Biomolecular chemistry and bioinformatics

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: Mgr. Gabriel Demo, Ph.D.

OBJECTIVES: The research aims to unravel the fundamental mechanism of the transcription-translation coupling in bacteria. These studies will significantly advance the current understanding how the lead ribosome closely trails the RNA polymerase (RNAP), thus promoting pause-free transcription, mRNA quality and efficient gene expression in bacteria.

FOCUS: Doctoral research projects focus on the mechanistic details and functional outcomes of coupled transcription-translation in bacteria. Students benefit from the shared cutting-edge core facilities of CEITEC that include (i) X-ray crystallography – crystallization robot Mosquito, Rigaku crystal hotel and diffraction system, (ii) cryo-EM equipment - Versa 3D dual beam microscope, Titan Krios and F20 electron microscopes (iii) High-field NMR systems, and (iv) biomolecular interactions equipment - confocal microscopes, near-field optical microscope (SNOM), surface plasmon resonance, microcalorimetric equipment.

EXAMPLES of potential student doctoral projects:

• Structural and functional identification of factors required to couple transcription and translation in bacteria
• Structal studies of various states of direct and bridged transcription-translation coupling in vitro and in vivo

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Gabriel Demo (gabriel.demo@ceitec.muni.cz) for informal discussion. MORE INFORMATION:https://www.ceitec.eu/structural-biology-of-coupled-transcription-translation-gabriel-demo

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 apod.) Různých poškození nebo zlomů v DNA je až půl milionu za den. Zvláště zlomy DNA vedou k nestabilitě genomu a mohou mít za následek zhoubné změny například vyvolání rakoviny. Jedním z mechanismů, který zaručuje bezchybnou opravu poškozené DNA je homologní rekombinace. Pro tento ročník vypisujeme jedno místo na některé z následujících témat. 1)RecQ4/RecQ helikáza, mutována u „Rothmund-Thomson Syndromu“, a její biochemická charakterizace. 2)Úloha Srs2 proteinu při opravě poškozené DNA. 3)„Bloom Syndrom“ protein a jeho role při odstraňování nebezpečných produktů. 4)Rad51 rekombinasa a co ji ovlivňuje. Při řešení těchto úkolů se zájemci seznámí s molekulárně biologickými, biochemickými, strukturálními a genetickými metodami.