XIV Discussions in Structural Molecular Biology

Institute of Biotechnology AS CR
Institute of Microbiology AS CR
South Bohemian University in České Budějovice
Czech Society for Structural Biology

proudly organize

XIV Discussions in Structural Molecular Biology 

Nové Hrady, Thursday March 17 – Saturday March 19 2016

for talks:
Phuong Pham Ngoc: Development of new protein scaffolds for directed evolution. Institute of Biotechnology CAS, Center BIOCEV, Vestec, Prague West
Tomáš Dršata: Computer simulations of nucleosome positioning and allosteric effects in DNA. Institute of Organic Chemistry and Biochemistry CAS, Prague
for posters:
Jakub Ptáček: Calcium ion is required for proper folding, dimerization and enzymatic activity of human glutamate carboxypeptidase II. Instititute of Biotechnology CAS, Center BIOCEV, Vestec, Prague West
Petr Louša: The kinetics of phosporylation of tyrosine hydroxylase and its interaction with 14-3-3 zeta protein studied by NMR, CEITEC MU, Brno
Nina Zemanová: Structural and biophysical characterization of the projection domain of neuronal tau protein, Faculty of Natural Sciences, Comenius University Bratislava

  • The whole program took place at Nový zámek.
  • All talks labeled (30′) take 30 minutes, all other take 20 minutes.
    • These times will be observed and include discussion, leave at least 5 minutes to your colleagegues!

XIV Discussions has been supported by program “Strategie AV21” by the Academy of Sciences of the Czech Republic.


10:30-12:30    Registration at Novy Zamek
12:30-13:30    Accommodation
Session 1    Chair person: Imrich Barák
13:59-14:00    Openning of XIV Discussions
14:00-14:30    Lenka Rezabkova (Paul Scherrer Institute(30′)
    Structural basis of katanin function at microtubule minus end
14:30-14:50    David Kopečný (Palacky University)
    Structure-function study on plant aldehyde dehydrogenase from moss Physcomitrella patens
14:50-15:20    Josef Houser (Masaryk University(30′)
    Lectins with beta-propeller fold in opportunistic pathogens
15:20-15:40    Rostislav Skrabana (Axon Neuroscience SE)
    Structural and binding properties of a quadruple epitope regulating tau protein oligomerization
15:40-16:00    break
Session 2    Chair person: Lenka Rezabkova
16:00-16:30    Imrich Barák (Institute of Molecular Biology, Slovak Academy of Sciences(30′)
    Asymmetric cell division during sporulation in Bacillus subtilis
16:30-16:50    Tomáš Kroupa (University of Chemistry and Technology, Prague)
    Interaction of the Mason-Pfizer monkey virus matrix protein and its budding deficient mutants with the plasma membrane
16:50-17:20    Ladislav Bumba (Institute of Microbiology(30′)
    Calcium-driven folding of RTX domain β-rolls ratchets translocation of RTX proteins through Type I secretion ducts
17:20-17:40    Lukáš Chrást (Masaryk University)
    Structure-function relationship of paradoxically thermostable haloalkane dehalogenase of psychrophilic origin
17:40-18:00    Phuong Pham Ngoc (Institute of Biotechnology AS CR, v.v.i.)
    Development of new protein scaffolds for directed evolution

18:30-21:30    dinner

 7:30- 8:45    breakfast

Session 3    Chair person: Jan Dohnalek
 9:00- 9:20    Jiří Brynda (Institute of Molecular Genetics of the ASCR, v. v. i.)
    Second generation of Carborane-Based Inhibitors of Carbonic Anhydrases
 9:20- 9:40    Leona Švecová (Institute of Biotechnology CAS, FNSPE CTU)
    X-ray structure of bilirubin oxidase from Myrothecium verrucaria with ligand in oxidation center
 9:40-10:00    Ondrej Cehlar (Institute of Neuroimmunology of SAS)
    The conformation of proline rich segment of neuronal protein tau studied by the X-ray crystallography, molecular dynamics simulations and biophysical methods
10:00-10:20    Tomas Koval (Biotechnologický ústav AV ČR, v.v.i.)
    Active site promiscuity in the S1-P1 nuclease family
10:20-10:40    Martin Kubala (Palacký University in Olomouc)
    Identification of the RH421-binding site on Na+/K+-ATPase
10:40-11:00    break
Session 4    Chair person: Frederic Vellieux
11:00-11:30    Piotr Wardega (NanoTemper a.g.(30′)
    Affinity. Stability. Conformation
11:30-11:50    Stanislav Kukla (Merck spol. s r.o.)
    Ultrafiltration master class
11:50-12:10    Raul Gomez (MALVERN Instruments, UK)
    Microcalorimetry: A versatile tool for the characterization of biomolecular interactions

