolds" Classical Quant. Grav. 31 (2014) 055008

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Mills EA and Plotkin SS "Density Functional Theory for Protein Transfer Free Energies" J. Phys. Chem. B (2013) 117 (42) 13278–13290, DOI: 10.1021/jp403600q http://pubs.acs.org/doi/abs/10.1021/jp403600q?prevSearch=plotkin&searchHistoryKey=

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Das A, Sin BK, Mohazab AR, and Plotkin SS  "Unfolded protein ensembles, folding trajectories, and refolding rate prediction" J. Chem. Phys. 139, 121925 (2013) http://jcp.aip.org/resource/1/jcpsa6/v139/i12/p121925_s1 PDF

Mohazab AR, Plotkin SS "Polymer Uncrossing and Knotting in Protein Folding, and Their Role in Minimal Folding Pathways" PLoS ONE 8(1): e53642 (2013). doi:10.1371/journal.pone.0053642

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Das A, Plotkin SS "Mechanical Probes of SOD1 Predict Systematic Trends in Metal and Dimer Affinity of ALS-Associated Mutants" J. Mol. Biol. 425, 850–874 (2013)

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Das A, Plotkin SS "SOD1 Exhibits Allosteric Frustration to Facilitate Metal Binding Affinity" Proc. Natl. Acad. Sci. USA 110, 3871 (2013)
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Chen S, Plotkin SS "Statistical Mechanics of Graph Models and their Implications for Emergent Spacetime Manifolds" Phys Rev D 87, 084011 (2013)

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Grad LI, Guest W, Yanai A, Pokrishevsky E, O’Neill MA, Gibbs E, Semenchenko V, Yousefi M, Wishart DS, Plotkin SS, Cashman NR, "Intermolecular Transmission of Superoxide Dismutase 1 Misfolding in Living Cells" Proc. Natl. Acad. Sci, 108, 16398–16403 (2011) (with supp mat)

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Hadizadeh S, Linhananta A, Plotkin SS, "Improved Measures for the Shape of a Disordered Polymer to Test a Mean-field Theory of Collapse" Macromolecules, 44, 6182–6197 (2011) (with supp mat) PDF
Guest W, Cashman NR, Plotkin SS, "A Theory for the Anisotropic and Inhomogeneous Dielectric Properties of Proteins" Phys. Chem. Chem. Phys., 13 (13), 6286 - 6295 (2011) PDF

Linhananta A, Hadizadeh S, Plotkin SS, "An Effective Solvent Theory Connecting the Underlying Mechanisms of Osmolytes and Denaturants for Protein Stability" Biophys J.100, 459–468 (2011) Supplemental material is here.

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Guest W, Plotkin SS, Cashman NR, "Toward A Mechanism of Prion Misfolding and Structural Models of PrPSc: Current Knowledge and Future Directions", J Toxicol Env Health Part A, 74:154–160 (2011) PDF

"Methods and Systems for Determining Localized Dielectric Properties of a Molecule" Inventors: William C. Guest, Neil R. Cashman, Steven S. Plotkin, Application #: 12/952,140  Publication #: US 2011/0125478 A1, Patent Filing date: Nov 22, 2010, Pub. Date: May 26, 2011.

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Guest W, Cashman NR, Plotkin SS, "Electrostatics in the Stability and Misfolding of the Prion Protein: Salt Bridges, Self-Energy, and Solvation" Biochem. Cell Biol 88, 371–381 (2010) Supplementary material is here. PDF
Morriss-Andrews A, Rottler J, Plotkin SS, "A Systematically Coarse-grained Model for DNA, and its Predictions for Persistence Length, Stacking, Twist, and Chirality" J Chem Phys 132, 035105 (2010) Supplementary material is here. PDF

"Methods and Systems for Predicting Misfolded Protein Epitopes" Inventors: Neil R. Cashman, Steven S. Plotkin, William C. Guest, Application #: 12/574,637, Publication #: US 2010/0233176 A1, Patent Filing date: Oct 6, 2009, Pub. Date: Sep. 16, 2010.

