Změnit instituci
Pokročilé nano a mikrotechnologie Pokročilé materiály Strukturní biologie Gen. a prot. rostlin. systémů Molekulární medicína Výzkum mozku a lidské mysli Molekulární vet. medicína

Struktura a dynamika proteinů - Lukáš Žídek

Vedoucí výzkumné skupiny
Researcher ID
Telefon: +420 54949 8393
E-mail: ,
Kancelář:
Zástupce vedoucího výzkumné skupiny
Researcher ID
Telefon: +420 54949 3847
E-mail:
Kancelář:

Research areas

  • Structure, dynamics and interactions of proteins
  • Intrinsically disordered proteins
  • Development and application of NMR methodology

Main objectives

  • Development of new methodologies for the investigation of biomolecular structures, interactions, and dynamics.
  • Investigations of the biomolecular structures and interactions and their relationship with physiological functions, diseases and therapies.
  • Production of pure and homogeneous proteins for the structural analysis.
  • Production of monoclonal antibodies, with emphasis on the quality of the antigen – antibody selection.  Selection of binding molecules from synthetic DNA libraries for diagnostic and therapeutic use.

Content of research

In collaboration with L. Krasný (Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic), we study subunits and sigma-factors unique for RNA polymerase of Gram-positive bacteria. We have determined structure of well-ordered N-terminal domain of delta subunit and characterized structural features of its intrinsically disordered C-terminal domain. In addition to the structural description, we characterized dynamics of both domains at various time scales using NMR relaxation. Investigation of other subunits and sigma-factors is in progress.

Multidisciplinary research of proteins involved in plant hormone signaling cascades is an example of a collaborative project within CEITEC (J. Hejtko, Functional Genomics and Proteomics of Plants). We have studied dynamics of receiver domain of the sensory kinase CKI1 and characterized its interactions with Mg(2+) ions and a phosphate analogue. We are involved in characterization of interactions of the CKI1 receiver domain with its down-stream partners and in structural studies of other sensory kinases (e.g. ETR1).

Traditionally, the strength of the group has been development of NMR methodology for atomic-resolution studies of proteins and nucleic acids. Recently, several fruitful collaborations witnessed that we are able to apply our know-how to solve real biological problems that were hard to attack by the conventional approaches. In the future, we would like to continue to develop in this direction and to complement the existing successful collaboration with our own projects. We plan to study dynamics, structural properties, function and regulation of Microtubule Associated Protein 2c (MAP2c), a cytoskeletal protein important for development of neuronal cells. The free form of the protein is disordered and relatively large (49 kDa), which makes it a challenging target for NMR. Our preliminary results show that the methodology developed in our group is sufficient for such a type of molecule.

Delta
  3D structure of the delta subunit of RNA polymerase from Bacillus subtilis including disordered C-terminal tail determined by NMR spectroscopy.