12:10-12:30   Vernon Smith (Bruker AXS GmbH)

State-of-the-Art Pixel Array Detectors for Crystallography

12:30-14:00    lunch
Session 5    Chair person: Filip Lankas
14:15-14:35    Zuzana Dunajová (Masaryk University)
    Molecular dynamics simulations of the transport of ligands through pathways of haloalkane dehalogenases DhaAwt and DhaA31
14:35-15:05    Tomáš Dršata (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.(30′)
    Computer simulations of nucleosome positioning and allosteric effects in DNA
15:05-15:25    Rudiger Ettrich (Institute of Microbiology, Academy of Sciences of the Czech Republic)
    Cation translocation in human ORAI channels: Modeling and simulations
15:25-15:55    Jiří Kozelka (Masarykova univerzita v Brně(30′)
    Lone-pair-π interactions in nucleic acids and proteins: physical origin and significance
15:55-16:15    break
Session 6    Chair person: Jiří Kozelka
16:15-16:45    Evžen Bouřa (IOCB(30′)
    Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein
16:45-17:15    Kvido Stříšovský (ÚOCHB AV ČR(30′)
    The ins and outs of membrane-immersed catalysis: structure, mechanism and inhibition of rhomboid intramembrane proteases
17:15-17:35    Sergei Kalynych (Central European Institute of Technology – Masaryk University)
    Large motions of the protruding domain in a native iflavirus
17:35-17:55    Jiri Novacek (Masaryk University)
    Structure and genome delivery mechanism of Staphylococcus aureus phage therapy agent phi812-K1 determined by cryo-electron microscopy
17:55-18:15    Tibor Füzik (CEITEC – Central European Institute of Technology, Masaryk University)
    Structural study of Tick-borne encephalitis virus using cryo-electron microscopy
18:30-19:45    dinner
19:45-21:00    General Assembly of the Czech Society for Structural Biology
Meeting will be held in the Czech and/or Slovak languages
1. Volba zapisovatele;
2. Schválení programu;
3. Výroční zpráva Rady ČSSB o činnosti a hospodaření;
4. Schválení výroční zprávy Rady ČSSB o činnosti a hospodaření;
5. Zpráva revizní komise;
6. Infrastruktury se vztahem ke strukturní biologii, přístupy, financování, vývoj Instructu;
7. Změna sídla ČSSB v souvislosti se zprovozněním centra Biocev, hlasování;
8. Různé
21:00-23:00    Poster session
Poster titles are listed below

 7:30- 8:45    breakfast
Session 7    Chair person: Karel Kubicek
 9:00- 9:30    Frederic Vellieux (Institute of Biotechnology AS CR, v.v.i., BIOCEV(30′)
    The Centre of Molecular Structure (IBT, CAS) at Biocev
 9:30- 9:50    Irena Kratochvilova (Institute of Physics AS CR)
    Freezing process in human cell nuclei: determination of cryoprotectant parameters strongly influencing the cell condition
 9:50-10:10    Lucie Bednarova (IOCB AV)
    Chiroptical Properties of the Antimicrobial Peptide Lasiocepsin and of its analogs
10:10-10:30    Olívia Petrvalská (Charles University in Prague)
    Structural Insight into the 14-3-3 Protein-Dependent Inhibition of Protein Kinase ASK1
10:30-10:50    break
Session 8    Chair person: Irena Kratochvilova
10:50-11:10    Milan Zachrdla (CEITEC, Masaryk University)
    Structure and Dynamics of Sigma Subunit of RNA Polymerase from Bacillus subtilis
11:10-11:30    open
11:30-11:50    Pavel Brazda (CEITEC MU)
    Recognition of pTyr1-CTD by the elongation factor Spt6
11:50-12:10    Student prizes & concluding remarks
12:15-13:30    lunch

