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:
Welcome Kenneth Pinto, PhD student in Cell and Developmental Biology!
Congratulations to Dr. Santanu Sasidharan on receiving the MITACS Fellowship!
Recently Awarded Grants:
- CIHR: Priority Announcement: Research on Prevention or Response to Covid-19 or Similar Future Pandemics: “A platform for developing mutation-resistant vaccines and antibodies for future viral variants, using SARS-CoV-2 as a model”
- Genome BC sequencing funding for SARS-CoV-2 research at Plotkin Lab
- CIHR: Priority announcement funding: Pandemic Preparedness and Health Emergencies Research: “A development platform for mutation-resistant vaccines and antibodies for SARS-CoV-2 future variants”
Recent Publications:
- Hsueh SCC, Nijland M, Aina A; Plotkin SS, “Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer’s Disease” Journal of Chemical Information and Modeling (2024)
- Conserved Epitopes in Coronaviruses and Vaccines and Antibodies Thereto. US Patent No.: US 63/447,146, Evolutionarily conserved epitopes in beta-coronaviruses and vaccines and antibodies thereto, Filed February 2023, Inventors: Steven S Plotkin, Pranav Garg, Ching-Chung Hsueh, Santanu Sasidharan. Full Application Filed February 21, 2024PCT/CA2024/050214Conserved Epitopes in Coronaviruses and Vaccines and Antibodies Thereto. US Provisional Patent Application No.: US 63/447,146, Evolutionarily conserved epitopes in beta-coronaviruses and vaccines and antibodies thereto, Filed February 2023, Inventors: Steven S Plotkin, Pranav Garg, Ching-Chung Hsueh, Santanu Sasidharan. Full Application Filed February 21, 2024
- Zhao B, Cowan CM, Coutts J; Christy DD, Saraph A, Hsueh SCC, Plotkin SS, Mackenzie IR, Kaplan JM, Cashman NR, “Targeting RACK1 to alleviate TDP-43 and FUS proteinopathy-mediated suppression of protein translation and neurodegeneration” Acta Neuropathologica Communications 11, Article number: 200 (2023)
- Aina A, Hsueh SCC, Gibbs E, Peng X, Cashman NR, Plotkin SS “De novo computational design of a β-helix tau protein scaffold: An oligomer-selective vaccine immunogen candidate for Alzheimer’s disease” ACS Chem. Neurosci. (2023)
- Aina A, Hsueh SCC, Plotkin SS “PROTHON: A local order parameter-based method for efficient comparison of protein ensembles” J. Chem. Inf. Model. 63, 11, 3453–3461 (2023)
- 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)
- 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, Hsueh SCC, Plotkin SS, “Testing the feasibility of targeting a conserved region on the S2 domain of SARS-CoV-2 spike protein”
- McAlary L, Nan JR, Shyu, C, Mine Sher M, Plotkin SS, Cashman NR, “Amyloidogenic regions in beta-strands II and III modulate the aggregation and toxicity of SOD1 in living cells” (in review)
- Hsueh SCC and Plotkin SS, “Reservoir-REMD facilitates kinetic rescue from metastable peptide conformations” (in review)
- 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.