Welcome 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.

Introductory lesson

Introductory lesson  

Alice Laníková, DSP Biomolecular chemistry: Study of the dynamics of intrinsically disordered proteins using advanced methods of nuclear magnetic resonance

Masaryk University

Abstract:

Intrinsically disordered proteins are challenging targets due to their high flexibility and lack of a stable three-dimensional structure. Investigating their conformational behaviour is necessary for a detailed understanding of the mechanisms underlying their function. The measurement of NMR relaxation is a powerful experimental approach that provides site-specific information about the dynamic behaviour throughout the molecule. Such experiments on biomolecules require the use of high magnetic fields that provide sufficient resolution and sensitivity; on the other hand, using high magnetic fields limits the information content of the relaxation experiments as they undersample slower motions (ns timescale). 
This presentation will address traditional NMR techniques for studying protein dynamics and introduce high-resolution relaxometry, a unique method that allows measurements at lower magnetic fields. This approach provides insight into the slow dynamics of biomolecules while preserving the necessary resolution and sensitivity. We applied this method to study the dynamics of two disordered proteins and their key interactions of our particular interest. First is the microtubule-associated protein 2c that regulates the dynamics of microtubules in brain neurons. The second studied protein is osteopontin, a multifunctional protein involved in both physiological and pathological processes, including biomineralisation, tumour progression and cardiovascular disease.

Martin Marek: Decoding how deep-sea animals produce light

Martin Marek: Decoding how deep-sea animals produce light

Masaryk University

Abstract: 

The engineering of light-emitting luciferase enzymes towards ultrasensitive bioassays is often possible only when the underlying catalytic mechanism is thoroughly known. Thus, atomic-level knowledge of a Michaelis enzyme-substrate complex, revealing molecular details of luciferin recognition and catalytic chemistry, is crucial for understanding and then rationally improving bioluminescent reactions. However, many known luciferases sample huge protein conformational space, often preventing complete structural characterization. Moreover, using a cognate luciferin is problematic since its conversion into an oxyluciferin in the presence of the luciferase will prevent the capture of the enzyme-luciferin conformation in an activated state. In this talk, I outline how to deal with such obstacles, focusing on the recent discoveries of marine bioluminescence mechanisms facilitated by a combination of engineered ancestral enzyme and the availability of a non-oxidizable luciferin analogue.

Juli Feigon: Structural Biology of Telomerase and Interactions at Telomeres

Juli Feigon is Distinguished Professor in the Department of Chemistry and Biochemistry at University of California, Los Angeles. Her lab continues to investigate structural biology of telomerase as well as the transcriptional regulator 7SK RNP and other non-coding RNAs.

Today´s SBS cancelled, please, come to hear presentation on Mendel Lectures that take place in Mendel´s refectory in the Mendel Museum Brno!!

More info here

9 October 2025 17:00

Jan Novotný: Elucidation of (supra)molecular structure by using paramagnetic effects in NMR

Jan Novotný: Elucidation of (Supra)Molecular Structure by Using Paramagnetic Effects in NMR

CEITEC, Masaryk University

Abstract:

Paramagnetic molecules play an important role both in living systems (active sites of redox enzymes, contrast agents in MRI, potential metallodrugs) and in various technological applications (chemical catalysts, materials for energy storage, single molecular magnets). However, studying their properties by  NMR analysis brings a number of challenges and often requires the use of advanced methods of quantum chemistry. In this contribution, we will demonstrate how the interpretation of pNMR spectra of coordination compounds and their supramolecular complexes allows us to understand the relationship between details of electronic structure and the observed hyperfine shift. Presented examples of our research illustrate effects of unpaired electron via different types of bond (contact shift) and trough-space (pseudocontact shift). 

Jan Petrovský, DSP Biomolecular chemistry : Cryo-EM Studies of Ap₄A RNA Capping and Anti-Plasmid Immunity by pAgo–Cas4 System

Masaryk University

Abtsract:

This study investigates the molecular mechanisms of Ap₄A-mediated RNA capping and anti-plasmid defense using cryo-electron microscopy. We reveal structural insights into how the Ap₄A cap is recognized and incorporated into the transcription process. We also pAgo–Cas4 interact and recognizes nucleic acid substrates involved in prokaryotic immunity.

Dominik Hrebik: Picking lentils out of ashes: Cryo-EM structures of viral membrane proteins from crowded environments

Dominik Hrebik: Picking lentils out of ashes: Cryo-EM structures of viral membrane proteins from crowded environments

CEITEC, Masaryk University

Abstract:

Cryo-electron microscopy single-particle analysis traditionally requires particles of high purity embedded in thin sections of vitreous ice. It has been thought that characterisation of more complex samples, such as heterogeneous enveloped viruses, necessitates cryo-electron tomography, which separates densities in the third dimension. However, data collection and processing of electron tomograms are slower than those for single-particle analysis. Recent advances in hardware and software now allow a wider range of structures to be resolved in crowded environments using single-particle analysis. By employing machine-learning-based picking of objects of interest and subsequent deep classifications, I determined in situ structures of individual proteins at up to 2.1 Å resolution from HIV-1 particles with an average thickness of approximately 120 nm. I demonstrate that it is possible to resolve the structure of the peripheral HIV-1 membrane protein, the matrix protein, with a molecular weight of less than 500 kDa, to sub-3 Å resolution. These structures have resolved a long-standing mystery in HIV-1 biology – the HIV-1 matrix protein binds a small conserved spacer peptide 2, with a previously unknown function. The binding triggers rearrangements of the matrix protein and viral membrane that regulate HIV-1 fusion with the host cell. Additionally, I will present potential future developments and applications of the approach, especially in the context of high-throughput in situ structural biology of membrane proteins and in-cell structural proteomics.

