Faculty of Physics University of Warsaw > Events > Seminars > Biophysics Seminar

Biophysics Seminar

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room B2.38, Pasteura 5 at 14:15

dr Lidia Wróbel (Laboratorium Proteostazy Komórkowej, Międzynarodowy Instytut Biologii Molekularnej i Komórkowej)

Cellular Proteostasis in Neurodegenerative Diseases

The cellular proteome and its organisation are remarkably complex. To maintain a homeostasis, cell must carefully balance its proteome by controlling protein quality and abundance.My lab is interested in the molecular basis of proteostasis with focus on protein clearance pathways in the context of human diseases. Protein degradation is a key mechanism to adapt protein levels to cellular or environmental changes. Efficient protein removal is crucial to avoid accumulation of misfolded and toxic protein species. The decline in protein clearance pathways is a key driver of age-related cellular dysfunction and accumulation of toxic protein species is associated with neurodegenerative diseases, including Alzheimer's and Parkinson's diseases.Maintenance of cellular proteostasis requires temporally and spatially controlled degradation of regulatory and erroneous proteins through ubiquitin-proteasome system and autophagy-lysosomal pathway. My lab focuses on understanding how ubiquitin-proteasome system is regulated in different cellular compartments and how does it crosstalk with autophagy. We also study the mechanisms regulating the nucleocytoplasmic trafficking of proteins important for cellular proteostasis.

room B2.38, Pasteura 5 at 14:15

dr Hossein Maleki-Ghaleh (Institute of Physical Chemistry, Polish Academy of Sciences)

Nanophysics and Nanochemistry in Biomaterials for Regenerative Medicine

Nanobiotechnology offers a promising approach to stimulating cellular responses for tissue regeneration, including bone, skin, and neural tissues. By designing nanoparticles with precise structural characteristics, we can fine-tune their physical and chemical properties, enabling the development of nanostructured systems that promote cell proliferation and differentiation. Among these, biodegradable calcium phosphate-based compounds are particularly interesting due to their bioactivity and ability to modulate key signaling pathways. Engineering their atomic structure allows for the control of optical, magnetic, and biochemical properties, enhancing cellular interactions. This presentation will highlight recent findings from my research, focusing on the role of nanophysics and nanochemistry in the development of advanced biomaterials for regenerative medicine.

room B2.38, Pasteura 5 at 14:15

Prof. Robert Szoszkiewicz (Laboratorium Fizykochemii Materiałów, Centrum Nauk Biologiczno-Chemicznych UW)

Internal Friction in Folding/Unfolding of Short Peptides and Small Proteins via Computer Simulations, Analytical Modeling and Single-Molecule Force Spectroscopy

This talk will summarize our recent developments in elucidating both experimental [1] and theoretical [2,3] information about friction coefficients and internal friction of selected simple peptides and proteins. Molecular internal friction obtained at the single molecule level is an interesting topic in physical chemistry/biophysics and material science since this parameter can be used as proxy for elucidating/discriminating various structures/conformations in the case of simple proteins at physiologically relevant conditions. Such information can later be useful for various drug delivery systems as well as novel cancer-fighting strategies. Acknowledgments: This work was supported by the National Science Center, Poland, with a grant number 2018/30/M/ST4/00005. MD simulations were carried out on the computer clusters Funk at CNBCh UW and ARES in Cyfronet AGH, Cracow (through its access grant to the RSz group). Data analysis has been partially performed on a dedicated workstation in RSz lab at UW. References: 1). R. Szoszkiewicz, Viscoelasticity of a single poly-protein probed step by-step during its mechanical unfolding and refolding under the force-clamp conditions, RSC Advances, 15, 2717–2726 (2025). Open access. https://doi.org/10.1039/d4ra08047e 2). A. Świątek, K. Kuczera, R. Szoszkiewicz, The effects of proline on internal friction in simulated folding dynamics of several alanine-based alpha-helical peptides. Journal of Physical Chemistry B (ACS), 128, 16, 3856–3869 (2024). Open access. https://doi.org/10.1021/acs.jpcb.4c00623 3). A. Wosztyl, K. Kuczera, R. Szoszkiewicz, Analytical Approaches for Deriving Friction Coefficients for Selected alpha-helical Peptides and Based Entirely on Molecular Dynamics Simulations, Journal Physical Chemistry B, 126, 8901-8912 (2022). Open access. 10.1021/acs.jpcb.2c03076

room B2.38, Pasteura 5 at 14:15

Prof. Jakub Włodarczyk (Pracownia Biofizyki Komórki, Instytut Biologii Doświadczalnej im. M. Nenckiego PAN)

