Biomolecular chemistry and bioinformatics

Supervisor: doc. RNDr. Radka Svobodová, 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. Mgr. Lumír Krejčí, Ph.D.

We invite applications for a PhD studentship from applicants with an enthusiastic interest in molecular biology and biochemistry. The successful candidate will work under the supervision of Dr. Krejčí to identify and characterize 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. RNDr. Robert Vácha, PhD.

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: doc. 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. Mgr. Lukáš Žídek, Ph.D.

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: RNDr. Mgr. Jozef Hritz, 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. Mgr. Štěpánka Vaňáčová, 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: Konstantinos Tripsianes, 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: prof. RNDr. Jiří Šponer, DrSc.

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

Our methods are:

• Classical Molecular Dynamics (MD) simulations
• Quantum-chemical (QM) method
• Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
• Structural bioinformatics

Specific experiments are possible in the field of prebiotic chemistry in collaborating laboratories - need to discussed. 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. See the full list of papers on this web page. We have excellent in-house computer facilities, which are regularly upgraded. We currently work in several mutually interrelated research areas.

• RNA structural dynamics, folding and catalysis
• Protein-RNA complexes
• DNA, with focus on G-quadruplexes
• 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: doc. Mgr. Lumír Krejčí, Ph.D.

Naše laboratoř se zaměřuje na studium molekulární podstaty zhoubných onemocnění, které souvisí s rekombinací a opravou poškozené DNA. DNA obsažená v lidské buňce je neustále poškozována vnějšími i vnitřními vlivy (radiace, UV záření ale i chybná replikace apod.) Různých poškození nebo zlomů v DNA je až půl milionu za den. Poškozená DNA zpomaluje nebo dokonce zastaví replikační vidlici a vede k nestabilitě genomu a je asociována se vznikem celé řady onemocnění, včetně rakoviny. Jedním z mechanismů, který zaručuje bezchybnou opravu poškozené DNA a její replikaci je homologní rekombinace. Experimentální práce zahrnuje širokou škálu molekulárně-biologických přístupů vč. amplifikace a klonování DNA, expresi proteinů a jejich purifikace, studium proteinových interakcí a další charakterizace pomocí biochemických, molekulárně biologických, biofyzikálních, strukturálních, buněčně biologických a genetických metod.