F1190

• P01: (21.09. Jiří Kozelka):
  
Otázky k testu
Otázky k tesu


Na vypracování testu bude 90 minut. S sebou je třeba mít kalkulačku. Bez vypočtení dihedrálního úhlu je test hodnocen nedostatečně.
1. Napište reakci, při níž vzniká peptidová vazba a popište základní charakteristiky peptidové vazby.
2. Nakreslete proteinovou páteř (alespoň pořadí tří aminokyselin) a nakreslete všechny dihedrální úhly proteinové páteře
3. Popište α-helix a β-skládaný list a jejich úlohu v terciární struktuře proteinu.
4. Jakou strukturní informaci nám dává Ramachandranův diagram?
5. Popište, čeho se týkal Anfinsenův experiment.(cíl experimentu, protein, činidla, závěr; ve kterém roce a za co byla Anfinsenovi udělěna 1/2 Nobelovy ceny?)
6. Nakreslete a popište jednu purinovou a jednu pyrimidinovou bázi nukleových kyselin (číslování, donory/akceptory vodíkových vazeb, dvojné vazby).
7. Popište základní stavební jednotky řetězce nukleových kyselin
8. Uveďte příklady párování bází ve dvojšroubovicích, triplexech nebo kvadruplexech.
9. Popište dvoujšroubovici DNA - velký žlábek, malý žlábek, konformace cukrů, náboj na cukr-fosfátové páteři, proti-ionty.
10. Kdo jsou objevitelé struktury DNA, kteří byli oceněni Nobelovou cenou?
11. Jaké znáte alternativní modely DNA a čím se od správného modelu liší?
12. Jaké interakce stabilizují strukturu DNA?
13. Napište rozpětí úhlů a délky vodíkových vazeb v biomolekulách.
14. Napište přibližnou tloušťku membrány a popište, o jaké se jedná prostředí (hydrofilní, hydrofobní ...).
15. Co je to Zwitterion?
16. Jakou má roli cholesterol v membránách?
17. Jaké jsou tři hlavní typy molekul v buněčných membránách?
18. V jakém stavu (tuhosti) jsou membrány za fyziologických podmínek?
19. Co vyjadřuje Lennard-Jonesův potenciál? Jakou funkcí je popisován? Načrtněte graf této funkce a komentujte jej.
20. Vypočtěte dihedrální úhel φ nebo ψ jestliže znáte:

       ATOM    868  N   VAL A  61      24.893  32.837  33.917  1.00 11.27           N
       ATOM    869  CA  VAL A  61      25.656  31.587  34.094  1.00  4.37           C
       ATOM    870  C   VAL A  61      25.678  31.013  35.496  1.00  6.02           C
       ATOM    871  O   VAL A  61      25.385  29.805  35.743  1.00 10.75           O
       ATOM    875  H   VAL A  61      25.316  33.618  33.435  1.00  0.00           H
       ATOM    884  N   THR A  62      26.053  31.843  36.442  1.00  7.02           N
       ATOM    885  CA  THR A  62      26.178  31.421  37.808  1.00  6.51           C
       ATOM    886  C   THR A  62      24.862  30.954  38.410  1.00  9.22           C
       ATOM    887  O   THR A  62      24.801  30.163  39.352  1.00  6.99           O
       ATOM    891  H   THR A  62      26.259  32.802  36.202  1.00  0.00           H
       ATOM    898  N   THR A  63      23.814  31.547  37.910  1.00  9.98           N
       ATOM    899  CA  THR A  63      22.457  31.212  38.388  1.00  6.69           C
       ATOM    900  C   THR A  63      22.033  29.830  37.865  1.00  8.14           C
       ATOM    901  O   THR A  63      21.499  28.984  38.604  1.00 13.48           O
       ATOM    905  H   THR A  63      23.931  32.243  37.188  1.00  0.00           H
       ATOM    912  N   PHE A  64      22.250  29.620  36.583  1.00 10.19           N
       ATOM    913  CA  PHE A  64      21.895  28.371  35.995  1.00  8.00           C
       ATOM    914  C   PHE A  64      22.774  27.253  36.518  1.00 25.26           C
       ATOM    915  O   PHE A  64      22.313  26.147  36.761  1.00  9.64           O
       ATOM    923  H   PHE A  64      22.668  30.344  36.016  1.00  0.00           H
       


