Biomolecular chemistry and bioinformatics

DNA forms not only the canonical duplex but also various non-canonical structures such as triplex, G-quadruplex, and i-motif. The are many external factors that influence folding and stability of the individual forms. Further, DNA structure can be affected by attachment of various artificial covalent or noncovalent ligands.

Our investigations are focused on detailed structural characterization of short purine oligonucleotides clipped by proper sequential blocks. For this purpose, modern NMR experiments combined with MD simulations are employed. The effect of modification of selected nucleotide on the structural properties of designed models is characterized to gain deeper understanding of key noncovalent interactions that contribute to the DNA folding.

Examples of PhD topics:
a) Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling
b) Designing modified DNA fragments

More information:
radek.marek@ceitec.muni.cz
jan.novotny@ceitec.muni.cz

Notes

Note: All candidates should contact R. Marek for informal discussion before initiating the formal application process.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

V současné době máme k dispozici nadkritické množství informací ohledně proteinových strukturních rodin. Konkrétně, pro většinu rodin známe stovky struktur jejích zástupců, přičemž tyto struktury pocházejí z různých organismů, některé z nich váží rozličné ligandy a mnohé obsahují různorodé mutace. Tyto informace umožňují analýzu „anatomie“ daných proteinových rodin. Například studium elementů sekundární struktury (šroubovic a skládaných listů), jejich vzájemného uspořádání, konzervovanosti a určování, které z těchto elementů jsou pro danou proteinovou rodinu klíčové a které se vyskytují jen raritně. Dále pak zkoumání proteinových tunelů a pórů, jejich charakteristik a četnosti jejich výskytu u jednotlivých zástupců proteinové rodiny. V rámci laboratoře LCC jsou vyvíjeny softwarové nástroje pro realizaci výše uvedených analýz, např. software MOLE, LiteMol, SecStrAnalyzer. Hlavním cílem disertační práce je zaměřit se na několik konkrétních biologicky významných proteinových rodin (např. cytochromy, poriny, dehalogenázy, proapoptotické proteiny) a provést jejich detailní analýzu. Dalším cílem je spolupráce při vývoji uvedených softwarových nástrojů.

Notes

Vypsáno pro přihlášení studentky Jany Porubské.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

V současné době jsou v rámci pokročilých bioinformatických, biochemických a biologických experimentů produkována rozsáhlá data – např. elektronové hustoty z kryoelektronové mikroskopie, obrazová data získaná optickou mikroskopií, proteinové struktury produkované molekulovou dynamikou nebo coarse-grained simulacemi. Taková data obsahují cenné informace pro vědeckou komunitu. Jejich získání je však často velmi časově i finančně náročné. V mnoha případech se jedná o data netriviálně komplikovaná (různě strukturované souborové hierarchie a závislosti mezi nimi) a velmi rozsáhlá. Stále častějším a do budoucna povinným požadavkem vědecké komunity je zpřístupňovat data dle FAIR principů. Tzn. že je nezbytné tato data vhodně strukturovat, anotovat a archivovat, aby byla pro komunitu dostupná, transparentně vyhledatelná, uložena ve standardních formátech a tím dále opakovaně využitelná. A právě vývojem workflow pro management uvedených dat se bude zabývat tato disertační práce.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

Bacterial and fungal infections are once again becoming a serious threat to humans. Especially with the emergence of new strains resistant to known antibacterial and antifungal drugs, the search for new treatments has become paramount. However, the classical drug development approaches have many limitations and have not provided successful candidates in the last decades. Hopefully, the situation can change due to a steady increase in computational power. Such unprecedented computational power, combined with new algorithms employing machine learning and artificial intelligence approaches, has the potential to revolutionize structural biology, biomolecular chemistry, and bioinformatics. However, many challenges need to be overcome to get the required outcome.

We are interested in combining in silico modelling approaches utilizing both physically based and machine learning approaches to understand the function of enzymes from pathogenic organisms. Detailed knowledge of protein behaviour and enzymatic reaction mechanisms is essential for developing potential inhibitors and, thus, novel drugs capable of blocking specific biochemical pathways that either kill the pathogen or help the immune system eradicate the infection.

We focus on systems with unknown experimental structures, where the combination of artificial intelligence approaches inspired by AlphaFold2 methodology and advanced molecular dynamics sampling can reveal a suitable structural model. The found model is then employed in the subsequent study of the reaction mechanisms by hybrid approaches utilizing reaction and classical potentials. We test the suitability of many approaches, from a traditional quantum mechanical description of the active site to modern ones based on machine learning approaches or reactive potentials such as ReaxFF. We employ the in-house developed PMFLib software to obtain free energies describing the reaction and activation energies of the studied processes.

