Denys Biriukov, Ph.D.
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Omlouváme se, ale tyto stránky jsou z důvodu odborného obsahu a účelu dostupné pouze v anglické verzi.
Open Ph.D. student position! Details can be found here.
We always welcome motivated B.Sc. and M.Sc. students interested in joining our group!
We are the Computational Glycobiology team, and our research focuses on uncovering the complex world of glycans (also known as sugars or carbohydrates) and their roles in various biological processes and related applications. Using cutting-edge multiscale molecular simulations, we study their structure, function, and dynamics in detail. Our computer simulations provide valuable insights into how glycans interact with other biomolecules, influencing key processes such as cell signaling, immune responses, and disease progression. We are also deeply committed to advancing simulation techniques, improving simulation models, and staying at the cutting edge of rapidly emerging methodologies like evolutionary algorithms and machine learning approaches.
Current projects
Core research
- Molecular recognition of bacterial peptidoglycan by peptides and proteins
- Tailoring polymeric implant coatings against bacteria attachment by studying bacterial glycans' affinity for functionalized polymers
- in collab. w/ Prof. Lukasz Cwiklik from the J. Heyrovsky Institute of Physical Chemistry in Prague and Prof. Andrzej Kotarba from the Jagiellonian University in Krakow
- High-throughput computing in molecular dynamics simulations of biological systems
- in collab. w/ Dr. Matti Javanainen from the Tampere University in Finland
Collaboration projects
- Modeling glycosaminoglycans in the context of glycocalyx, extracellular matrix, and the design of biocompatible hydrogels
- in collab. w/ Dr. Hector Martinez-Seara from IOCB Prague
- Designing pore-forming antimicrobial peptides against drug-resistant bacteria
- in collab. w/ Prof. Robert Vácha from CEITEC MU
- Developing novel simulation models for glycans within the de novo comprehensive force field for biological systems that accounts for electronic polarisation in a mean-field way via charge scaling
- in collab. w/ Prof. Pavel Jungwirth from IOCB Prague
Team members
Team leader
- Dr. Denys Biriukov, Ph.D.
Postdocs
- Jacob Clark, Ph.D. (joining in Fall 2026)
Part-time researchers
- Tamara Polačková
Master students
- Bc. Andrej Baláži
- Bc. Vojtěch Klapetek
- Bc. Tereza Tutková
Bachelor students
- Kryštof Kučera
Alumni
2026, bachelor's thesis: Tamara Polačková, “Computer simulations of glycan binding to cellular membranes"
2024, bachelor's thesis: Tereza Tutková, “Molecular modeling of bacterial glycans and their interactions"
Selected publications
Caspase-4 binds to LPS membranes with positive curvature for non-canonical inflammasome activation
Began, J.; Boegli, A.; Anton, L.; Biriukov, D.; Vairamuthu, J.; Santos, J. C.; Broz, P. Immunity 2026, 59, 542–558.e8
Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by Nuclear Magnetic Resonance, Cryo-Electron Microscopy, and Molecular Dynamics
Biriukov, D.; Osifová, Z.; Nguyen, M. T. H.; Mason,P. E.; Dračínský, M.; Jungwirth, P.; Heyda, J.; Morandi, M. I.; Vazdar, M. Aggregate 2026, 7:e70276
Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity
Riopedre-Fernandez, M.; Biriukov, D.; Dračínský, M.; Martinez-Seara, H. Carbohydr. Polym. 2024, 325, 121568
Transient formation of supramolecular complexes between hyaluronan and oligopeptides at submicromolar concentration
Riopedre-Fernandez, M.; Chu, B.; Kuffel, A; Marchioro, A.; Biriukov, D.; Martinez-Seara, H. Commun. Chem. 2026, 9, 34.
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions
Riopedre-Fernandez, M.; Kostal, V.; Martinek, T.; Martinez-Seara, H.; Biriukov, D. J. Chem. Inf. Model. 2024, 64 (18), 7122–7134
Lipid Scrambling Pathways in the Sec61 Translocon Complex
Javanainen, M.; Šimek, J.; Tranter, D.; O’Keefe, S.; Karki, S.; Biriukov, D.; Šachl, R.; Paavilainen, V. O. J. Am. Chem. Soc. 2025, 147 (19), 15970–15984
Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations
Rivel, T.; Biriukov, D.; Kabelka, I.; Vácha, R. J. Chem. Inf. Model. 2025, 65 (2), 908–920
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field
Nencini, R.; Tempra, C.; Biriukov, D.; Riopedre-Fernandez, M.; Chamorro, V. C.; Polák, J.; Mason, P. E.; Ondo, D.; Heyda, J.; Ollila, O. H. S.; Jungwirth, P.; Javanainen, M.; Martinez-Seara, H. О. J. Chem. Theory Comput. 2024, 20 (17), 7546–7559
Funding
2026 – 2028: The Czech Science Foundation, project 26-20435S, “Physics-based inverse design of new peptides selective for the bacterial peptidoglycan”, allocated funding: ~285,000 EUR.
2024 – 2026: The Czech Science Foundation, project 24-11274S, “Tailoring polymeric implant coatings against bacteria attachment: a knowledge-based approach”, allocated funding: ~115,000 EUR. Co-investigator – Prof. Lukasz Cwiklik from J. Heyrovsky Institute of Physical Chemistry in Prague; total allocated funding: ~390,000 EUR.