 


 

F5351


• P1: (12.10. Jiří Kozelka): DNA coby polyelektrolyt: Manningova teorie kondenzace protiiontů
• P2: (30.11. Jiří Kozelka): Rhodopsin

 


 

F8390


 

F7790

 
Semináře CB061/CB060 a F7790 se v podzimním semestru 2017 (18.9-19.12.2017) konají v níže uvedených datech (zatím) od 14.00 do 16.00 v místnosti 205 budovy A11 na Univerzitním kampusu Bohunice (UKB).
 
Prezentace by měly splňovat následující kriteria:
The presentations should follow these criterions:
• neměly by být kratší 20 minut a delší 30 minut
  shouldn't be shorter 20 minutes and longer 30 minutes
• měly by být srozumitelné širšímu vědeckému publiku
  should be comprehensible to wider audience
• měly by obsahovat:
  should include:
  • stručné představení přednášejícího
    short intro of the presenter (the host of the seminar - Žídek / Kubíček - will also introduce the presenter before the presentation)
  • úvod do problematiky
    Introduction
  • popis problému, způsob jeho řešení a cíle
    Description of the problem, aims of the study and your approach to solve your project
  • výsledky
    Results
  • závěr
    Conclusion
• jsou vedeny v anglickém jazyce
  by default, all lectures are in English
• přednášející se dostaví v dostatečném předstihu před zahájením semináře a zkontroluje, že veškerá audiovizuální technika funguje a je kompatibilní s připravenou přednáškou
  the presenter is responsible for checking the room and AV-devices being compatible with her/his presentation and make sure that everything is ready to start on time

 

1. 05.10.2017
   Karel Kubíček
   Show/Hide Abstract
   Tandem SH2 domain of elongation factor from C. Glabrata

   The recruitment of distinct processing factors to RNA polymerase II (RNAPII) is governed by dynamic post-translational modifications upon its highly flexible CTD domain (1) composed of repetitive sequence Y1-S2-P3-T4-S5-P6-S7 (2). This led to the formulation of the so-called “CTD-code” (3). How the CTD of RNAPII recruits, (de)activates, or displaces relevant processing factors, remains still poorly understood. Genome-wide mapping of CTD phosphorylation patterns revealed that Y1 and S2 phosphorylation levels are raising simultaneously during early elongation. Increased Y1 phosphorylation releases factors associated with RNAPII at the beginning of genes, and impairs assembly of the termination factors. In addition, phosphorylated Y1 mark is recognized by a tandem SH2 (tSH2) domain of elongation factor Spt6, consistent with Spt6 occupancy within Tyr1-phosphorylated region of genes in vivo (4).

   Via a combination of structural methods, we have acquired and confirmed by biochemical assays data that are explaining the role of the individual SH2 domains. Additionally, physico-chemical driving forces of recognition Y1-phosphorylated CTD by the tSH2 domain of the elongation factor Spt6 structure of the CTD complexed with Spt6.

   References
   (1) Egloff, S. and Murphy, S.: Cracking the RNA polymerase II CTD code. Trends Genet., 24: 280-8 (2008).
   (2) Jasnovidova, O. ,and Stefl, R., The CTD code of RNA polymerase II: a structural view. WIREs RNA, 4: 1–16 (2013).
   (3) Buratovski, S.: The CTD code. Nat Struct Biol., 10:679-80 (2003).
   (4) Mayer, A., Heidemann, M., Lidschieber, M., Schreieck, Sun, M., Hintermair, C., Kremmer, E., Eick, D. and Cramer, P.: CTD Tyrosine Phosphorylation Impairs Termination Factor Recruitment to RNA Polymerase II. Science, 336:1723-5 (2012).
   