Possible PhD topics include:

• Structure, protein dynamics, and reaction mechanisms of fucosyltransferases
• Pharmacologically relevant glycosyltransferases in Mycobacterium tuberculosis

Notes

Téma vyhrazeno pro studenta Július Zemaník.

Supervisor

RNDr. Petr Kulhánek, Ph.D.

Correlative Light Electron Microscopy (CLEM) uses a combination of an optical (fluorescence) microscope and a cryo-electron microscope. Two images of the sample are taken simultaneously – one with the optical light, the other with the electron beam. This technology allows to capture not only dynamic changes but also the molecular ultrastructure of living systems. New developments in accurate positional referencing of specimens on mounting grids, advances in the instrumentation, and the availability of software packages for cross-platform data correlation allow to image the ultrastructure of nucleolar sub-compartments and to track specific proteins found in phase-separated organelles. In this project, we will implement the CLEM technology to investigate and visualize phase-separated organelles involved in transcription by RNA polymerase II and investigate their regulatory mechanism during transcription. This biophysically focused project will also involve other imaging approaches, including single-particle reconstruction cryo-electron microscopy and cryo-electron tomography, which will help to obtain an overall picture of condensate-based transcription at different resolutions.

Supervisor

prof. Mgr. Richard Štefl, Ph.D.

We invite enthusiastic application for a PhD position with interest in molecular biology and biochemistry. The successful candidate will work under the supervision of Dr. Krejčí to identify and characterise novel inhibitors of DNA repair nucleases, their mechanisms of action and therapeutic implications.

The PhD position candidate should hold or be about to complete a Masters degree in molecular biology, biochemistry or similar field. The applicant is also expected to demonstrate essential training in a range of molecular biology techniques relevant to basic research, should be well-organised, motivated and passionate about pursuing a career in biomedical research.

We offer fully funded positions with competitive salary in a well established laboratory. The lab hosts international team members, has a strong publication track record and international collaborations. The offered projects contribute to a rapidly advancing, very competitive field. The successful candidate can start immediately.

Supervisor

doc. Mgr. Lumír Krejčí, Ph.D.

The primary objective of our research is to delve into the collective and site-specific dynamics of both intrinsically disordered and globular proteins, with the overarching goal of elucidating their biological function and allosteric control mechanisms. Our focus lies in comprehending how knowledge of protein dynamics can inform the design of mutations within a protein to reshape its ensemble of conformational states and thereby modulate its function. Central to our investigative approach is the recognition of how evolution has shaped protein dynamics and how fundamental processes such as allosteric regulation are intricately intertwined with the dynamic coupling of different regions within an enzyme. To achieve this, we employ a combination of solution- and solid-state NMR techniques, allowing us to zoom in on the dynamic coupling mechanisms underlying allostery. Through this interdisciplinary methodology, we endeavor to gain a comprehensive understanding of how protein dynamics intersect with allosteric regulation, offering valuable insights for the development of targeted therapeutic interventions. These insights hold particular promise for addressing diseases characterized by protein dynamics and function.

Supervisor

prof. Mgr. Lukáš Žídek, Ph.D.

OBJECTIVES: The aim is to elucidate the relationship between molecular properties of amphiphilic peptides and their ability to translocate and form transmembrane pores in membranes with various lipid compositions. The obtained understanding will be used for the development of new antimicrobial peptides, which can serve as a new type of antibiotic drugs.



DESCRIPTION: Antibiotic-resistant bacteria cause more than 700 000 deaths per year, and the forecast is 10 million per year in 2050. Moreover, emerging strains of bacteria resistant to all available antibiotics may lead to a global post-antibiotic era. Because of this threat, the WHO and the UN are encouraging the research and development of new treatments. Antimicrobial peptides are promising candidates for such new treatments. We will study the molecular mechanism of action of antimicrobial peptides and determine the critical peptide properties required for membrane disruption via the formation of transmembrane pores and spontaneous peptide translocation across membranes. Based on the obtained insight, we will design new peptides and test their abilities. The most effective peptides will be evaluated for antimicrobial activity and human cell toxicity using growth inhibition and hemolytic assays, respectively. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models. The simulations will be complemented by in vitro experiments using fluorescent techniques.