Sarah Butcher: Fake it! Chimeric TBEV structure and function

Sarah Butcher: Fake it! Chimeric TBEV structure and function

University of Helsinky, Finland

Abstract:

"Fake it! Chimeric TBEV structure and function" describes creating a chimeric virus to study how structural proteins affect tick-borne encephalitis virus (TBEV) pathogenicity and tropism. The study concludes that factors beyond the virus's surface proteins are critical in determining its behavior within the brain.

Serge Perez: The diversity and structural complexity of GlycosAminoGlycan (GAG and ProteoGlycans 'PG)

Serge Perez: The diversity and structural complexity of GlycosAminoGlycan (GAG and ProteoGlycans 'PG)

University Grenoble Alpes, France

Abstract:

The diversity and structural complexity of GlycosAminoGlycan (GAG and ProteoGlycans 'PG) constitute a significant part of the ExtraCellular Matrix and Glycocalix. Within the context of a European Cooperation in Science and Technology Action (INNOGLY), scientists of the Glycosaminoglycans (GAG) research community addressed the questions of what remains to be solved to understand the structure and function of GAGs fully and address their role in proteo-glycans  (PG) and further in the glycocalyx and peri- and ExtraCellular matrix.  

The presentation will discuss those pending issues that will benefit from the development of new approaches, namely in chemistry and biology, with emphasis on

(i)             The synthesis of GAG oligosaccharides to build large and diverse GAG libraries,

(ii)            GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores,

(iii)  Biophysical methods to investigate binding interfaces

(iv)  Molecular modelling to identify bioactive GAG sequences and to expand our knowledge and understanding of glycocode governing GAG molecular recognition

(v)      Artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics.

(vi)  The functional characterisation of the new PGs recently identified by glycoproteomics,

(vii)    The selectivity of interactions mediated by GAG chains,

(viii)       The display of GAG chains and PGs at the cell surface and their impact on the availability and activity of soluble ligands and on their move through the glycocalyx layer to reach their receptors

Tereza Buráňová, DSP Biomolecular chemistry: Mysteries of Lectins in Opportunistic Pathogens: Two Domains – One Purpose?

Masaryk University

Asbtract:

LecB (PA-IIL) is one of two characterized lectins (saccharide-binding proteins) from the bacterium Pseudomonas aeruginosa. Both proteins (LecA and LecB) play a significant role in bacterial infection and biofilm formation in immunocompromised patients, such as those with cystic fibrosis. Several LecB homologs have been described, including lectins produced by Burkholderia cenocepacia. Nevertheless, there remain uncharacterized LecB-like proteins in the pathogenic bacteria, some of which contain an additional domain of unknown function. Characterizing these proteins could provide insight into infection mechanisms and lead to the development of novel disease treatment approaches.

This project aims to structurally and functionally characterize three potential two-domain lectins that contain a LecB-like domain with an emphasis on their binding properties. The genes encoding these hypothetical carbohydrate-specific proteins originating in opportunistic human and insect pathogens were identified by bioinformatic analysis. The genes were then cloned into expression vectors and expressed in Escherichia coli. Additionally, new gene constructs were prepared to characterize each domain separately. The examined proteins (whole proteins, as well as separate domains) are undergoing production and purification optimization. Various methods are being used to investigate the thermostability, homogeneity, and binding properties of the purified proteins. The contribution focuses on the current state of knowledge regarding those two-domain proteins.

Jiří Vondrášek: Bridging Domains and Disorder: Bioinformatics and Modeling of Protein–DNA and Protein–Protein Interactions

Prof. RNDr. Jiří Vondrášek CSc: Bridging Domains and Disorder: Bioinformatics and Modeling of Protein–DNA and Protein–Protein Interactions

Ústav organické chemie a biochemie AV ČR, v. v. i., Czech Republic

Abstract:

Proteins operate at the interface of order and disorder, with their functions often shaped by modular domains, flexible linkers, and intrinsically disordered regions. Our research combines bioinformatics, computational molecular biology, and molecular modeling to uncover the principles that govern this continuum.

I will present two case studies. First, our investigations into transcription factors, a protein family central to gene regulation, show how extended sequence signals, DNA shape features, and disordered segments cooperate to fine-tune DNA recognition. These results, originating from work of my student in collaboration with our SIB partner, highlight the critical role of larger structural and sequence context in specificity and regulation.

