Profile
Ratmir Derda received his B.Sci. in Physics from Moscow Institute of Physics and Technology in 2001 and Ph.D. in Chemistry from the University of Wisconsin-Madison in 2008, under the supervision of Laura L. Kiessling. From 2008 to 2011, he was a postdoctoral researcher at Harvard University working under the supervision of George M. Whitesides and and Donald E. Ingber. He is currently Assistant Professor at the Department of Chemistry and Principal Investigator at the Alberta Glycomics Centre and SENTINEL Bioactive Paper Network. His recent awards include Young Investigator Award from Boulder Peptide Society (2014), University of Alberta Award for Outstanding Mentorship in Undergraduate Research & Creative Activities (2014) and Canadian Rising Star in Global Health award from Grand Challenges Canada (2011) GlycoNet Funded ProjectsProducts
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Genetically-encoded fragment-based discovery (GE -FBD) of glycopeptide ligands with differential selectivity for antibodies related to mycobacterial infectionsTP-18 University of Alberta | Publication | 2018-01-01 | | Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing University of Alberta | Publication | 2018-01-01 | Bifang He, Katrina F Tjhung, Nicholas J Bennett, Ali Chou, Andrea Rau, Jian Huang, Ratmir Derda | DNA-Encoded Multivalent Display of Chemically Modified Protein Tetramers on Phage: Synthesis and in Vivo ApplicationsPhage display links the phenotype of displayed polypeptides with the DNA sequence in the phage genome and offers a universal method for the discovery of proteins with novel properties. However, the display of large multisubunit proteins on phages remains a challenge. A majority of protein display systems are based on monovalent phagemid constructs, but methods for the robust display of multiple copies of large proteins are scarce. Here, we describe a DNA-encoded display of a ∼ 200 kDa tetrameric l-asparaginase protein on M13 and fd phages produced by ligation of SpyCatcher-Asparaginase fusion (ScA) and PEGylated-ScA (PEG-ScA) to barcoded phage clones displaying SpyTag peptide. Starting from the SpyTag display on p3 or p8 coat proteins yielded constructs with five copies of ScA displayed on p3 (ScA-p3), ∼100 copies of ScA on p8 protein (ScA-p8) and ∼300 copies of PEG-ScA on p8 protein (PEG-ScA-p8). Display constructs of different valencies and chemical modifications on protein (e.g., PEGylation) can be injected into mice and analyzed by deep sequencing of the DNA barcodes associated with phage clones. In these multiplexed studies, we observed a density and protein-dependent clearance rate in vivo. Our observations link the absence of PEGylation and increase in density of the displayed protein with the increased rate of the endocytosis by cells in vivo. In conclusion, we demonstrate that a multivalent display of l-asparaginase on phages could be used to study the circulation life of this protein in vivo, and such an approach opens the possibility to use DNA sequencing to investigate multiplexed libraries of other multisubunit proteins in vivo.CR-03 University of Alberta | Publication | 2021-12-20 | Guilherme Meira Lima, "Alexey Atrazhev ", Susmita Sarkar, Mirat Sojitra, Revathi Reddy, "Karin Torres-Obreque ", "Carlota de Oliveira Rangel-Yagui ", Matthew Macauley, "Gisele Monteiro ", Ratmir Derda | Siglec-6 mediates the uptake of extracellular vesicles through a noncanonical glycolipid binding pocket. Immunomodulatory Siglecs are controlled by their glycoprotein and glycolipid ligands. Siglec-glycolipid interactions are often studied outside the context of a lipid bilayer, missing the complex behaviors of glycolipids in a membrane. Through optimizing a liposomal formulation to dissect Siglec–glycolipid interactions, it is shown that Siglec-6 can recognize glycolipids independent of its canonical binding pocket, suggesting that Siglec-6 possesses a secondary binding pocket tailored for recognizing glycolipids in a bilayer. A panel of synthetic neoglycolipids is used to probe the specificity of this glycolipid binding pocket on Siglec-6, leading to the development of a neoglycolipid with higher avidity for Siglec-6 compared to natural glycolipids. This neoglycolipid facilitates the delivery of liposomes to Siglec-6 on human mast cells, memory B-cells and placental syncytiotrophoblasts. A physiological relevance for glycolipid recognition by Siglec-6 is revealed for the binding and internalization of extracellular vesicles. These results demonstrate a unique and physiologically relevant ability of Siglec-6 to recognize glycolipids in a membrane.CR-03, CR-27 University of Alberta | Publication | 2023-04-22 | Edward Schmidt, "Dimitra Lamprinaki ", Kelli McCord, Maju Joe, Mirat Sojitra, "Ayk Waldow ", "Jasmine Nguyen ", John Monyror, Elena Kitova, "Fahima Mozaneh ", "XY Guo ", Jaesoo Jung, "Jhon Enterina ", Gour Chand Daskhan, Ling Han, "Crystal Chrystler ", "Christopher Cromwell ", Basil Hubbard, Lori J. West, "Marianne Kulka ", Simonetta Sipione, John Klassen, Ratmir Derda, Todd L. Lowary, Lara Mahal, "Megan Riddell ", Matthew Macauley | Diversity of phage-displayed libraries of peptides during panning and amplification. Harvard University | Publication | 2011-01-01 | | Multizone paper platform for 3D cell cultures. Harvard University | Publication | 2011-01-01 | Ratmir Derda, Tang SK, Laromaine A, Mosadegh B, Hong E, Mwangi M, Mammoto A, Ingber DE, Whitesides GM | Uniform amplification of phage with different growth characteristics