EXAMPLES of potential projects: * Antimicrobial peptides and formation of membrane pores * Synergistic mechanisms between antimicrobial peptides * Membrane disruption by antimicrobial peptides in non-equilibrium conditions



MORE INFORMATION about the group: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor

prof. RNDr. Robert Vácha, PhD.

Díky vysoce výkonným bioinformatickým, biochemickým a biologickým experimentálním metodikám jsou v současné době produkována extrémně velká data – např. data z kryoelektronové mikroskopie, obrazová data z nukleární magnetické rezonance nebo světelné mikroskopie, proteinové struktury generované coarse-grained simulacemi apod. Tato data jsou cenná nejen pro jejich autory, ale i pro celou vědeckou komunitu. Proto je velmi žádoucí uvedená data této vědecké komunitě zpřístupnit. Nezbytným krokem pro zpřístupnění těchto dat je jejich popis metadaty. Bez metadatového popisu by byla orientace v datech nemožná. Cílem disertační práce je vývoj metodik a workflow pro práci s těmito metadaty: jejich extrakce z (primárních) dat, popis pomocí ontologií a integrace v rámci obecnějších metadatových schémat, případně návrh systému/jazyka, který umožní s metadaty z různých zdrojů transparentně a unifikovaně pracovat.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

Bacterial glycans, commonly found on cell surfaces, are a characteristic trait of many bacteria. They play a crucial role in adhesion, colonization, and evasion of the immune system. This Ph.D. project employs state-of-the-art molecular simulations to investigate how bacterial glycans and lipopolysaccharides interact with polymeric materials. The primary goal is to leverage molecular insights to propose innovative functionalization techniques for implant coatings, making them less prone to bacterial adherence. The student will develop and employ novel atomistic/coarse-grained models to accurately depict both bacterial glycans and polymeric surfaces. The student will master and perform multiscale molecular dynamics simulations, incorporating enhanced sampling methods such as well-tempered metadynamics and accelerated weight histogram techniques. The project will be conducted in collaboration with multiple experimental groups, enriching its practical applicability.

All interested candidates should first contact Dr. Denys Biriukov (denys.biriukov@ceitec.muni.cz)

Supervisor

Denys Biriukov, Ph.D.

Peptidová/proteinová afinita k membránám je závislá na konkrétní sekvenci a membránovém složení. Bohužel porozumění tohoto komplexního vztahu nám dosud chybí. Cílem tohoto projektu odhalit tento vztah a využít ho k vývoji nových antimikrobiálních peptidů, biomarkerů a senzorů.

Student získá znalosti v oblasti fluorescence, lipidových váčků, QCM.

Supervisor

prof. RNDr. Robert Vácha, PhD.

OBJECTIVES: The aim is to elucidate the relationship between protein sequence and preferred composition and curvature of human membranes,i.e., find peptide motifs that are selective to specific membranes in cells (plasma membrane, endoplasmic reticulum, Golgi apparatus, mitochondria, etc.). The obtained understanding will be used for the development of new protein biomarkers, sensors, scaffolds, and drugs.



DESCRIPTION: The control of biological membrane shape and composition is vital to eukaryotic life. Despite a continuous exchange of material, organelles maintain a precise combination and organization of membrane lipids, which is crucial for their function and the recruitment of many peripheral proteins. Membrane shape thus enables the cell to organize proteins and their functions in space and time, without which serious diseases can occur. Moreover, membrane curvature and lipid content can be specific to cancer cells, bacteria, and enveloped virus coatings, which could be utilized for selective targeting. We will develop a new method, using which we will elucidate the relationship between the protein sequence and the preferred membrane. The relationship will lay the foundations for the design of new protein motifs sensitive to membranes with a specific curvature and composition. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models.



EXAMPLES of potential projects: * Determination of helical motifs for specific membrane compositions * Development of implicit membrane model for fast determination of protein-membrane affinity * Helical peptides and their sensitivity for membrane curvature



MORE INFORMATION: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor

prof. RNDr. Robert Vácha, PhD.

The research goal is investigation of structure, dynamics, and biologically relevant properties of proteins, using NMR spectroscopy and other high-resolution approaches. Currently, our group is mostly interested in studies of molecular motions using NMR relaxation and relaxation dispersion; in studies of protein disorder using NMR approaches providing sufficient resolution (usually based on non-uniformly sampled high-dimensional spectra); and in studies of interactions of intrinsically disordered proteins with their binding partners (using NMR, cryo-EM, and biophysical methods). The systems currently studied in the laboratory include bacterial RNA polymerases and microtubule associated proteins.

