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Plotkin Research Group

Principal Researcher

Steven Plotkin Steve Plotkin Protein misfolding and neurodegenerative disease; Molecular-genetic basis of multicellularity

Post Doctoral Researchers

Luke McAlary Molecular interplay of liquid-liquid phase separation and pathogenic aggregation of TDP43 in ALS

Graduate Researchers

Pranav Garg Models of cell differentiation and development
Tiam Heydari Mechanisms of germ cell specification in early metazoans
Neil Cashman

Publications:

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).

Guest W, Cashman N, 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)

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)[4]

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)

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)

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)

Silverman JM, Gibbs E, Martens KM, Balducci C, Wang J, Yousefi M, Peng X, Lamour G, Cowan CM, Forloni G, Hsiung GR, Plotkin SS, Wellington CL and Cashman NR "A Neutralizing Epitope For Toxic And Propagating Amyloid-beta Oligomers," Submitted June 2016.

PI on project grants:

PrioNet Canada: “Prion-Like Propagated Misfolding of SOD1 in ALS Pathogenesis”

“Prion Protein Conversion in disease: The “Demiglobule” Hypothesis”

Co-inventor:

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

"N-terminal epitopes in Amyloid beta and conformationally-selective antibodies thereto" Inventors: Plotkin SS and Cashman NR, 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, Filed: February 1, 2016

"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.

"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.

Andriy Kovalenko

PI on project grants:

“Immunological Lead Towards Characterization of Toxic Oligomers for Therapeutic Targeting in Neurodegenerative Diseases”

“Targeting Prion-Like Propagated Misfolding of SOD1 for ALS Immunotherapy”
Joerg Rottler

Publications:

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)

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

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

Habibi M, Plotkin SS, and Rottler J "Soft vibrational modes predict force-induced protein unfolding mechanisms" Submitted

Cecilia Clementi

Publications:

Clementi C, Plotkin SS, "The Effects of Non-native Interactions on Protein Folding Rates: Theory and Simulation" Prot. Sci. 13, 1750-1765 (2004)

Alumni of The Plotkin Research Group

Post-Doctoral Researchers

Erik Abrahamsson

Dr. Abrahamsson received his Ph.D. in Chemistry from Göteborg University in Sweden. He is a co-author of our BioVEC molecular visualization software.

Atanu Das

Dr. Das is interested in Protein folding, misfolding and aggregation, as well as DNA modification and repair. He is currently a PDF in the group of Dmitrii E. Makarov at UT Austin, Department of Chemistry.
das(at)phas.ubc.ca

Reza Ejtehadi

Dr. Ejtehadi is interested in soft condensed matter physics, biological macromolecules, complex systems, and simulations and computational physics. He is currently an associate professor at Sharif University.

Mahdi Ghelichi Protein misfolding and dysregulation in cancer
Yuri Gusev

Dr. Gusev received his Ph.D. in Mathematical Physics from the University of Manitoba; his current research at Perimeter Institute involves quantum gravity.

Mona Habibi

Simulation of mechanically-induced protein unfolding and monomerization for misfolding-prone proteins, mhabibi(at)phas.ubc.ca

(Supervised jointly with Prof. Joerg Rottler)

Daniel Luesebrink Dimer binding affinity calculations for SOD1; approach to equilibrium
Eric Mills Density functional theory of solvation; protein unfolding thermodynamics
millsea(at)phas.ubc.ca
Xubiao Peng

Energy landscape theory for protein misfolding: applications to ALS and cancer

Sabbatical Visitors

Prof. Hector Dominguez

Materials Science Institute
Universidad Nacional Autónoma de México

Metal-protein interactions (August 2015 - July 2016)

Peter Lenz Protein science; Molecular mechanisms in cancer

Apichart Linhananta

Lakehead University

Osmolyte-Induced Protein Stability (January - July 2009)

Visiting Researchers

Matthias Huber

Mechanisms of protein folding (June 2004 - April 2005)
matthias.huber(at)phys.chem.ethz.ch

Graduate Researchers

Vibudh Agrawal Algorithmic discovery of genetic regulatory elements
Si Chen

Statistical mechanics of graphs and emergent manifolds, quantum gravity. sichen(at)phas.ubc.ca

John Dupuis

Saponsin-like protein-membrane interactions
johndupuis1 (at) hotmail (dot) com

*Supervised jointly with Rickey Yada

Miguel Garcia

Magnetic sensing proteins. miguel(at)phas.ubc.ca

William Guest

Misfolding and aggregation in prion protein and SOD1 (M.D./Ph.D. Program)
Shared with Faculty of Medicine, Neil Cashman
wguest(at)interchange.ubc.ca

Shirin Hadizadeh Osmolyte effects on protein stability
shirin(at)physics.ubc.ca
Rawnak Hoque Bioinformatics of cancer expression data
Todd Kilstrom

Computational Protein misfolding; Protein stability and instability
todd(dot)kilstrom(at)gmail(dot)com

*Supervised jointly with Neil Cashman

Ali Mohazab
High-dimensional distance metrics, applications to protein folding (Ph.D. Program)
alirm(at)phas.ubc.ca
Alex Morriss-Andrews

Rigid body simulations of coarse-grained DNA
(Co-supervised, with Joerg Rottler, Physics)
aandrews(at)physics.ucsb.edu

Baris Oztop Protein folding rates and mechanisms
boztop(at)fen.bilkent.edu.tr
Alena Shmygelska Energy parameters and search algorithms for protein structure prediction (Co-supervised, with Holger Hoos, Comp. Sci.)

Graduate Rotation Students - GSAT Program

Matthew Bundala matus.bundala (at) gmail.com
Min Feng feng.min110 (at) gmail.com

Undergraduate Researchers

Stefan Avall s_avall(at)yahoo.ca
Kyle Bower Steiner minimal networks in high-dimension
Christopher Chang Genetics of stem cell niches in C-elegans
Alvin Cheung

 

Sebastian Cogswell sebcogs(at)yahoo.com
Philip Edgcumbe

edgcumbe(at)interchange.ubc.ca

John Flores Dimer stability of superoxide dismutase and ALS
Zach Hamilton Disordered protein ensembles; membrane bound proteins
Johanna Hansen johanna(at)physics.ubc.ca
Johnathan Hoggarth TDP-43 liquid-liquid phase separation and stress granule formation in ALS
Justin Hsu justinhsu(at)telus.net
Derek Inman Molecular dynamics simulations of superoxide dismutase misfolding
dinman(at)interchange.ubc.ca
Benjamin Lindner benlin(at)interchange.ubc.ca
Sebastian Ohse sohse(at)interchange.ubc.ca
Gene Polovy Energetic analysis of alpha-spectrin repeat proteins
gpolovy(at)gmail.com
David Rudko rudko(at)interchange.ubc.ca
Brian Sin

Unfolded protein ensembles; protein folding kinetics

Kwinten Van Gassen

Protein energetics and loop entropy
vangassen.k(at)gmail.com

Brittany Welsh

Molecular genetics; evolution

Jim Xu

Protein Dimer Binding Free Energy Calculations

Christopher Yearwood cyearwoo (at) physics.ca
Rachel Zhao Novel therapeutic targets for intrinsically-disordered, prion-like proteins involved in Alzheimer’s and ALS
Waterfall at UBC Memorial Japanese Garden Pond at UBC Japanese Memorial Garden
The above photos are from the UBC Japanese Memorial Garden on campus.
To see more, please visit the photo gallery under "Fun".
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