seznam / vizitky

Jméno a pozice

E-mail

Telefon

prof. Mgr. Lukáš Žídek, Ph.D.
vedoucí pracoviště
+420 54949 8393
prof. RNDr. Vladimír Sklenář, DrSc.
představitel vedení pro infrastruktury
+420 54949 7022
RNDr. Mgr. Jozef Hritz, Ph.D.
senior researcher
+420 54949 3847
Mgr. Petr Padrta, Ph.D.
odborný pracovník
+420 54949 6355
Dr. Tanvir Shaikh
manažer pro koordinaci a správu projektů, senior researcher
+420 54949 7577
RNDr. Mgr. Arnošt Mládek, Ph.D.
odborný pracovník ve výzkumu
+420 54949 5398
Mgr. Zuzana Gelová
odborná pracovnice - PhD studentka
Mgr. Kateřina Hanáková
odborná pracovnice, odborná pracovnice - PhD studentka
+420 54949 8442
Ing. Dominika Ledvinová
odborná pracovnice - PhD studentka
+420 54949 8442
Mgr. Zuzana Jaseňáková
odborná pracovnice - PhD student
+420 54949 2615
Mgr. Kateřina Melková
odborná pracovnice - PhD student
+420 54949 2523
Mgr. Vojtěch Zapletal
odborný pracovník - PhD student
+420 54949 8147, +420 54949 2523
Mgr. Šimon Džatko
odborný pracovník - PhD student
+420 54949 7832
Mgr. Martin Gajarský
odborný pracovník - PhD student
+420 54949 7832
Mgr. Michaela Krafčíková
odborná pracovnice - PhD student
+420 54949 7832
Mgr. Olga Otrusinová
PhD student
+420 54949 2615
Mgr. Zuzana Trošanová
odborná pracovnice - PhD student
Séverine Jansen, PhD.
senior researcher
+420 54949 2615
RNDr. Hana Konečná
odborná pracovnice
+420 54949 5050
Bc. Tereza Chmelíková
Student
Mgr. Michaela Markvartová
Bc. Hana Štégnerová
Vladimír Jonas
Sudhir Kumar Pal
Mgr. Jakub Šebera, Ph.D.
Mgr. Pavlína Víšková
odborná pracovnice - PhD student
Bc. Hana Zigová
Student
Mgr. Daniel Krafčík
odborný pracovník - PhD student

VYBRANÉ PUBLIKACE

2017

  • GAJARSKY, M; ZIVKOVIC, ML; STADLBAUER, P; PAGANO, B; FIALA, R; AMATO, J; TOMASKA, L; SPONER, J; PLAVEC, J; TRANTIREK, L, 2017:Structure of a Stable G-Hairpin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 (10), p. 3591 - 3594.
  • GROCHALOVA, M; KONECNA, H; STEJSKAL, K; POTESIL, D; FRIDRICHOVA, D; SRBOVA, E; ORNEROVA, K; ZDRAHAL, Z, 2017:Deep coverage of the beer proteome. JOURNAL OF PROTEOMICS 162 , p. 119 - 124.
  • LINKE, F; HARENBERG, M; NIETERT, M M; ZAUNIG, S; VON BONIN, F; ARLT, A; SZCZEPANOWSKI, M; WEICH, H A; LUTZ S; DULLIN, C; JANOVSKÁ, P; KRAFČÍKOVÁ, M; TRANTÍREK, L; OVESNÁ, P; KLAPPER, W; BEISSBARTH, T; ALVES, F; BRYJA, V; TRÜMPER, L; WILTING, J, KUBE, D, 2017:Microenvironmental interactions between endothelial and lymphoma cells: a role for the canonical WNT pathway in Hodgkin lymphoma. Leukemia 31 (2), p. 361 - 372.
  • NAGY, G; OOSTENBRINK, C; HRITZ, J, 2017:Exploring the binding pathways of the 14-3-3 zeta : protein Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. PLOS ONE 12 (7)
  • NAGY, G; OOSTENBRINK, C; HRITZ, J, 2017:Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. PLoS ONE 7 (12)
  • NIKLASSON, M; MADDALO, G; SRAMKOVA, Z; MUTLU, E; WEE, S; SEKYROVA, P; SCHMIDT, L; FRITZ, N; DEHNISCH, I; KYRIATZIS, G; KRAFCIKOVA, M; CARSON, BB; FEENSTRA, JM; MARINESCU, VD; SEGERMAN, A; HARALDSSON, M; GUSTAVSSON, AL; HAMMARSTROM, LGJ; JENSEN, AJ; UHRBOM, L; ALTELAAR, AFM; LINNARSSON, S; UHLEN, P; TRANTIREK, L; VINCENT, CT; NELANDER, S; ENGER, PO; ANDANG, M, 2017:Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses. CANCER RESEARCH 77 (7), p. 1741 - 1752.