Molecular Fingerprint of Stress Resilience

Stress resilience refers to the ability of neuronal networks to maintain their function despite exposure to stress. In this study, we investigate whether stress resilience is an actively developed dynamic process. To assess resilient and anhedonic behavioral phenotypes emerging after chronic unpredictable stress, we quantitatively analyzed the structural and functional plasticity of excitatory synapses in the hippocampus using a combination of proteomic, electrophysiological, and imaging techniques. Our results demonstrate that stress resilience is a dynamic, multifactorial process involving structural, functional, and molecular adaptations at the synaptic level. Specifically, we show that chronic stress modulates the palmitoylation of synaptic proteins, with distinct profiles observed in resilient versus anhedonic phenotypes. Moreover, stress resilience is associated with compensatory structural plasticity in the postsynaptic compartments of synapses. Finally, we identify a signaling pathway that promotes resilience, shedding light on the molecular mechanisms underlying adaptive responses to chronic stress.

room B2.38, Pasteura 5 at 14:15

Paweł Płatek (Centrum Transferu Technologii i Wiedzy, Uniwersytet Warszawski)

UW — Ochrona własności intelektualnej i komercjalizacja rezultatów prac badawczych

Spotkanie w ramach Seminarium Zakłądu Biofizyki ma na celu przybliżenie osobom uczestniczącym kluczowych aspektów związanych z ochroną własności intelektualnej oraz procesem komercjalizacji wyników badań naukowych zgodnie z zasadami Regulaminu Zarządzania Własnością Intelektualną na Uniwersytecie Warszawskim. Podczas prezentacji omówione zostaną podstawowe pojęcia dotyczące własności intelektualnej, w tym patenty, prawa autorskie oraz znaki towarowe. Ponadto, przedstawione zostaną najlepsze praktyki w zakresie zarządzania własnością intelektualną na UW i procesem komercjalizacji innowacji. Spotkanie będzie również okazją do zapoznania się z przykładami udanych projektów komercjalizacyjnych oraz korzyściami płynącymi z efektywnego zarządzania własnością intelektualną w środowisku akademickim.

room B2.38, Pasteura 5 at 14:15

dr Tomasz Góral (Cryomicroscopy and Electron Diffraction Core Facility, Centre of New Technologies, University of Warsaw)

Cryo-EM Core Facility at CeNT UW: Major Achievements and Future Prospects

In 2019 one of the very first cryo-EM microscopes in the country – the 200kV Glacios equipped with a Falcon3EC camera and a phase plate solution was installed in the University of Warsaw. In the next few years the Cryomicroscopy and Electron Diffraction Core Facility was established and started providing many local structural biologists and chemists with direct access to this ground-breaking and Noble-winning technology. To date, there have been only two cryo-EM Core Facilities operating in Poland which provide services with all cryo-EM modalities. This seminar aims to summarise our activities over the last 5 years highlighting our major achievements based on publications that include results obtained on the Glacios microscope. We also discuss our current services and prospects for the future given the 1M PLN-worth SPUB grant that we recently got awarded from the Ministry of Science.

room B2.38, Pasteura 5 at 14:15

dr hab. Agnieszka Korgul (Faculty of Physics, UW)

New Therapeutic Strategies for Glioblastoma Multiforme: The Potential of Alpha Radiation in Oncology