We are inetrested structure and dynamics of well-ordered and domains of subunits and sigma factors of RNA polymerase from B. subtilis, characterization of structural features and dynamics of disordered domain, and in importance of electrostatic interactions for structural properties and biological function of the protein. Currently we extend our interest to mycobacterial RNA polymerase.

Microtubule associated protein 2c (MAP2c) is a key factor regulating microtubule dynamics in developing brain neurons, and an example of an intrinsically disordered proteins with an important physiological function and detectable structure-function relationship. The first goal is to study MAP2c in a natural complexity and by methods providing atomic resolution. Such methods include paramagnetic relaxation interference, to detect and describe transient local structures of MAP2c important for its function, and real-time NMR, to monitor kinetics of MAP2c phosphorylation by relevant kinases of different signalling pathways. The second goal is to characterize interactions of MAP2c with biologically important binding partners, especially with isoforms and a monomeric form of regulatory protein 14-3-3. The third goal is to test the effect of cellular environment on MAP2c by recording NMR spectra at near-to-native conditions (in cells and/or cell lysates) and/or by performing cryo-electron tomography on monolayered neurons.

EXAMPLES OF POTENTIAL PHD TOPICS:

• Interactions underlying physiological function of Microtubule Associated Protein 2c
• Structure, dynamics and interactions of bacterial RNA polymerase subunits and sigma factors

Supervisor

prof. Mgr. Lukáš Žídek, Ph.D.

BACKGROUND: Several neurodegenerative diseases are associated with the formation of fibrous protein aggregates. The fibrillization of amyloid beta peptide into amyloid plaques and the agregation of hyperphosphorylated tau protein into neurofibrillar tangles are main neuropatological signs of Alzheimer disease. Studying of how different factors influence the formation of biomolecular complexes is the key for understanding underlying molecular mechanism of neurodegerative processes. The described activities are part of international research projects allowing to spend the part of PhD study at the collaborative groups in Europe or North and South America and to learn specific research techniques, there.

OBJECTIVES: The research aims to elucidate molecular mechanisms of conformational changes leading to the modified potential of biomolecular complex formation. Interdisciplinary approach combining computational biophysical chemistry, structural biology, bioinformatics and biophysical interaction techniques will be applied.

FOCUS: Doctoral research projects focus on the monitoring of post-translational modification of studied proteins, their interaction with adaptor proteins and induced conformational changes. Students benefit from outstanding research facilities of CEITEC-MU that include cryoEM tomography, NMR, AFM, and biophysical interaction methods.

EXAMPLES of potential student doctoral projects:

• Are Tau fibrils induced by phosphorylation and the interaction with 14-3-3 proteins relevant for Alzheimer disease?
• A Tau conformational changes induced by phosphorylation and 14-3-3 proteins relevant in neurodegenerative diseases
• Oligomerization states within the 14-3-3 protein family
• Computational prediction of biomolecular complexes and their statibities

MORE INFORMATION: jozef.hritz@ceitec.muni.cz

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Jozef Hritz (jozef.hritz@ceitec.muni.cz) for informal discussion.

Supervisor

doc. RNDr. Mgr. Jozef Hritz, Ph.D.

The internal and external RNA modifications play crucial roles in a number of essential processes of eukaryotic organisms. They regulate the production of germ cells, cellular differentiation, response to stress, and defects in this pathway have been linked to a number of human diseases.

The aim of PhD projects is to study in details on how specific terminal RNA modifications regulate cellular differentiation and to study the protein-protein interactions of factors involved in the regulation of adenosine methylation (m6A) in coding and noncoding RNAs.

Prospective student should ideally have done masters in molecular biology/biochemistry and have laboratory experience in nucleic acids and/or protein purification and analysis. The most highly valued feature will, however, be excitement for science and a strong drive in tackling important biological questions.

EXAMPLES OF POTENTIAL PHD TOPICS:

• The role of posttranscriptional RNA modifications in cell differentiation
• The role of protein-protein interactions in the dynamics of m6A RNA modification

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor

MORE INFORMATION: https://www.ceitec.eu/rna-quality-control-stepanka-vanacov

Supervisor

prof. Mgr. Štěpánka Vaňáčová, Ph.D.

We apply structural biology methods in order to gain a mechanistic view of CK1ε action in the Wnt signalling pathways. CK1ε represents an attractive therapeutic target but currently two key steps in the CK1ε-mediated Wnt signal transduction are unclear: how CK1ε gets activated and/or engages target proteins in response to Wnt signal and how CK1ε phosphorylates its key substrate Dishevelled (DVL).