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Abrahamsson E, Plotkin SS, ”BioVEC: A Program for Biomolecule Visualization with Ellipsoidal Coarse-graining” J. Mol. Graph. Mod. 28, 140-145 (2009) [Supplementary Video] PDF
Mohazab AR, Plotkin SS, "Structural Alignment using the Generalized Euclidean Distance Between Conformations" Int. J. Quant. Chem. 109, 3217–3228 (2009) PDF
Li L, Guest W, Huang A, Plotkin SS, Cashman N, "Immunological Mimicry of PrPc-PrPSc Interactions: Antibody-Induced PrP Misfolding" Protein Engineering, Design and Selection 22(8):523-529 (2009) PDF
Mohazab AR, Plotkin SS, "Minimal Folding Pathways for Coarse-grained Biopolymer Fragments" Biophys J, 95 (12) 5496 (2008) PDF
Mohazab AR, Plotkin SS, “Minimal Distance Transformations Between Links and Polymers: Principles and Applications” J. Phys Condens Mat 20 (24) 244133 (2008)
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Plotkin SS, "Generalization of Distance to Higher Dimensional Objects" Proc. Natl. Acad. Sci. 104, 14899 (2007) PDF
Plotkin SS, "Determination of Barrier Heights and Prefactors from Protein Folding Rate Data" Biophys J. 88, (6) (2005) PDF
Oztop B, Ejtehadi MR, Plotkin SS, "Protein Folding Rates Correlate with Heterogeneity of Folding Mechanism" Phys. Rev. Lett. 93, 208105 (2004) (Experimental references) PDF
Ejtehadi MR, Avall SP, Plotkin SS, "Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models" Proc. Natl. Acad. Sci. 101, 15088-15093 (2004) PDF
Clementi C, Plotkin SS, "The Effects of Non-native Interactions on Protein Folding Rates: Theory and Simulation" Prot. Sci. 13, 1750-1765 (2004)

The appendices to this paper were converted into electronic supplementary material for some reason. Unfortunately 2 figures were lost during this conversion. Here they are: figure 11 and figure 12

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Plotkin SS, Wolynes PG, "Buffed Energy Landscapes: Another Solution to the Kinetic Paradoxes of Protein Folding" Proc. Natl. Acad. Sci. 100, (8) 4417-4422 (2003) PDF
Plotkin SS, Onuchic JN, "Understanding Protein Folding with Energy Landscape Theory II: Quantitative Aspects" Quart. Rev. Biophys. 35, 205-286 (2002) PDF
Plotkin SS, Onuchic JN, "Understanding Protein Folding with Energy Landscape Theory, Part I: Basic Concepts" Quart. Rev. Biophys. 35, 111-167 (2002) PDF
Plotkin SS, Onuchic JN, ``Structural and Energetic Heterogeneity in Protein Folding I: Theory'' J. Chem. Phys. 116 (12), 5263-5283 (2002) PDF
Plotkin SS, "Speeding Protein Folding Beyond the Go Model: How a Little Frustration Sometimes Helps" Proteins: Structure, Function, Genetics 45 (4), 337-345 (2001) PDF
Plotkin SS, Onuchic JN, "Investigation of Routes and Funnels in Protein Folding by Free Energy Functional Methods" Proc Natl Acad Sci 97 (12): 6509-6514 (2000) PDF
Plotkin SS, Wolynes PG, "Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding" Phys Rev Lett 80 (22): 5015-5018 (1998) PDF
Plotkin SS, Wang J, Wolynes PG, "Statistical Mechanics of Correlated Energy Landscape Models for Random Heteropolymers and Proteins" Physica D 107 (2-4): 322-325 (1997) PDF
Wang J, Plotkin SS, Wolynes PG "Configurational Diffusion on a Locally Connected Correlated Energy Landscape; Application to Finite, Random Heteropolymers" Journal De Physique I 7 (3): 395-421 (1997) PDF
Plotkin SS, Wang J, Wolynes PG, "Statistical Mechanics of a Correlated Energy Landscape Model for Protein Folding Funnels" J Chem Phys 106 (7): 2932-2948 (1997) PDF
Plotkin SS, Wang J, Wolynes PG, "Correlated Energy Landscape Model for Finite, Random Heteropolymers" Phys Rev E 53 (6): 6271-6296 Part B (1996) PDF

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