Glioblastoma multiforme (GBM, glioblastoma multiforme) is the most common and aggressive primary brain tumour, characterised by rapid growth, high invasiveness and high genetic diversity. Current therapeutic approaches, including surgery, radiotherapy and chemotherapy, although being intensively developed, often do not provide sustained clinical benefit. The average survival time for patients from diagnosis is only 12-18 months, highlighting the urgent need to develop innovative and more effective treatment strategies for this cancer.This seminar will discuss a variety of methods using ionising radiation in cancer therapy, with a particular focus on alpha particles. Alpha radiation, characterised by high linear energy transfer (LET), has unique therapeutic potential as these particles induce complex and difficult to repair DNA damage. This makes them particularly effective in eliminating cancer cells resistant to conventional therapies such as X-rays and electrons.Radiobiological issues will also be addressed, including differences in the mechanisms of DNA damage induced by alpha radiation compared to low LET radiation. Particular attention will be paid to dosimetric aspects, which are key to accurately delivering radiation doses to tumour sites while minimising damage to healthy tissue. Examples of the use of alpha radiation in modern therapeutic strategies will also be discussed, which may represent an important step in the treatment of glioblastoma multiforme.

Bio: Dr Agnieszka Korgul, Prof. UW, is an employee of the Department of Nuclear Physics, Faculty of Physics, University of Warsaw, with over 20 years of experience in research and teaching in nuclear physics. She collaborates with renowned research centres such as CERN, GSI, ORNL, MSU and RIKEN. She has authored more than 100 publications in Philadelphia-listed journals. She is also President of the Polish Nucleonic Society. Her research focuses on basic research, among others, related to nuclear medicine and dosimetry.

room B2.38, Pasteura 5 at 14:15

dr hab. Anna Niedźwiecka (Institute of Physics, Polish Academy of Sciences)

Everything you always wanted to know about intrinsically disordered proteins (but were afraid to ask)

Intrinsically disordered proteins (IDPs) are an important class of biomolecules that regulate biological processes in higher organisms. The lack of a fixed spatial structure facilitates their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From a biophysical point of view, IDPs are biopolymers with a wide configuration state space and their actual conformation depends on the non-covalent interactions of their amino acid side chain groups at a given temperature and chemical conditions.

During this seminar I will discuss the pitfalls in interpreting the molecular properties of IDPs and how we can understand the hydrodynamic parameters of proteins as a function of their structural features. I will also present our recent results on the properties, interactions and propensity to liquid-phase separation of cytoplasmic proteins involved in the regulation of human gene expression, as well as extracellular coral acid-rich proteins responsible for biomineralisation in the skeletal organic matrix, studied by fluorescence correlation spectroscopy and confocal imaging.

Short Bio
Anna Niedźwiecka, PhD DSc
Interactions and Structural Dynamics of Biomolecules
Web of Science Core Coll.: 50 publications, 2048 citations, 4 publications cited > 100 times, H‐index 17; Google Scholar: 64 works cited 3169 times, H‐index 21
• D.Sc. (Habilitation) 2016 in biology, Institute of Biochemistry and Biophysics PAS
• Ph.D. 2003 in physics, with honours, University of Warsaw, Faculty of Physics
• M.Sc. 1994 in biophysics, with honours, University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics
- 2018‐ Associate professor in Laboratory of Biological Physics, Institute of Physics PAS
- 2023‐2026 Vice‐Chair of Scientific Council of Institute of Physics PAS
- 2020‐2021 Head of laboratory at Institute of Physics PAS with accreditation for testing laboratory from Polskie Centrum Akredytacji (PCA) according to PN‐EN ISO/IEC 17025
- 2008‐2014 Scientific coordinator of the NanoFun Project POIG.02.02.00‐00‐025

room B2.38, Pasteura 5 at 14:15

dr Angelika Kaczyńska (WPD Pharmaceuticals)