2016

  • CERVENKA, I; VALNOHOVA, J; BERNATIK, O; HARNOS, J; RADSETOULAL, M; SEDOVA, K; HANAKOVA, K; POTESIL, D; SEDLACKOVA, M; SALASOVA, A; STEINHART, Z; ANGERS, S; SCHULTE, G; HAMPL, A; ZDRAHAL, Z; BRYJA, V, 2016:Dishevelled is a NEK2 kinase substrate controlling dynamics of centrosomal linker proteins. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113 (33), p. 9304 - 9309.
  • PEKAROVA, B; SZMITKOWSKA, A; DOPITOVA, R; DEGTJARIK, O; ZIDEK, L; HEJATKO, J, 2016:Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants. MOLECULAR PLANT 9 (1), p. 71 - 85.
  • RUBIO-MARRERO, EN; VINCELLI, G; JEFFRIES, CM; SHAIKH, TR; PAKOS, IS; RANAIVOSON, FM; VON DAAKE, S; DEMELER, B; DE JACO, A; PERKINS, G; ELLISMAN, MH; TREWHELLA, J; COMOLETTI, D, 2016:Structural Characterization of the Extracellular Domain of CASPR2 and Insights into Its Association with the Novel Ligand Contactin1. JOURNAL OF BIOLOGICAL CHEMISTRY 291 (11), p. 5788 - 5802.
  • SHASMAL, M; DEY, S; SHAIKH, TR; BHAKTA, S; SENGUPTA, J, 2016:E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed. SCIENTIFIC REPORTS 6
  • SLANINOVA, V; KRAFCIKOVA, M; PEREZ-GOMEZ, R; STEFFAL, P; TRANTIREK, L; BRAY, SJ; KREJCI, A, 2016:Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle. OPEN BIOLOGY 6 (2)
  • VAVRINSKA, A; ZELINKA, J; SEBERA, J; SYCHROVSKY, V; FIALA, R; BOELENS, R; SKLENAR, V; TRANTIREK, L, 2016:Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions (vol 64, pg 53, 2016). JOURNAL OF BIOMOLECULAR NMR 65 (1), p. 49 - 49.
  • VAVRINSKA, A; ZELINKA, J; SEBERA, J; SYCHROVSKY, V; FIALA, R; BOELENS, R; SKLENAR, V; TRANTIREK, L, 2016:Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 64 (1), p. 53 - 62.

2015

  • KOZAKOVA, L; VONDROVA, L; STEJSKAL, K; CHARALABOUS, P; KOLESAR, P; LEHMANN, AR; ULDRIJAN, S; SANDERSON, CM; ZDRAHAL, Z; PALECEK, JJ, 2015:The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. CELL CYCLE 14 (6), p. 920 - 930.
  • ZDARSKA, M; DOBISOVA, T; GELOVA, Z; PERNISOVA, M; DABRAVOLSKI, S; HEJATKO, J, 2015:Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development. JOURNAL OF EXPERIMENTAL BOTANY 66 (16), p. 4913 - 4931.

