NCBR PhD Info Day

We cordially invite you to the NCBR PhD Info Day. You will learn a lot of helpful information essential for the smooth progress of your studies and you will have a unique opportunity to ask anything you need to know. The attendance is mandatory for all 1st to 4th-year PhD candidates enrolled in the following doctoral programmes: Biomolecular Chemistry and Bioinformatics, Genomics and Proteomics, Experimental Plant Biology, and Life Sciences.

Student Mobility & Funding PhD Info Day

Basic rules for participation on foreign stays (obligatory for all PhD students as a course XD110 Placement abroad), funding opportunities and internal processes will be explained by International relations contact Kristýna Bajgarová & Veronika Papoušková, NCBR scientific secretary.

Uncovering the Dicer Activity Cycle- Nikola Miková

Uncovering the Dicer Activity Cycle

Mgr. Nikola Miková, CEITEC,MU

Abstract: 

Mammalian Dicer plays a central role in small RNA biogenesis, yet the full sequence of structural and functional events that constitute its activity cycle is not fully understood. This presentation will discuss our progress in filling in this cycle, with a focus on how structured domains and intrinsically disordered regions of Dicer contribute to its conformational dynamics and RNA processing. Particular attention will be given to the transition from Dicer-mediated RNA cleavage to the subsequent loading of miRNA into Argonaute, a central effector of miRNA-mediated gene regulation.

Machine Learning in Protein Engineering- Dr. Stanislav Mazurenko

Machine Learning in Protein Engineering

Dr. Stanislav Mazurenko,Team leader, AI in Protein Engineering, Loschmidt Laboratories, Faculty of Science MU

Abstract: 

Life sciences are undergoing a transformational shift driven by the emergence of machine learning–based solutions to long-standing problems. These methods are reshaping how we engineer the molecules of life: predict protein structures, annotate protein sequences, evaluate the effects of substitutions on various protein properties, and extract biological insights from simulations and experiments. In this talk, we will explore the state of the art in using machine learning for protein science, highlighting how these tools are changing the way we understand, design, and engineer proteins. We will also delve into ongoing challenges and open research questions in the domain, from data limitations and model interpretability to the integration of physics-based and data-driven approaches. The talk is delivered as part of a Habilitation Lecture.

Cell*: Bringing Web-Based Structural Biology from Molecules to Whole Cells- David Sehnal

Cell*: Bringing Web-Based Structural Biology from Molecules to Whole Cells

David Sehnal, NCBR, MU

Abstract:

Recent breakthroughs in cryo-electron microscopy, tomography, and computational modeling have expanded structural biology far beyond isolated proteins. Researchers can now study large macromolecular machines, viral capsids, and cellular environments containing tens of millions of atoms. Yet interactively exploring and sharing these massive, multiscale datasets without specialized desktop software remains a major challenge.

Mol* (molstar.org) is an open-source web platform co-developed by NCBR and CEITEC together with PDBe and RCSB PDB. It has become a widely used platform for molecular graphics in the browser, supporting structural analysis and visualization in resources including the Protein Data Bank, AlphaFold DB, and many others.

In this seminar, we present the key outcomes of the GAČR JUNIOR STAR project Cell* (2022–2026), hosted at NCBR. Cell* extends the Mol* ecosystem from individual proteins to cellular-scale environments, delivering practical tools for structural biology, imaging, education, and scientific communication.

Harnessing Natural Products as Supramolecular Building Blocks in Pharmacy and Beyond- Ondřej Jurček

Harnessing Natural Products as Supramolecular Building Blocks in Pharmacy and Beyond

Ondřej Jurček, Faculty of Pharmacy, MU

Abstract:

Natural systems possess chiral binding pockets which play key roles in many biological functions, for example, in selective molecular recognition as parts of transport proteins or in substrate-specific transformations as parts of enzymes. To understand and mimic these natural systems and their (supra)molecular mechanisms of action, the development of their artificial counterparts containing stereogenic and metal centres is desirable. Almost 60 years ago, studying small crown-like molecules for binding alkaline metal cations, the field of supramolecular chemistry has emerged, ultimately leading to a better understanding of complexity of intermolecular interactions in design and construction of hierarchically higher supramolecular systems with functions. But, only recently, the subfield of metallo-supramolecular self-assembly advanced from using relatively simple symmetric, rigid, and achiral coordination ligands to more challenging systems using unsymmetric, flexible, and chiral organic building blocks. The understanding of multicomponent self-assembly mechanisms is the key to design and development of advanced structural architectures able to mimic (or repair deleterious) natural processes.