Trojan Horse Strategy in Targeted Therapy: A New Approach to Combat Brain Cancer

Glioblastoma (GBM) is the most common and aggressive primary brain tumor, with current therapeutic approaches often failing to deliver durable clinical benefits. This highlights the urgent need for innovative treatment strategies. Targeted therapies employing the "Trojan Horse" approach have emerged as a promising avenue, offering the potential to improve specificity and reduce side effects by focusing on tumor-specific antigens.This presentation outlines the preclinical advancements of immunotoxins developed by WPD Pharmaceuticals, specifically designed to target overexpressed proteins such as IL-13RA2 and EphA2—markers frequently found in glioblastoma cells but absent in normal brain tissue. Initial studies demonstrate these immunotoxins' ability to inhibit tumor cell growth and induce apoptosis in receptor-positive GBM cells. The integration of innovative delivery methods, including intracerebral administration and composite carriers, further enhances drug precision and effectiveness. Moreover, combination therapy approaches that pair these immunotoxins with other drugs are being explored to maximize therapeutic outcomes.This pioneering work underscores the potential of the “Trojan Horse” strategy in transforming the treatment landscape for GBM, offering hope for improved patient outcomes through highly specific and locally delivered therapeutic interventions.

Dr Angelika Kaczyńska is a highly qualified biotechnologist specializing in innovative anti-cancer therapies. Dr Kaczyńska earned her PhD with distinction from the University of Gdańsk, where she focused on combination therapies for breast cancer. She has extensive experience in the pharmaceutical industry, particularly in managing research and development (R&D) projects. Since 2018, she has been affiliated with WPD Pharmaceuticals, where she holds the position of Project Manager. She graduated with distinction from the postgraduate studies Academy of Management Excellence at Koźminski University. Dr Kaczyńska is the author of numerous scientific publications and conference presentations. She is a recipient of multiple awards for scientific achievements, including the InnoDoktorant Award, the We Educate the Best Award, the Jerzy Masłowski Award, the Gullapalli Young Investigator Award, and a scholarship co-funded by UNESCO.

room B2.38, Pasteura 5 at 14:15

prof. Piotr Koprowski (Nencki Institute of Experimental Biology PAS)

You Shall Not Pass: A Story of a Potassium Channel Gated and Blocked by Hydrophobicity

Ion channels play a crucial role in cellular function by conducting ions across membranes. The invention of the patch-clamp technique has made it possible to study their activity at the single-molecule level. Among the evolutionary conserved classes of ion channels, those selective for potassium ions are particularly intriguing. Traditionally, potassium channels have been described as water-filled pores with physical gates that regulate ion flow. However, recent studies challenge this paradigm, showing that potassium channel pores can obstruct ion conduction without fully closing by leveraging hydrophobicity to repel water molecules.The large-conductance calcium-activated potassium (BK) channel exemplifies this mechanism. In our collaborative studies using molecular dynamics simulations and patch-clamp experiments, we demonstrated that paxilline, a high-affinity hydrophobic inhibitor of the BK channel, promotes channel pore dehydration. Furthermore, we identified two additional hydrophobic weak small-molecule inhibitors—dibenzoylmethane and chalcone—that block BK channels. These findings suggest a common inhibition mechanism based on water expulsion, opening new avenues for understanding potassium channel pharmacology.

BIO:Piotr Koprowski is a Professor at the Laboratory of Intracellular Ion Channels at the Nencki Institute of Experimental Biology PAS. He graduated from the Department of Biology at the University of Warsaw in 1997 and earned his Ph.D. in 2003 at the Institute of Biochemistry and Biophysics PAS, focusing on mitochondrial DNA repair. During this time, his interest shifted toward ion channels, leading him to investigate bacterial mechanosensitive channels at the Nencki Institute. From 2004 to 2007, he pursued postdoctoral training at the University of California, Berkeley, where he further explored mechanosensitive channels. Upon returning to the Nencki Institute, he continued his research on these channels until 2015, when his focus shifted to human potassium channels. Currently, his research is centered on the regulation and pharmacology of potassium channels, with a particular interest in their protein partners, structural dynamics, and potential therapeutic targeting.

room B2.38, Pasteura 5 at 14:15

dr Marta Wojtyś (IFD UW)

