Welcome to the website for The Plotkin Research Group

We do research at the interface of biology and physics.

Our current projects involve the molecular-genetic study of the evolution of multicellularity, protein misfolding in neurodegenerative disease, and more recently, viral evolution and molecular therapeutics to SARS-CoV-2. Please see our Research Page for more details.

Plotkin Lab News:

Our team welcomes two new researchers:

• Santanu Sasidharan, Post Doctoral Fellow, Evolution of the SARS-CoV-2 Virus
• Kai Xiao, PhD Student, Evolution of the SARS-CoV-2 Virus

Recently Awarded Grants:

• Digital Technology SuperCluster funding for SARS-CoV-2 research at Plotkin Lab ($511K)
• Genome BC sequencing funding for SARS-CoV-2 research at Plotkin Lab ($195K)

Recent Publications:

• Hsueh SCC, Aina A, Plotkin SS, “Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS” J Phys Chem B, 26, 49, 10384–10399 (2022) Cover article
• McAlary L, Shephard, VK, Sher M, Rice LJ, Yerbury JJ, Cashman NR, Plotkin SS “Assessment of protein inclusions in cultured cells using automated image analysis” STAR Protocols 3 (4), 101748 (2022)
• Gibbs E, Zhao B, Roman A, Plotkin SS, Peng X, Hsueh SSC, Aina A, Wang A, Shyu C, Yip CK, Nam S, Kaplan JM, Cashman NR “Rational Generation of Monoclonal Antibodies Selective for Pathogenic Forms of Alpha-Synuclein” Biomedicines, 10, 2168 (2022)
• Hsueh SCC, Aina A, Roman AY, Cashman, NR, Peng X, Plotkin SS “Optimizing Epitope Conformational Ensembles Using α-Synuclein Cyclic Peptide “Glycindel” Scaffolds: A Customized Immunogen Method for Generating Oligomer-Selective Antibodies for Parkinson’s Disease” ACS Chem. Neurosci., 13, 2261−2280 (2022) Cover article
• Garg P, Semmler S, Baudouin C, Vande Velde C, Plotkin SS “Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6” J. Mol. Bio., Vol 434, Issue 6 (2022)
• Hsueh SCC, Nijlad M, Peng X, Hilton B, Plotkin SS, “First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants” Front. Mol. Biosci. 9:845013. (2022)

• Evolutionarily conserved epitopes in beta-coronaviruses and vaccines and antibodies thereto, US Provisional Patent Application No.: US 63/447,146, Inventors: Steven S Plotkin, Pranav Garg, Ching-Chung Hsueh, Filed February 2023
• Antibodies Targeting Rack1 and Methods of Use Thereof” US Provisional Patent Application No. 63/438,178, Inventors: Neil R Cashman, Steven S Plotkin, Ching-Chung Hsueh, Beibei Zhao, Filed Jan 2023
• Immunogens Targeting Oligomeric Tau and Methods of Generation and Use Thereof, Provisional Patent P69765US00, Filed Dec 2022

Recent Submissions:

• Garg P, HsuehSCC, Plotkin SS, “Predicting the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein” (submitted)
• Aina A, Hsueh SCC, Plotkin SS “PROTHON: A local order parameter-based method for efficient comparison of protein ensembles” (submitted)
• Aina A, Hsueh SCC, Peng X, Plotkin SS “De novo computational design of a β-helix tau protein scaffold: An oligomer-selective vaccine immunogen candidate for Alzheimer’s disease” (submitted)
• Pokrishevsky E, DuVal MG, McAlary L, Louadi S, Pozzi S, Roman A, Plotkin SS, Dijkstra A, Julien JP, Allison WT, Cashman NR “Tryptophan Residues in TDP-43 and SOD1 Mediate the Cross-seeding and Toxicity of SOD1” (under revision)
• DuVal MG, McAlary L, Habibi M, Garg P, Sher M, Cashman NR, Allison WT and Plotkin SS “Physical Properties of Novel Aggressive and Beneficial SOD1 Mutants Predict Phenotypes Consistent with ALS” (submitted, bioRxiv)

Recent Recorded Presentations:

We are grateful to the Digital Technology Supercluster, Canadian Institutes of Health Research, Genome BC, Mitacs, and Westgrid/Compute Canada for supporting our research.