in individual compartments consisting of monodisperse droplets. Harvard University | Publication | 2010-07-01 | | High-throughput discovery of synthetic surfaces that support proliferation of pluripotent cells. Harvard University | Publication | 2010-02-01 | Ratmir Derda, Musah S, Orner BP, Klim JR, Li L, Kiessling LL | Paper-supported 3D cell culture for tissue-based bioassays. Harvard University | Publication | 2009-11-01 | Ratmir Derda, Laromaine A, Mammoto A, Tang SK, Mammoto T, Ingber DE, Whitesides GM | Defined substrates for human embryonic stem cell growth identified from surface arrays. University of Wisconsin - Madison | Publication | 2007-05-01 | Ratmir Derda, Li L, Orner BP, Lewis RL, Thomson JA, Kiessling LL | Synthetic Cross-linking of Peptides: Molecular Linchpins for Peptide Cyclization University of Alberta | Publication | 2018-11-01 | | Freeze-Float Selection of Ice Nucleators University of Alberta | Publication | 2018-12-01 | | Bacteriophages and viruses as a support for organic synthesis and combinatorial chemistry. University of Alberta | Publication | 2012-01-01 | | Spatial control of cell fate using synthetic surfaces to potentiate TGF-beta signaling. University of Alberta | Publication | 2011-07-01 | | Three-Dimensional Paper-Based Model for Cardiac Ischemia. University of Alberta | Publication | 2014-02-01 | Mosadegh B, Dabiri BE, Lockett MR, Ratmir Derda, Campbell P, Parker KK, Whitesides GM | Flow-Through Synthesis on Teflon-Patterned Paper To Produce Peptide Arrays for Cell-Based Assays University of Alberta | Publication | 2014-02-01 | Frédérique Deiss, Wadim L. Matochko, Natasha Govindasamy, Ratmir Derda | Prospective identification of parasitic sequences in phage display screens. University of Alberta | Publication | 2014-02-01 | | Quantitative synthesis of genetically encoded glycopeptide libraries displayed on M13 phage. University of Alberta | Publication | 2012-09-01 | | Antimicrobial susceptibility assays in paper-based portable culture devices. University of Alberta | Publication | 2014-01-01 | | Phage Display of the Serpin Alpha-1 Proteinase Inhibitor Randomized at Consecutive Residues in the Reactive Centre Loop and Biopanned with or without Thrombin. University of Alberta | Publication | 2014-01-01 | Scott BM, Matochko WL, Gierczak RF, Bhakta V, Ratmir Derda, Sheffield WP | Platform for high-throughput testing of the effect of soluble compounds on 3D cell cultures. University of Alberta | Publication | 2013-09-01 | Deiss F, Mazzeo A, Hong E, Ingber DE, Ratmir Derda, Whitesides GM | Aqueous multiphase systems of polymers and surfactants provide self-assembling step-gradients in density. University of Alberta | Publication | 2012-06-01 | Mace CR, Akbulut O, Kumar AA, Shapiro ND, Ratmir Derda, Patton MR, Whitesides GM | Mechanochemical Control of Mesenchymal Condensation and Embryonic Tooth Organ Formation University of Alberta | Publication | 2011-10-01 | Mammoto T, Mammoto A, Tat T, Gibbs A, Ratmir Derda, Mannix R, Bruijn M, Yung CW, Huh D, Ingber DE | Light-responsive bicyclic peptides University of Alberta | Publication | 2018-08-01 | Mohammad R Jafari, Hongtao Yu, Jessica M Wickware, Yu-Shan Lin, Ratmir Derda | GlyNet: a multi-task neural network for predicting protein–glycan interactions.Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan–protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet's output of continuous values provides more detailed results than the standard binary classification models. After incorporating a simple threshold to transform such continuous outputs the resulting GlyNet classifier outperforms those standard classifiers. GlyNet is the first multi-output regression model for predicting protein–glycan interactions and serves as an important benchmark, facilitating development of quantitative computational glycobiology.TP-22 University of Alberta | Publication | 2022-05-16 | "Eric Carpenter ", Shaurya Seth, "Noel Yue ", "Russell Greiner ", Ratmir Derda | Uniform amplification of phage display libraries in monodisperse emulsions. University of Alberta | Publication | 2012-09-01 | Matochko WL, Ng S, Jafari MR, Romaniuk J, Tang SK, Ratmir Derda | Deep sequencing analysis of phage libraries using Illumina platform. University of Alberta | Publication | 2012-09-01 | Matochko WL, Chu K, Jin B, Lee SW, Whitesides GM, Ratmir Derda | Fluorine bonding enhances the energetics of protein-lipid binding in the gas phase Fonds de recherche du Québec, University of Alberta | Publication | 2014-12-01 | | Genetically-encoded fragment-based discovery of glycopeptide ligands for DC -SIGNTP-22 University of Alberta | Publication | 2018-08-01 | Simon Ng, Nicholas Bennett, Jessica Schulze, Nan Gao, Christoph Rademacher, Ratmir Derda | Selection of galectin-3 ligands derived from genetically encoded glycopeptide librariesTP-22 University of Alberta | Publication | 2018-09-01 | Daniel Ferrer Vinals, Pavel I. Kitov, Zhijay Tu, Chunxia (Cecilia) Zou, Christopher W. Cairo, Hans Chun-Hung Lin, Ratmir Derda | Discovery of Light-Responsive Ligands through Screening of a Light-Responsive Genetically Encoded Library. University of Alberta | Publication | 2014-02-01 | | Portable self-contained cultures for phage and bacteria made of paper and tape. University of Alberta | Publication | 2012-11-01 | | Discovery of Light-Responsive Ligands through Screening of a Light-
Responsive Genetically Encoded Library University of Alberta | Publication | 2014-12-01 | |
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