Inhibitory fosforylazy nukleozydów purynowych (PNP) oraz syntetazy adenylobursztynianowej (AdSS) jako potencjalne nowe leki w eradykacji Helicobacter pylori

Helicobacter pylori to gram-ujemna, mikroaerofilna, spiralna bakteria zidentyfikowana 40 lat temu. Kolonizuje błonę śluzową żołądka oraz dwunastnicy połowy ludzkiej populacji na świecie, a jej obecność w organizmie może wywołać poważne choroby takie jak: wrzody żołądka i dwunastnicy oraz nowotwory żołądka. W 2017 roku WHO zaliczyła szczepy H. pylori oporne na klarytromycynę do grupy priorytetowych patogenów w kategorii konieczności wprowadzenia nowych leków do terapii. Dlatego bardzo istotne jest poszukiwanie nowych celów molekularnych do zaprojektowania nowych leków do eradykacji H. pylori. Metabolizm H. pylori opiera się jedynie na tzw. drodze zapasowej (ratunkowej) pozyskiwania puryn, jako jedynej umożliwiającej syntezę kwasów nukleinowych. Obecność w tym szlaku enzymów, fosforylazy nukleozydów purynowych (PNP) oraz syntetazy adenylobursztynianowej (AdSS), kodowanych przez geny, odpowiednio deoD i purA, jest kluczowa dla przeżycia H. pylori. W swojej prezentacji opowiem czy możliwe jest całkowite zahamowanie wzrostu H. pylori, kiedy celem dla potencjalnych nowych leków będą kluczowe enzymy drogi zapasowej pozyskiwania puryn, PNP i/lub AdSS.

room B2.38, Pasteura 5 at 14:15

prof Krzysztof Kuczera (University of Kansas)

Helix Folding in One Dimension: Through the Lens of Hydrogen Bond Dynamics

We present an analysis of α-helix folding in the coarse-grained coordinate of number of formed helical hydrogen bonds (NHB) for four alanine peptides (ALA)n, with n = 5, 8, 15 and 21, residues. Based on multi-microsecond all-atom molecular dynamics trajectories in aqueous solution, we represent the system dynamics in a space of hydrogen-bonding microstates. Transitions changing the hydrogen bond count by 1–2 dominate and the coil formation, NHB 1 → 0, is the fastest process. Graf analysis indicates that, at a sufficiently long lag time, folding in the NHB coordinate is consecutive, with direct folding, 0 → 3, for ALA5 and bottlenecks at transitions 4 → 6 for ALA8, 0 → 5 for ALA15 and 0 → 9 for ALA21. Kinetic coarse graining identified crucial folding intermediates and time scales of their formation. Folding is initiated preferentially at both peptide termini. The kinetic model was also used to estimate diffusion and friction coefficients for helix propagation. Use of the low-dimensional hydrogen bonding picture provides a different, complementary way of describing the complex and fascinating mechanism of helix formation as compared to structural analysis.

Bio:Dr. Krzysztof Kuczera received his PhD in Physics from the Institute of Physics of the Polish Academy of Sciences in 1985. He was a postdoctoral fellow at Harvard University over 1986-1991, with Professor Martin Karplus. Since 1992 he has been at the University of Kanas, becoming Professor of Chemistry and Molecular Biosciences in 2007. His research interests are in computer modeling of biomolecular structure, dynamics and interactions. The goals are to relate the simulations to observable experimental properties, and ultimately to explain biological function and design potent and specific drugs. He is the author of more than 130 publications and presenter of more than 180 scientific talks. In the area of teaching he is implementing active learning strategies in chemistry and biochemistry courses has trained 4 postdocs, 15 graduate and 24 undergraduate students. He has been a visiting professor at Baylor University, the University of Texas and Warsaw University.

room B2.38, Pasteura 5 at 14:15

dr Simon Drew (IFD UW)

Biophysical characterisation of copper-binding proteins: the good, the bad, and the irrelevant

This presentation will provide an overview of my past research, with a special emphasis on applications of EPR spectroscopy to copper-binding peptides and proteins involved in health and disease. I will also outline my current interests and future research goals.