2. 12.10.2017
   Assoc. Prof. Mikael Lund
   Show/Hide Abstract
   Coarse-grain

3. 26.10.2017
   Mgr. Kateřina Melková (prof. Mgr. Lukáš Žídek, Ph.D.)
   Show/Hide Abstract
   Microtubule Associated Proteins 2c and Tau: insight into molecular basis of functional diversity of homologous regulatory intrinsically disordered proteins

   Microtubule Associated Proteins (MAP) play a key role in regulation of microtubule dynamics. Products of two genes, MAPT and MAP2, are expressed in nerve cells in multiple isoforms generated by alternative splicing. The former gene encodes protein Tau, which is associated with neurodegenerative processes accompanying the Alzheimer's disease, and therefore attracted great attention in the past few decades. Its longest, 441-residue isoform, lacking exons 6, 8, and 10, has been previously characterized in detail [1,2]. Our recently published study of the shortest, 467-residue isoform MAP2c of the latter gene [3] revealed that the cAMP-dependent protein kinase PKA phosphorylates Tau and MAP2c differently. This finding is in a good agreement with the distinct functions and localizations of Tau and MAP2c, and suggests that PKA may represent a branch point in signaling cascades controlling microtubule dynamics. On the NCBR seminar I will be presenting recently published results providing detailed description of molecular properties of MAP2c. We used high-resolution NMR techniques and small angle X-ray scattering to acquire atomic-resolution data reflecting structural and dynamic features of MAP2c, and analyzed the experimental results using the ASTEROIDS algorithm [4]. We obtained representative structural ensembles characterizing both local conformations of MAP2c and its global shape, determined by electrostatic interactions of regions distant in the sequence. The results allowed us to directly compare MAP2c with Tau.

   References
   [1] Mukrasch, M.D. et al., PloS Biology 7 (2009) e1000034
   [2] Lippens, G. et al., Biomolecules 6 (2016) biom6020028
   [3] Jansen, S. et al., J. Biol. Chem. 292 (2017) 6715-6727
   [4] Nodet, G. et al., J. Am. Chem. Soc. 131 (2009) 16968-16975
   

   
   Mgr. Vojtěch Zapletal (prof. Mgr. Lukáš Žídek, Ph.D.)
   Show/Hide Abstract
   Conformational study on intrinsically disordered and hybrid proteins

   Intrinsically disordered proteins (IDPs) characterized by polypeptide chains that fail to fold into stable and well defined tertiary structure in an isolated state have been under our interest. In spite of the lack of stable structure, IDPs play key roles in processes such as molecular recognition, regulation of transcription and they are related to neurodegenerative diseases.

   Microtubule associated protein 2c (MAP2c) is an IDP regulating stability and dynamics of microtubules in the cytoskeleton of neurons and other cells. MAP2c is a 49 kDa homolog of tau protein which differs in localization, expression, and binding properties. Important structural and functional regions were revealed in MAP2c. Typical experimental methods for studies of IDPs are nuclear magnetic resonance (NMR) and small angle X-ray scattering (SAXS). We used 5D NMR experiments to obtain chemical shifts. We also performed paramagnetic relaxation enhancement (PRE) experiments to get the information about intramolecular distances and SAXS experiments to monitor the overall size and shape of the MAP2c in solution. The pools of possible chain conformations were generated by the program Flexible - Meccano, which builds consecutively a polypeptide chain assuming that peptide planes are rigid entities connected through Cα atoms. The ensemble of structures was selected by the program ASTEROIDS which uses a genetic algorithm to produce and ensemble of IDPs consistent with experimental data, measured with a simple quadratic fitness function measuring the deviation of the back calculated parameters from the measured ones.

   Most of IDPs are in fact intrinsically disordered regions (IDRs) that are tethered to ordered domains (ODs). It is imperative that the biophysical properties of these regions be studied in their naturally occurring contexts, which is tethered to ODs. It is difficult to cope with such systems for the experimental techniques and for computational methods. In our next study, we generated structural ensembles of the δ-subunit of RNA polymerase using molecular dynamics simulations. The reliability of the obtained ensembles generated under different force field parameters was checked by the comparison of the corresponding calculated properties with their experimental values. Namely we monitored: NMR chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, relaxation rates, and SAXS data.