Our preliminary data suggest that we can efficiently apply methods of integrated structural biology to (i) probe the DVL conformational landscape using in vitro and in vivo FRET sensors coupled to SAXS and CryoEM, (ii) understand the (auto)phosphorylation regulatory mechanisms of CK1ε, (iii) analyse by NMR the functional consequences of DVL phosphorylation and (iv) monitor DVL phosphorylation by real-time NMR under controlled cellular conditions. The position is part of a multidisciplinary project that combines (i) cellular and molecular biology, (ii) proteomic analysis, (iii) biochemistry and structural biology, and received generous funding in a very competitive grant scheme.

Keywords: CK1ε, WNT, DVL phosphorylation, SAXS, cryo-EM, cryo-electron microscopy, real-time NMR

Contact:
Kostas Tripsianes, PhD | CEITEC - Central European Institute of Technology | Masaryk University | Kamenice 5/A35/1S081, CZ-62500 Brno | phone: 00420 549 49 6607

Supervisor

Konstantinos Tripsianes, Ph.D.

Our scientific goal is understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.

To achieve our goal, we use a wide portfolio of theoretical/computational approaches. Our research is closely related to experiments, mostly via extensive collaborations, though in the prebiotic chemistry we have in house experiments. We offer thesis essentially on any topic that is currently active in the laboratory. You can get the most up-to-date idea about our current research from the WOS or SCOPUS databases, where you can find all our publications (Sponer, J.), see all our collaborators, etc. The laboratory is located at the Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno, where we have a powerfull and regularly upgraded set of high-perfomance computer clusters dedicated exclusively to our group

Our methods are:

• Classical Molecular Dynamics (MD) simulations. Besides standard simulations, we have years of experience in using all classes of enhanced-sampling techniques. We play also a prominent role in development of DNA/RNA simulation force fields and our versions are used world-wide
• Quantum-chemical (QM) method. We are using a wide spectrum of methods, ranging from ultra-accurate computations of small model systems, through large-scale QM studies on biomolecular building blocks with hundreds of atoms up to sophisticated methods that are used in studies of excited states and photochemistry; the later technique is especially relevant to study the origin of life chemistry under UV light. Again, please see the papers we have published in last years.
• Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
• Structural bioinformatics

Specific experiments are possible in the field of prebiotic chemistry in collaborating laboratories. Modern computations are extensively combined with many experimental techniques (NMR, X-Ray, high-energy lasers, biochemical techniques) mostly via numerous collaborations. We collaborate with 30 foreign and Czech laboratories. We publish about 20 papers annually and belong to the most cited Czech research groups. We currently work in several mutually interrelated research areas.

• RNA structural dynamics, folding and catalysis
• Protein-RNA (or DNA) complexes. We try to go beyond the ensemble-averaged picture of experimental methods in order to understand how rarely accessed dynamical conformations invisible to experiments allow to separate affinity for reactivity or selectivity.
• DNA, with focus on G-quadruplexes, specifically advanced studies of quadruplex folding mechanisms
• Diverse types of quantum-chemical studies on nucleic acids systems
• Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe), with a specific attention paid to the formamide pathway to template-free synthesis of the first RNA molecules. This specific project includes also in house experimental research.

Besides studies of specific systems, we are also involved extensively in method testing/development, mainly in the field of parametrization of molecular mechanical force fields for DNA

NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Sponer (sponer@ncbr.muni.cz) for an informal discussion.

Laboratory web page https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/info-about-the-department

List of publications https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/publications

Supervisor

prof. RNDr. Jiří Šponer, DrSc.

Our laboratory is focusing on study of molecular mechanisms of genome instability associated diseases
linked to DNA repair defects. DNA in cells is constantly damaged not only from external but also internal sources resulting in accumulation of hundreds of thousand lesion per cell and day. One of the mechanisms involved in genome stability is homologous recombination and its defects are linked to development of various cancers and diseases (BLM, RTS, FA, etc.).

PhD project might involved following topics: 1)RecQ4 helicase, mutated in „Rothmund-Thomson Syndrome“, a its biochemical and biological characterisation; 2) Development of new nuclease inhibitors and their preclinical characterisation; 3) Rad51 paralogs and their role in genome stability and cancer development; 4) Role of G4 structures and their metabolism in genome stability.

Our approaches involve broad range of molecular-biological, biochemical, biophysical, cell biological, genetic and structural methods.

Supervisor

doc. Mgr. Lumír Krejčí, Ph.D.