Bio:Simon obtained a PhD specialising in paramagnetic resonance spectroscopy from the School of Physics, Monash University, Australia, in 2002. This was followed by postdoctoral research in magnetic resonance imaging (2002–2004) and bioinorganic chemistry (2004–2006) at the Centre for Magnetic Resonance, University of Queensland, Australia. From 2006–2009, he was a research fellow in the Department of Pathology, University of Melbourne, Australia, gaining wet-lab experience in the biosciences. In 2010–2011, he obtained valuable international experience at the Max Planck Institute for Bioinorganic Chemistry, Germany, before returning to the University of Melbourne to start an independent laboratory in the Florey Department of Neuroscience and Mental Health (2012–2016) and the Department of Medicine (2017–2018). He subsequently relocated to the Institute of Biochemistry and Biophysics, Polish Academy of Sciences (2018–2021) and was a visiting scientist at the Pasteur Institute, Paris (2022–2023). He remains an honorary research fellow in the Department of Medicine (Royal Melbourne Hospital), University of Melbourne.

room B2.38, Pasteura 5 at 14:15

dr Piotr Brągoszewski (Narodowy Instytut Onkologii)

Safeguarding mitochondrial protein transport: proteolytic mechanisms in action

Most mitochondrial proteins begin as precursors in the cytosol and are imported into the organelle through specialized translocation channels. If a protein misfolds during this process, it may stall, blocking further import and disrupting mitochondrial function and protein homeostasis. We compared molecular mechanisms handling failed import events in yeast and human cells. Our experiments revealed that yeast cells primarily rely on the cytosolic ubiquitin-proteasome system, while human cells depend more on mitochondrial factors. Our findings suggest that understanding these mechanisms could provide insights into human diseases related to protein misfolding.

room B2.38, Pasteura 5 at 14:15

dr Monika Wojciechowska (CeNT UW)

Antibiotic resistance is doing well - a challenge and proposed strategies to combat the global threat

Combating antibiotic-resistant pathogens has become one of the greatest challenges facing modern science. The overuse of antibiotics has led to a sharp increase in bacterial resistance, particularly after the COVID-19 outbreak. As a result, the development of new, effective antibacterial agents is crucial. Membrane-active peptides hold significant potential for creating new antimicrobials. However, their therapeutic use is limited by factors such as susceptibility to proteolytic degradation and potential toxicity to mammalian cells.By stabilizing the conformations of membrane-active peptides and adapting their specific properties, we have been able to mitigate these limitations. The peptides we have modified show activity against both Gram-negative and Gram-positive strains and are non-hemolytic. Our findings pave the way for designing new classes of amphipathic peptides and will contribute to the development of novel antibacterial agents

room B2.38, Pasteura 5 at 14:15

prof Joanna Sułkowska (CeNT UW)