4. 09.11.2017
   Helena Covelo Molares (doc. Mgr. Štěpánka Vaňáčová, Ph.D.)
   Show/Hide Abstract
   Understanding the role of dynamic RNA methylation on gene expression regulation

   N⁶-methyladenosine (m⁶A) is the most prevalent internal messenger RNA (mRNA) modification and it is the first example of reversible RNA methylation. m⁶A is deposited on the RNA by a methyltransferase complex and it can be removed by the action of two demethylases, FTO and AlkBH5. The functions of m⁶A in the cells are mediated by RNA binding proteins. Two principal modes of m⁶A recognition have been proposed: 1) direct binding to m⁶A modified RNA or 2) indirectly recognition of secondary structures altered by m⁶A modification. On the functional level, m⁶A regulates mRNA fate -stability, translation or splicing- and biological processes such as mammalian cell differentiation or stress responses.

   In our lab, we characterized the transcriptome-wide RNA targets of the m⁶A demethylase FTO using the CLIP-Seq technique (cross-linking and immunoprecipitation coupled to high throughput sequencing). FTO preferentially binds to intronic regions of pre-mRNAs, around alternative spliced (AS) exons and in the proximity of poly(A) sites. Furthermore, we performed RNA-Seq analysis of FTO knockout (KO) mammalian cell line and uncovered that depletion of FTO leads to changes in pre-mRNA splicing, which are dependent of FTO catalytic activity in vivo.

   To get further insights into the cellular pathways regulated by m⁶A and the dynamics of m⁶A deposition/removal on RNA, we are analyzing the stable and transient protein interactome of FTO and METTL3, one of the mammalian m⁶A methyltransferases. To that end, we are using an approach called BioID, which uses a fusion protein between the ‘bait’ protein and a biotin ligase to biotinylate proteins based on proximity. The biotinylation allows their selective enrichment and analysis by mass spectrometry.

   
   Nandan Mysore Varadarajan, M.Sc. (doc. Mgr. Štěpánka Vaňáčová, Ph.D.)
   Show/Hide Abstract
   Uridylation mediated cytoplasmic RNA quality control in mammalian cells.

   A living cell consists of various types of RNA (coding and non-coding RNAs). RNA stability and processing is essential part of the molecular mechanism involving growth, differentiation and proliferation. Post transcriptional modification facilitates to maintain this stability and helps in processing of RNAs in the cell. Main focus of this study in the lab is uridylation of RNA in the cytoplasm of mammalian cells. There are various kinds of small RNAs which are subjected to Uridylation which helps in processing; these include U6snRNA (1), degradation of replication dependent histone mRNA (2)(3)(4) and pre-microRNA. U-tailing generally leads to degradation of the target RNA. (5). Recent reports have shown that uridylation also plays a role in RNA processing such as let7-miRNAs (6)(7). Uridylated abbarent forms of RNAs were subjected to degradation by an enzyme having 3' to 5' exonuclease activity, which was recognised to be DIS3L2 (8).
   DIS3L2 targets precursors of Let7-miRNAs by identifying the polyudridine residues at the 3' end of the precursors. DIS3L2 belongs to RNase II family of enzymes and has a sequence homology to Rrp44P of yeast (9). DIS3L2 is localized in the cytoplasm of the cells (8). DIS3L2 CLIP data revealed that most, if not all classes of RNAs in the cell were found to be uridylated, suggesting that DIS3L2 binds to a broad array of uridylated RNAs. As per earlier reports (10) the CLIP data analysis reiterated that pre-Let7 forms of miRNA are uridylated at the 3'ends.
   The current study focuses on discovering the fates of miRNA in a global scale with respect to a catalytical mutant of DIS3L2. For this we use PAN-AGO CLIP and RNA seq analysis to understand miRNA regulation by TUT-DIS3L2 pathway.