2014

  • BERNATIK, O; SEDOVA, K; SCHILLE, C; GANJI, RS; CERVENKA, I; TRANTIREK, L; SCHAMBONY, A; ZDRAHAL, Z; BRYJA, V, 2014:Functional Analysis of Dishevelled-3 Phosphorylation Identifies Distinct Mechanisms Driven by Casein Kinase 1 epsilon and Frizzled5. JOURNAL OF BIOLOGICAL CHEMISTRY 289 (34), p. 23520 - 23533.
  • BORKOVCOVA, P; PEKAROVA, B; VALKOVA, M; DOPITOVA, R; BRZOBOHATY, B; JANDA, L; HEJATKO, J, 2014:Antibodies against CKI1(RD), a receiver domain of the sensor histidine kinase in Arabidopsis thaliana: From antigen preparation to in planta immunolocalization. PHYTOCHEMISTRY 100 , p. 6 - 15.
  • GARDNER, CL; HRITZ, J; SUN, CQ; VANLANDINGHAM, DL; SONG, TY; GHEDIN, E; HIGGS, S; KLIMSTRA, WB; RYMAN, KD, 2014:Deliberate Attenuation of Chikungunya Virus by Adaptation to Heparan Sulfate-Dependent Infectivity: A Model for Rational Arboviral Vaccine Design. PLOS NEGLECTED TROPICAL DISEASES 8 (2)
  • HRITZ, J; BYEON, IJL; KRZYSIAK, T; MARTINEZ, A; SKLENAR, V; GRONENBORN, AM, 2014:Dissection of Binding between a Phosphorylated Tyrosine Hydroxylase Peptide and 14-3-3 zeta: A Complex Story Elucidated by NMR. BIOPHYSICAL JOURNAL 107 (9), p. 2185 - 2194.
  • LUI, VWY; PEYSER, ND; NG, PKS; HRITZ, J; ZENG, Y; LU, YL; LI, H; WANG, L; GILBERT, BR; GENERAL, IJ; BAHAR, I; JU, ZL; WANG, ZH; PENDLETON, KP; XIAO, X; DU, Y; VRIES, JK; HAMMERMAN, PS; GARRAWAY, LA; MILLS, GB; JOHNSON, DE; GRANDIS, JR, 2014:Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 (3), p. 1114 - 1119.
  • OBR, M; HADRAVOVA, R; DOLEZAL, M; KRIZOVA, I; PAPOUSKOV, V; ZIDEK, L; HRABAL, R; RUML, T; RUMLOVA, M, 2014:Stabilization of the beta-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity. RETROVIROLOGY 11
  • YURENKO, YP; NOVOTNY, J; MITORAJ, MP; SKLENAR, V; MICHALAK, A; MAREK, R, 2014:Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 10 (12), p. 5353 - 5365.
  • ZABRADY, M; HRDINOVA, V; MULLER, B; CONRAD, U; HEJATKO, J; JANDA, L, 2014:Targeted In Vivo Inhibition of Specific Protein-Protein Interactions Using Recombinant Antibodies. PLOS ONE 9 (10)

2013

  • HABA, NY; GROSS, R; NOVACEK, J; SHAKED, H; ZIDEK, L; BARDA-SAAD, M; CHILL, JH, 2013:NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein. BIOPHYSICAL JOURNAL 105 (2), p. 481 - 493.
  • NOVACEK, J; JANDA, L; DOPITOVA, R; ZIDEK, L; SKLENAR, V, 2013:Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. JOURNAL OF BIOMOLECULAR NMR 56 (4), p. 291 - 301.
  • PAPOUSKOVA, V; KADERAVEK, P; OTRUSINOVA, O; RABATINOVA, A; SANDEROVA, H; NOVACEK, J; KRASNY, L; SKLENAR, V; ZIDEK, L, 2013:Structural Study of the Partially Disordered Full-Length delta Subunit of RNA Polymerase from Bacillus subtilis. CHEMBIOCHEM 14 (14), p. 1772 - 1779.
  • PAPOUSKOVA, V; NOVACEK, J; KADERAVEK, P; SANDEROVA, H; RABATINOVA, A; ZIDEK, L; KRASNY, L; SKLENAR, V, 2013:Structural study of partially disordered delta subunit of RNA polymerase unique for gram-positive bacteria. FEBS JOURNAL 280 , p. 146 - 147.

2012

  • FERUS, M; CIVIS, S; MLADEK, A; SPONER, J; JUHA, L; SPONER, JE, 2012:On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (51), p. 20788 - 20796.
  • PAVLIKOVA, N; BLAHOVA, L; KLAN, P; BATHULA, SR; SKLENAR, V; GIESY, JP; BLAHA, L, 2012:Enantioselective effects of alpha-hexachlorocyclohexane (HCH) isomers on androgen receptor activity in vitro. CHEMOSPHERE 86 (1), p. 65 - 69.