Second, I will discuss our long-term project on multi-domain proteins, with a focus on inter-domain linkers. These flexible elements serve as dynamic regulators of protein architecture, mediating structural communication, adaptability, and stability. By combining predictive bioinformatics with molecular simulations, we reveal how linkers and disordered regions are key design features in protein evolution.

Finally, I will introduce the Integrated Database of Small Molecules (IDSM), a resource interlinking chemical space with biological interaction data from UniProt and Rhea. By connecting protein architecture with systems-level chemical biology, we aim to derive general rules for molecular recognition and function.

Viktor Bartošík, DSP Biomolecular chemistry: Structural characterization of disordered protein regions using NMR

Masaryk University

Abstract:

Characterising intrinsically disordered protein regions is complicated, but nonetheless essential for completing our understanding of molecular processes. This talk will focus on two systems. The fully disordered microtubule associated protein 2c (MAP2c) both stabilises microtubules and binds cAMP-dependent protein kinase (PKA). The disordered c-terminal domain of delta subunit of RNA polymerase improves transcription specificity, increasing fitness and virulence of the bacterium Staphylococcus aureus and other gram-positive bacteria.

This presentation will demonstrate traditional NMR structure determination on MAP2c-PKA, and ensemble-based characterization on RNAP delta c-terminal domain.

Special attention is placed on comparing the delta of S. aureus with the much less pathogenic Bacillus subtilis. Additionally, a combination of NMR relaxation rates with MD simulations helps us determine the dynamics of the RNAP delta c-terminal domain.

David Šafránek (FI,MU): Revealing the Logic of Gene Regulation

David Šafránek: Revealing the Logic of Gene Regulation

Faculty of Informatics, Masaryk University

Abstract:

Deciphering the dynamics of gene regulation requires the integration of heterogeneous knowledge—data analysis, literature mining, and computational modelling. Genetic regulatory networks (GRNs) capture causal influences among gene products, but reconstructing their short- and long-term behaviour is difficult due to the scarcity of quantitative kinetic information. In such situations, qualitative logical modelling offers a practical and mechanistically interpretable alternative.

In this talk, we will discuss how logic-based models—particularly Boolean networks—combined with abstraction techniques, symbolic algorithms, and model-checking methods can be used to model and analyse GRN dynamics. Starting from a well-studied cell-cycle regulatory network, we will illustrate how these methods scale from small motifs to larger systems involving dozens of interacting components that integrate signalling pathways with gene-level regulation. We will also present several tools developed at the Sybila Laboratory for the inference, refinement, and dynamical analysis of logic-based GRN models.

Ondřej Woznica: Protecting Your Brain Babies: Intellectual Property for Researchers and Other Brave Souls

Ondřej Woznica: Protecting Your Brain Babies: Intellectual Property for Researchers and Other Brave Souls

TTO and Faculty of Law, Masaryk University

Abstarct: This workshop introduces the essentials of intellectual property (IP): what it is, how to protect it, and what you need to know when using it. We will address practical questions such as: What is copyright? How do you obtain a patent? Can copyrighted works be used in teaching? What does a Creative Commons license mean? By understanding these fundamentals, you will gain the ability to identify intellectual property and apply this knowledge in your everyday academic practice. Building on this foundation, the workshop will then focus on technology and knowledge transfer within the university environment by exploring how research outputs can be effectively shared and utilized beyond academia.

NCBR ASSEMBLY (christmas party)

Christmas annual assembly

Toon Lemmens, DSP Biomolecular chemistry and Michaela Mikysková, DSP Biomolecular chemistry

Toon Lemmens, DSP Biomolecular chmistry: Unraveling the dynamic characteristics of RNA through molecular dynamics simulations.

Masaryk university

Abstract:

RNA is a fundamental and indispensable actor in the transfer of information and functioning of life, giving rise to uniquely diverse and complex structural and interaction networks. Here, the multifaceted nature of RNA is demonstrated through two distinct applications. First, the RRM (RNA recognition motif) of protein TbRGG2, featuring a single binding pocket that recognizes poly(U)-RNA, mediates protein–RNA interactions. Secondly, the kink-turn, a multifunctional recurrent structural motif, is characterized by a complex network of tertiary hydrogen bonds facilitating wide-ranging structural dynamics. Both systems were studied through atomistic molecular dynamics (MD) simulations, a powerful computational method based on calibrated set of empirical potentials, referred to as force fields (FF). Standard MD simulations were employed revealing a fast diffusion mechanism governing the interaction between the single binding pocket of RRM and poly(U)-RNA. Simultaneously, the structural complexity of Kt7 (kink-turn 7) was exploited to benchmark the system and evaluate the shortcomings of a broad selection of published RNA FFs. In addition, the kink-turn’s dynamic features such as unkinking and A-minor state transitions are being investigated through several enhanced sampling methods further unraveling RNAs distinctive characteristics. 

Michaela Mikysková, DSP Biomolecular chemistry

Masaryk University

Lessons cancelled

TBA