Easing these efforts, nature readily offers convenient chiral building blocks (e.g., numerous terpenoids, carbohydrates, or amino acids) which can be utilized. In our work, we provide a concept to design chiral, unsymmetric, flexible ligands employing natural bile acids in the construction of large supramolecular coordination complexes.^1-4 Implementing this concept we have introduced several building coordination ligands (L), which in connection to palladium cations (Pd) form large macrocycles of general formula Pd_nL_2n, where n = 3-6,^1-3 or unique bioactive cages Pd₆L₈ and Pd₁₂L₁₆ of a size of small proteins containing up to 160 stereogenic centres.⁴ 

In the line of our interest, we also study other metallo-supramolecular systems made of natural products, e.g., using macrocyclic carbohydrates for preparation of porous metal-organic frameworks (MOFs) as carriers of Ru(III)-based metallo-drugs,^5,6 or using folic acid in development of non-toxic supramolecular metallo-supergels which have shown application potential beyond the scope of supramolecular pharmacy.⁷

References:

1) O. Jurček, P. Bonakdarzadeh, E. Kalenius, J. M. Linnanto, M. Groessl, R. Knochenmuss, J. A. Ihalainen, K. Rissanen, Angew. Chem. Int. Ed. (2015) 54, 15462–15467.

2) O. Jurček, Nonappa, E. Kalenius, P. Jurček, J. M. Linnanto, R. Puttreddy, H. Valkenier, N. Houbenov, M. Babiak, M. Peterek, A. P. Davis, R. Marek, K. Rissanen, Cell Rep. Phys. Sci. (2021) 2, 100303.

3) O. Jurček, S. Chattopadhyay, E. Kalenius, J. M. Linnanto, A. Kiesilä, P. Jurček, P. Radiměřský, R. Marek, Angew. Chem. Int. Ed. (2024) 136, e202409134.

Single-Molecule Imaging of Telomere Maintenance in Living Cells- Tomáš Janovič

Single-Molecule Imaging of Telomere Maintenance in Living Cells

Tomáš Janovič, NCBR, MU

Abstract:

Telomeres protect chromosome ends and are essential for genome stability. Their function relies on a network of telomere-associated proteins that must assemble, exchange, and act at chromosome ends with precise spatial and temporal control. Yet, much of our current understanding comes from in vitro biochemical and structural studies, leaving the behavior of these molecular machines in living human cells poorly understood.

Our group combines genome engineering, quantitative fluorescence microscopy, single-molecule imaging, and structural approaches to investigate how telomeres are organized and maintained in their native cellular environment. We have developed a panel of human cancer cell lines in which individual telomere-associated proteins are endogenously HaloTagged, enabling us to quantify their abundance and directly visualize their behavior at native chromosome ends. Using high-speed single-molecule imaging, we have uncovered distinct dynamic behaviors among shelterin components, revealing stable and highly mobile populations that contribute to chromosome-end protection and regulation of telomerase access.

We are extending this approach to the CST complex, which cooperates with DNA polymerase α/primase to complete telomere replication. Live-cell single-molecule imaging shows that CST is highly mobile in the nucleoplasm and associates with telomeres only infrequently. Stable CST binding at telomeres is a rare event, closely resembling the transient interactions observed for telomerase.

Together, these studies establish a broader research program focused on understanding how telomere-associated molecular machines assemble, move, and function at chromosome ends in intact cells. By integrating quantitative imaging, genome engineering, and structural approaches, we aim to connect molecular dynamics with nanoscale organization and ultrastructure, revealing fundamental mechanisms that preserve genome stability.

Petr Stadlbauer, Institute of Biophysics & Faculty of Sciences, UP

The Life and Death of a G-Quadruplex

Petr Stadlbauer, Institute of Biophysics & Faculty of Sciences, UP

Abstract:

TBW

Artificial Intelligence in Biomolecular Research and Education- Petr Kulhánek

Artificial Intelligence in Biomolecular Research and Education

Petr Kulhánek, NCBR, MU

Abstact:

TBW

Molecular Mechanisms of Protein Complexation and Aggregation in Neurodegeneration- Jozef Hritz

Molecular Mechanisms of Protein Complexation and Aggregation in Neurodegeneration

Jozef Hritz, NCBR & CEITEC, MU

Abstract:

TBW

Understanding and Tuning Polymeric Implant Surfaces: From Cell-Free Models to Molecular Dynamics- Lukasz Cwiklik

Understanding and Tuning Polymeric Implant Surfaces: From Cell-Free Models to Molecular Dynamics

Lukasz Cwiklik, JH Institute, AS CZ

Abstract:

TBW

NCBR christmas assembly

Traditional NCBR christmas assembly for students as well as for employees of NCBR department.

CEITEC15 Conference

15 Years of CEITEC: Development, Impact, and Future Direction

CEITEC MUNI, University Campus, Building E35, Atrium

The CEITEC15 Conference marks the 15th anniversary of CEITEC.

The event will bring together partners, collaborators, alumni, scientists, and institutional stakeholders to reflect on the development of CEITEC and its role in research and innovation.

cancelled