2011

  • NOVACEK, J; ZAWADZKA-KAZIMIERCZUK, A; PAPOUSKOVA, V; ZIDEK, L; SANDEROVA, H; KRASNY, L; KOZMINSKI, W; SKLENAR, V, 2011:5D C-13-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. JOURNAL OF BIOMOLECULAR NMR 50 (1), p. 1 - 11.
  • PEKAROVA, B; KLUMPLER, T; TRISKOVA, O; HORAK, J; JANSEN, S; DOPITOVA, R; BORKOVCOVA, P; PAPOUSKOVA, V; NEJEDLA, E; SKLENAR, V; MAREK, J; ZIDEK, L; HEJATKO, J; JANDA, L, 2011:Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana. PLANT JOURNAL 67 (5), p. 827 - 839.

2010

  • MOTACKOVA, V; SANDEROVA, H; ZIDEK, L; NOVACEK, J; PADRTA, P; SVENKOVA, A; KORELUSOVA, J; JONAK, J; KRASNY, L; SKLENAR, V, 2010:Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 78 (7), p. 1807 - 1810.
  • PRECECHTELOVA, J; NOVAK, P; MUNZAROVA, ML; KAUPP, M; SKLENAR, V, 2010:Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 132 (48), p. 17139 - 17148.

2009

  • MACEK, P., CHMELIK, J., KRIZOVA, I., KADERAVEK, P., ZIDEK, L., WILDOVA, M., HADRAVOVA, R., CHALOUPKOVA, R., PICHOVA, I., RUML, T., RUMLOVA, M., SKLENAR, V., 2009:NMR structure of the N-terminal domain of capsid protein from the Mason-Pfizer monkey virus. Journal of Molecular Biology 392 (1), p. 100 - 114.
  • MATEJKOVA, M; ZIDKOVA, J; ZIDEK, L; WIMMEROVA, M; CHMELIK, J; SKLENAR, V, 2009:Investigation of Thermal Denaturation of Barley Nonspecific Lipid Transfer Protein 1 (ns-LTP1b) by Nuclear Magnetic Resonance and Differential Scanning Calorimetry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 57 (18), p. 8444 - 8452.

GRANTY

  • Podjednotky určující DNA specificitu bakteriální RNA polymerázy s flexibilními doménami: funkce a dynamika (GA13-16842S), Czech Science Foundation - Standard Grants, 2013 - 2017
  • Určení struktury lidské 14-3-3zeta v komplexu s dvojitě fosforylovanou lidskou tyrosin hydroxylázou 1 (4SGA8679), South Moravian Region - SoMoPro, 2014 - 2016
  • Efektivní výpočty volných energií a konfiguračního vzorkování protein-proteinových interakcí (I 1999-N28), Czech Science Foundation - International Projects, 2015 - 2017
  • iNEXT - Infrastructure for NMR, EM and X-ray crystallography for translational research (653706), H2020 - Excellent science - Research Infrastructures, 2015 - 2019

1. Atomic resolution study of transient structures and complexes of Microtubule Associated Protein 2c

Supervisor:  prof. Mgr. Lukáš Žídek, Ph.D.
Consultant: RNDr. Mgr. Jozef Hritz, Ph.D.

Annotation:

Microtubule Associated Protein 2c (MAP2c) is an intrinsically disordered protein important for development of nerve cells, expressed prenatally in dendrites. Dynamics, interactions, and structural features of MAP2c has been studied previously in our group. The aim of the thesis is to use nuclear magnetic resonance spectroscopy, X-ray crystallography, and other relevant techniques to characterize with atomic resolution structures of MAP2c present in complexes with interacting partners and transiently in solution.

Keywords: Microtubule Associated Protein 2c, MAP2c, NMR spectroscopy, X-ray crystallography, transient structures, nerve cells

2. Impact of 14-3-3 protein on the formation of protein aggregates involved in neurodegenerative diseases

Supervisor:  RNDr. Mgr. Jozef Hritz, Ph.D.
Consultant: doc. Mgr. Vítězslav Bryja, Ph.D., Mgr. Jan Přibyl, Ph.D.