   References
   1. Trippe R, Guschina E, Hossbach M, Urlaub H, Luhrmann R, Benecke BJ. 2006. Identification, cloning, and functional analysis of the human U6 snRNA-specific terminal uridylyl transferase. RNA 12: 1494–1504.
   2. Schmidt MJ, West S, Norbury CJ. 2011. The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation. RNA 17: 39–44.
   3. Minasaki R, Eckmann CR. 2012. Subcellular specialization of multifaceted 3′end modifying nucleotidyltransferases. Curr Opin Cell Biol 24: 314–322.
   4. Su W, Slepenkov SV, Slevin MK, Lyons SM, Ziemniak M, Kowalska J, Darzynkiewicz E, Jemielity J, Marzluff WF, Rhoads RE. 2013. mRNAs containing the histone 3′ stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3′ end. RNA 19: 1–16.
   5. Lee M, Kim B, Kim VN: Emerging roles of RNA modification: m(6)A and U-tail. Cell 2014, 158:980-987..
   6. Heo I, Joo C, Cho J, Ha M, Han J, Kim VN: Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 2008, 32:276-284
   7. Hagan JP, Piskounova E, Gregory RI: Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat Struct Mol Biol 2009, 16:1021-1025.
   8. Ustianenko D., Hrossova D., Potesil D., Chalupnikova K., Hrazdilova K., Pachernik J., et al. (2013). Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs. RNA 19, 1632–1638. 10.1261/rna.040055.113
   9. Dziembowski A, Lorentzen E, Conti E, Seraphin B. 2007. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 14: 15–22.
   10. Lee H, Han S, Kwon CS, Lee D: Biogenesis and regulation of the let-7 miRNAs and their functional implications. Protein Cell 2016, 7:100-113.

5. 23.11.2017 biophysics
   Mgr. Miroslav Jurásek (doc. RNDr. Robert Vácha, Ph.D.)
   Show/Hide Abstract
   Regulation of Dishevelled protein

   Dishevelled (DVL) is a highly conserved protein that has a vital role in cell-cell communication in tissues. DLV is one of the key components of Wnt signaling pathway, where it plays an essential role in signal transduction from the membrane-bound receptors to downstream effectors. This way, DVL is situated at the branching point between canonical (β-catenin dependent) and non-canonical (planar cell polarity) signaling and thus might serve as a switch between different pathways. DVL is known to interact with more than 50 different binding partners, however, structural base of their regulatory effect are largely unknown. DVL consists of three structured domains (Dishevelled-Axin (DIX), Post-synaptic-Density-95-Discs-large and Zonula-occludens 1 (PDZ), and Dishevelled-EGL-10-Pleckstrin (DEP)) and highly conserved C-terminus. Interestingly, intrinsically disordered regions, that interconnects domains, also contain highly conserved regions.

   One of the recently described mechanisms of DVL regulation is an autoinhibition of the PDZ domain by the highly conserved C-terminus, which results in so-called closed conformation. However, to this date, no mechanism for regulation of DVL closing have been proposed. Recently, our collaborators from the group of Vítězslav Bryja have found two novel phosphorylation sites in PDZ domain that affect the closing of DVL. We employed molecular dynamics simulations to study the structural effect of phosphorylation and phosphomimetics (substitution of phosphorylated amino acids by glutamic or aspartic acid) on PDZ. We found modest differences between effects of phosphorylation and mimetics. We observed two major effects of phosphorylation/mimetics on PDZ structure: 1) disruption of the binding site on a surface of PDZ and 2) change in conformation of loop close to the binding site. Based on coarse-grained simulations we proposed, that secondary binding site at PDZ domain might be important for peptide binding and should be affected by the conformational change in the loop.

6. 30.11.2017
   Mgr. David Buchta (Mgr. Pavel Plevka, Ph.D.)
   Show/Hide Abstract
   Echovirus 18 structure

   Enteroviruses are human pathogens that cause millions of infections every year. Echovirus 18 (E18) is among the five most frequent enteroviruses detected in the US. It can cause aseptic meningitis, leukoencephalitis, and acute exanthema. However, no treatments against E18 are available and its structure is unknown. Here, we present the structure of an E18 virion and A particle determined to a resolution of 3.3 Å using cryo-electron microscopy.