Knot or not? Application of Machine Learning models in structural biology

Recent advances in Machine Learning methods in structural biology opened up new perspectives for protein analysis. Utilizing these methods allows us to go beyond the limitations of empirical research, and take advantage of the vast amount of generated data. We use a complete set of potentially knotted protein models identified in all high-quality predictions from the AlphaFold Database to search for any common trends that describe them [1,2]. We show that the vast majority of knotted proteins have the simplest type of knot and that the presence of knots is preferred in neither Bacteria, Eukaryota, or Archaea domains. On the contrary, the percentage of knotted proteins in any given proteome is around 0.4%, regardless of the taxonomical group. Moreover, we show through structural biology methods (X-ray, Cryo-EM), that AF can predict new types of knot in proteins [3] and neural network type models (NN) can be used to detect topology based on geometry [4] and LSTM is a good approach to. design protein with non-trivial topology [5]. In addition, I briefly discuss the use of quantum methods in combination with classical molecular dynamics and AF approach to determine the methylation reactions pathway based on knotted tRNA methyltransferases [6,7,8].1. Everything AlphaFold tells us about protein knots, A Perlinska, M Sikora, JI Sulkowska Journal of Molecular Biology (2024)2. AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods, W Niemyska, P Rubach, BA Gren, ML Nguyen, W Garstka, F Bruno da Silva, EJ Rawdon, JI Sulkowska, Nucleic Acids Research (2022) 3. First crystal structure of double knotted protein TrmD-Tm1570 – inside from degradation perspective, B da Silva, I Lewandowska, A Kluza, S Niewieczerzal, R Augustyniak, JI Sulkowska, 2024 JACS (under review)4. Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks, Bruno da Silva, F., Gabrovšek, B., Korpacz, M., Luczkiewicz, K., Niewieczerzal, S., Sikora, M., & Sulkowska, J. I. Macromolecules (2024), 57(9)5. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model, M Sikora, E Klimentova, D Uchal, D Sramkova, AP Perlinska, ML Nguyen, M Korpacz, R Malinowska, S Nowakowski, P Rubach, P Simecek, JI SulkowskaProtein Science (2024), 33 (7)6. Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study, M Jedrzejewski, B Belza, I Lewandowska, M Sadlej, AP Perlinska, R Augustyniak, T Christian, Y Hou, M Kalek, JI Sulkowska, Computational and Structural Biotechnology Journal (2023)7. Mg2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study, AP Perlinska, M Kalek, Y-M Hou, JI Sulkowska, ACS Catalysis (2020) 10(15):8058-80688. Methyl Transfer by Substrate Signaling from a Knotted Protein FoldT Christian*, R Sakaguchi*, AP Perlinska*, G Lahoud, T Ito, EA Taylor, S Yokoyama, JI Sulkowska, Y-M Hou, Nature Structural & Molecular Biology (2016) 23: 941-948

Bio: Dr hab. Joanna Sułkowska, prof. UW is a head of the "Interdisciplinary laboratory for modeling biological systems" at the Centre of New Technologies at the University of Warsaw. In 2007 she defended with distinction her doctoral dissertation in the field of biophysics, devoted to the characteristics of mechanical properties of proteins. In 2016 she obtained her habilitation at the Faculty of Chemistry of the University of Warsaw and professor position in 2018. For several years, as part of a postdoctoral internship, she worked at the University of California, San Diego. She spent several months as a visiting professor at MIT and the California Institute of Technology. She is an author of over 80 scientific publications, including Nature Structure & MB, JACS, PNAS, PRL, NAR, where she combines theoretical approach with experimental data. For her greatest scientific achievement so far, she considers a discovery and characterization of non-trivial topology in proteins such as knots, slipknots, lassos and theta curves, the determination of mechanisms of their formation and relationships with biological function. She has also worked successfully on antagonists for GPCR-type proteins (CB1 and CB2).Joanna Sulkowska has been awarded many times for her scientific achievements. She received e.g. Installation and Young Investigator award from the European Molecular Biology Organization (EMBO), grants from the National Science Centre, the Foundation for Polish Science, and the Ministry of Science and Higher Education in Poland (Idea Plus based on ERC Starting grant application). She is the winners of the 2018 National Science Centre Award in Poland in the field of Life Sciences (for people under 40 years), and award from MNiSW, 2020. She received the international prize Unesco-L'Oreal ''Rising talent''. She was chosen as a person of the year “MocArty – 2017” by Polish RMF Classic. She was also ranked among the group of 50 brave people and in the initiative Jutronauci by Gazeta Wyborcza (PL) in 2017. She gave as well many public lectures.

room B2.38, Pasteura 5 at 14:15

Denis Koltsov (HORIBA)

Particle Tracking Analysis in biophysics and other areas

Since the first commercial implementations of particle tracing analysis in 2010s the uptake of this method has grown and took over some of the particle- and dispersion-based areas of science and production. This presentation focuses on the application of particle sizing, counting and tracking for biological and pharma applications with relevant method descriptions, capabilities and limitations. We also outline common experimental setups and unique features of three-laser system for number concentration measurements, sizing very polydisperse samples and using florescence methods for tagging. This presentation is aimed to bring the best PTA technology to mainstream universities and companies