Annotation:

The neuronal cells of patients suffering from neurodegenerative diseases are characteristic by possession of aggregates of several proteins such as tau and Abeta protein. They form toxic aggregates to the different extend depending on the environment and their state (e.g. different post-translational modifications or specific conformational state). The main aim of this PhD project will be to quantify the extent of aggregation of three selected proteins in vitro and in the cell environment. Dependence of aggregation on phosphorylation and the potential interaction with various forms of 14-3-3 proteins will be analyzed mostly by biophysical interaction techniques and the atomic force microscopy. The biological relevance of the in-vitro findings will be tested in cell cultures by fluorescence microscopy.

Keywords: tau and Abeta protein, post-translational modifications, phosphorylation, 14-3-3 proteins, atomic force microscopy, neurodegenerative diseases, AFM

3. Structural basis of function of receiver domains of plant hybrid histidine kinases

Supervisor: prof. Mgr. Lukáš Žídek, Ph.D.
Consultants: RNDr. Mgr. Jozef Hritz, Ph.D., doc. RNDr. Jan Hejátko, Ph.D.

Annotation

The aim of the thesis is to study the role of conformational changes in function of the receiver domain of hybrid histidine kinase CKI1 from the model plant Arabidopsis thaliana and compare it with homologous histidine kinases from the same organism. Although the activation has been studied in structurally similar bacterial domains, little is known about the mechanism and structural basis of this event in plant systems, differing in several significant aspects. Our previous results show that the activation of the receiver domain is associated with a dramatic reduction of conformational dynamics of a loop in a vicinity of the phosphorylation site. NMR and computational approaches will be employed to study the structural changes during activation, to relate the dynamics of the loop to the function of other residues important for signal transduction, and to investigate interactions.

Keywords: hybrid histidine kinase, CKI1, Arabidopsis thaliana, NMR, conformational changes

4. Structural changes of the selected protein fibrils induced by phosphorylation and the interaction with 14-3-3 proteins

Supervisor:  RNDr. Mgr. Jozef Hritz, Ph.D.
Consultant: doc. Mgr. Vítězslav Bryja, Ph.D., Dr. Tanvir Shaikh

Annotation:

Several neurodegenerative diseases are asociated with the formation of fibrous (fibrillar) protein agreggates. 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 protein fibrils is the key for understanding this neurodegerative processes. The main aim of this PhD project will be characterization of structural changes in the formation of protein fibrils due to different phosphorylation state and the interaction with 14-3-3 proteins. Interdisciplinary approach combining molecular biology and structural biology (mainly cryoEM tomography) methods will be applied. Molecular binding mode involving 14-3-3 will be elucidated by NMR.

Keywords: neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography, NMR

5. Structure, dynamics and interactions of subunits of RNA polymerase of Gram-positive bacteria

Supervisor:  prof. Mgr. Lukáš Žídek, Ph.D.
Consultant: Mgr. Pavel Kadeřávek, Ph.D.

Annotation:

Certain RNA polymerase subunits (including sigma factors) are specific for Gram-positive bacteria. Such subunits are critical determinants of the enzyme specificity for DNA promoter sequence. Structures of delta subunits and of the vegetative sigmaA 1.1. domain, both containing highly dynamical regions, have been solved and further characterized in the group. The results suggest an important role of the conformational flexibility in functions of the subunits, but mechanistic details remain to be revealed. The aim of the thesis is to study dynamics and interactions of the subunit in order to understand their roles on the atomistic level, and provide structural data for other sigma factors and/or their domains. Standard and advanced methods of nuclear magnetic spectroscopy, recently developed in the group for such applications, will be combined with X-ray crystallography and cryo-electron microscopy

Keywords: Gram-positive bacteria, RNA polymerase subunits, NMR spectroscopy, X-ray crystallography, cryo-electron microscopy

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