   
   Mgr. Dominik Hrebík (Mgr. Pavel Plevka, Ph.D.)
   Show/Hide Abstract
   Structure and genome release mechanism of podovirus P68 infecting Staphylococcus aureus

   Bacteriophages from the family Podoviridae are composed of a head and a short non-­contractile tail attached to one of the 5-­fold icosahedral vertices of the head. Here we present the structures of Staphylococcus aureus phage P68 before and after genome ejection. The structure of the full particle was solved by cryo-­electron microscopy to resolution of 3.3 Å for head, and 3.9 Å for tail, using single particle analysis and localized reconstruction. One structural protein which was poorly resolved in the cryo-EM electron map was solved by X-ray crystallography to 1.9 Å resolution. In situ structure of the phage P68 is showing unique phage structural proteins with a novel morphology, and their interconnections which were not observed before. The structures of the full and empty phage shows changes of the portal complex and of the tail machinery that are required for genome release and membrane penetration.

   
   Mgr. Karel Škubník (Mgr. Pavel Plevka, Ph.D.)
7. 07.12.2017 biophysics
   Mgr. Michal Růžička (Mgr. Kamila Réblová, Ph.D.)
   Show/Hide Abstract
   Study of Structural and Elastic Properties of DNA Mutation Motifs Using Computational Methods

   Mutations in human genes can be responsible for inherited genetic disorders and cancer. It has been shown that certain DNA sequences are more prone to mutate [1]. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which however often reflects particular population where an effect of a common ancestor plays a role. To detect coldspots and hotspots unaffected by population bias we analysed presence of germline mutations obtained from HGMD database in the 5-nucleotide segments which repeatedly occurring in genes associated with common inherited disorders [2], particularly in PAH, LDLR, CFTR, F8, and F9 genes.

   Using molecular dynamics simulations and free energy calculations we have analyzed global bending properties of selected coldspots and hotspots with G/T mismatch base pair. Coldspots were observed to be inherently more flexible than hotspots. In addition, we observed that mismatch G/T pair opens more easily towards minor groove than a canonical G=C base pair in the bent DNA conformation. This property might be critical for effective mismatch repair as aberrant DNA recognized by MutSα protein is noticeably bent and mismatch base pair is disrupted and shifted towards minor groove where it is recognized by conserved amino acids from MutSα.

   References
   [1] Rogozin, I. B. and Y. I. Pavlov (2003). "Theoretical analysis of mutation hotspots and their DNA sequence context specificity." Mutation Research-Reviews in Mutation Research 544(1): 65-85.
   [2] Krawczak, M., E. V. Ball, et al. (1998). "Neighboring-nucleotide effects on the rates of germ-line single-base-pair substitution in human genes." American Journal of Human Genetics 63(2): 474-488.

   
   Bc. Jakub Institoris ()
   Show/Hide Abstract
   Generování a charakterizace emulsních kapének s využitím mikrofluidních čipů a laserů.

8. 14.12.2017
   Dragana Vukić, M.Sc. (Mary O'Connell, Ph.D., MS)
   Show/Hide Abstract
   ELUCIDATING THE REGULATION OF ADAR1

   Adenosine deaminases acting on double-stranded RNA (ADARs) catalyze one of the most abundant RNA modifications present in mammalian cells, that is the conversion of adenosine by hydrolytic deamination to inosine (I), a process known as RNA editing. Previous results from our group have demonstrated the importance of Adar1 function in mice, as mice lacking the Adar1^-/- gene die at embryonal stage (day E12.5) with increased type I interferon (IFN), IFN stimulated genes (ISGs) and apoptosis. This phenotype was rescued by generating a double mutant in mice with Mavs (adaptor protein during innate immune response).

