 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. | |
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) | |
| 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) | |
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) | |
| "Methods and Systems for Determining Localized Dielectric Properties of a Molecule" Inventors: Guest, Cashman, Plotkin, Application: PCT 12/952,140 (Provisional patent filed Nov 2010) | |
| 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. | |
| 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. | |
"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 |
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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) | |
| Mohazab AR, Plotkin SS, "Structural alignment using the generalized Euclidean distance between conformations" Int. J. Quant. Chem. 109, 3217–3228 (2009) | |
| 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) | |
| Mohazab AR, Plotkin SS, "Minimal folding pathways for coarse-grained biopolymer fragments" Biophys J, 95 (12) 5496 (2008) | |
| 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) | |
| Plotkin SS, "Determination of barrier heights and prefactors from protein folding rate data" Biophys J. 88, (6) (2005) | |
| Oztop B, Ejtehadi MR, Plotkin SS, "Protein folding rates correlate with heterogeneity of folding mechanism" Phys. Rev. Lett. 93, 208105 (2004)
(Experimental references)
Here is streaming video of a seminar of mine including some this work. There is a fairly lengthy review of basic protein folding ideas (part 1) below. |
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| 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) | |
| 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) | |
| Plotkin SS, Onuchic JN, "Understanding Protein Folding with Energy Landscape Theory II: Quantitative Aspects" Quart. Rev. Biophys. 35, 205-286 (2002) | |
| Plotkin SS, Onuchic JN, "Understanding Protein Folding with Energy Landscape Theory, Part I: Basic Concepts" Quart. Rev. Biophys. 35, 111-167 (2002) | |
| Plotkin SS, "Speeding Protein Folding Beyond the Go Model: How a Little Frustration Sometimes Helps" Proteins: Structure, Function, Genetics 45 (4), 337-345 (2001) | |
| Plotkin SS, Onuchic JN, ``Structural and Energetic Heterogeneity in Protein Folding I: Theory'' J. Chem. Phys. 116 (12), 5263-5283 (2002) | |
| 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) | |
| Plotkin SS, Wolynes PG, "Non-Markovian configurational diffusion and reaction coordinates for protein folding" Phys Rev Lett 80 (22): 5015-5018 (1998) | |
| 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) | |
| 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) | |
| 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) | |
| Plotkin SS, Wang J, Wolynes PG, "Correlated energy landscape model for finite, random heteropolymers" Phys Rev E 53 (6): 6271-6296 Part B (1996) | |
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