   In humans, mutations in ADAR1 lead to development of an autoimmune disorder; Aicardi Goutier Syndrome, where patients have increased immune response that appears similar to a viral infection but there is no virus present. For most of the ADAR1 mutations in AGS, a decrease in editing activity has been demonstrated, however the mutation at position D1113H in ADAR1 does not affect editing activity. Therefore, this raises an interesting question as how this mutation can cause the disease? One possibility is that the mutation perturbs protein-protein interactions. To test this hypothesis, different experimental approaches were undertaken such as pull-downs and co-immunoprecipitations under different conditions with subsequent mass spectrometry analysis to determine the ADAR1 complexes. We obtained comprehensive interactome data, which agreed with previously published data. However, we also found novel ADAR1 interactions which changed with induction of the immune response. This data has provided greater insights into the biological role of ADAR1, under normal conditions and during the innate immune response. In addition, our results allowed us to address the current ‘hot’ question in the field: “how does inactive ADAR1 protein rescue lethality”?

   
   Zuzana Trošanová (RNDr. Mgr. Jozef Hritz, Ph.D.)
   Show/Hide Abstract
   Thermodynamic and kinetic study of 14-3-3ζ dimerization

   14-3-3 proteins are regulatory proteins involved in many signaling pathways. They play a key role in nervous system and neurodegeneration. The 14-3-3 family of proteins consists of seven isoforms in mammals and interact with large number of protein clients. The three dimensional structure showed dimeric form of 14-3-3. In order to study monomer-dimer equilibria of 14-3-3ζ, we developed fluorescent assays based on FRET and self-quencning phenomenas. These assays provide us information about thermodynamic (dissociation constant, K_d) and kinetic (dissociation rate constant, k_off) parameters of dimer-monomer equilibria. Moreover, in order to determine dissociation rate constant, micsroscale thermophoresis was used.

 

 
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F1190 Úvod do biofyziky prof. Dr. Jiří Kozelka, PhD., Mgr. Karel Kubíček, PhD. RNDr. Bc. Arnošt Mládek, prof. RNDr. Vojtěch Mornstein, CSc. Soubor prezentací k přednášce (cca 96MB)	F5351 Základy molekulární biofyziky prof. Dr. Jiří Kozelka, PhD., prof. RNDr. Jiří Šponer, DrSc. Mgr. Lukáš Trantírek, Ph.D., RNDr. Bc. Arnošt Mládek Soubor prezentací k přednášce (cca 73MB)	F5370 Biofyzikální praktikum UFKL Mgr. Lukáš Trantírek, Ph.D., RNDr. Silvie Trantírková, Ph.D. Mgr. Karel Kubíček, PhD. Materiály k praktiku (1.4MB)
F6342 Základy lékařské biofyziky prof. RNDr. Vojtěch Mornstein, CSc. Soubor prezentací k přednášce (cca 6.7MB)	F8380 Základy molekulového modelování a bioinformatiky Mgr. Kamila Réblová, Ph.D., Mgr. Naděžda Špačková, Ph.D. Soubor prezentací k přednášce (cca 48MB)	F9600 Spektroskopické studium biopolymerů Mgr. Karel Kubíček, PhD., prof. RNDr. Tomáš Polívka, Ph.D. doc. RNDr. Oldřich Vrána, CSc. Soubor prezentací k přednášce (cca 20MB)
F9601 Optické studium jednotlivých molekul doc. RNDr. František Vácha, Ph.D. Soubor prezentací k přednášce (cca 37MB)	F9602 Interakce elektromag. pole se živou hmotou Mgr. Dušan Hemzal, Ph.D. Soubor prezentací k přednášce (cca 14MB)	F9603 Od diagnózy k léku Mgr. Karel Kubíček, Ph.D. Soubor prezentací k přednášce (cca 204MB)
FA601 Fotosyntéza prof. RNDr. Ondřej Prášil, CSc. Soubor prezentací k přednášce (cca 50MB)	FA602 Strukturní biologie: biofyzikální aspekty Mgr. Lukáš Trantírek, Ph.D. Soubor prezentací k přednášce (cca 12MB)	FA603 Elektronová mikroskopie v biologii Ing. Jana Nebesářová, CSc. Soubor prezentací k přednášce (cca 77MB)
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