Posters will be presented on Friday 21:00 – 23:00

Valery Andrushchenko (Institute of Organic Chemistry and Biochemistry)
Eu3+-induced DNA Condensation and Chirality Transfer

Borislav Angelov (Institute of Physics, ELI beamlines, AVCR)
Time-Resolved Crystallography of Proteins at the laser driven X-ray sources in ELI beamlines

Cyril Bařinka (Institute of Biotechnology CAS, v.v.i.)
Human histone deacetylase 6: profiling of deacylase specificity

Jakub Benysek (UOCHB AV ČR)
Novel inhibition scaffolds targeting human cysteine cathepsins

Lada Biedermannová (Institute of Biotechnology – BIOCEV Centre)
Atlas of Protein Hydration – Connecting Information from Crystallography and Ab Initio Calculations

Michal Buša (ÚOCHB AV ČR)
Functional characterisation of novel cysteine protease inhibitor from Fasciola hepatica

Jan Dohnálek (Institute of Biotechnology CAS, v.v.i.)
Towards structure of HelD – a partner protein of RNAp in gram positive bacteria

Pavla Fajtová (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.)
Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: designing active-site inhibitors with anti-schistosomal activity

Tereza Gerguri (Masaryk University, CEITEC, NCBR)
Novel structure of membrane nanodisc

Mária Gondová (Masaryk University)
Crystal structure of honey bee hexamerin 70b at 3.2 Å resolution

Eva Hájková (Univerzita Palackého v Olomouci)
Nucleoside N-ribohydrolases and adenosine kinases in maize (Zea mays)

Jiří Hausner (Charles University in Prague)
Dynamics of ClC-ec1 D417C mutant form studied by hydrogen/deuterium exchange

Marie Hlavničková (Biotechnologický ústav AV ČR, v.v.i.)
Inhibitory binders derived from ABD-domain scaffold targeting human IL-17RA receptor as an alternative for modulation of Th17-mediated pro-inflammatory axis

Zuzana Jaseňáková (Masaryk Univesity – CEITEC)
Structural study of the intracellular domains of the ethylene receptor ETR1 from Arabidopsis thaliana

Petr Jeřábek (Charles University in Prague)
Structure and dynamics of the membrane-anchored cytochrome P450 1A2–cytochrome b5 complex

Barbora Kalouskova (Charles University in Prague)

Eva Krascsenitsova (Institute of Molecular Biology)
How Min systems from Clostridia species helps to find the mid-cell site during cell division?

Magdalena Krejcikova (Masaryk University)
Structural details of the interaction between pTyr1-CTD and the elongation factor Spt6

Monika Krupova (ÚOCHB AVČR)

Adrian Leontovyč (Institute of Organic Chemistry and Biochemistry)
Towards structural characterization of SmSP2 protease from parasitic blood fluke Schistosoma mansoni

Petr Louša (Masaryk University)

Václav Mareška (UCT Prague)
Electronic sculpting of AT2R ligands by metadynamics

Sara Matić (University of Zagreb)
Computational study of specific ion effect on the graphene oxide surface

Kateřina Mudroňová (Charles University in Prague)
Effect of the ribose versus 2’-deoxyribose residue in guanosine-5’-monophosphates on the formation of G-quartets stabilized by K+ and Na+

Ivana Nemčovičová (Biomedicínske Centrum SAV)
Characterization of a novel bidirectional NK activating ligand CD160

Joanna Oniskiewicz (Masaryk University)
Recognition of different methylation states on histone H3 lysine 4 by Set3 protein

Sudhir Kumar Pal (Institute of Microbiology, Academy of Sciences of the Czech Republic)
Structure and Dynamics of the Methyl-transeferase subunit of the E.coli restriction-modification system EcoR124I

Kirubakaran Palani (Institute of Organic Chemistry and Biochemistry AS CR)
Artificial proteins modulate allostery of PDZ3 and SH3 in two domains constructs. A computational characterization of novel chimeric proteins

Marketa Pazderkova (Charles University in Prague)
Spectroscopic study of protein fibrils

Samuel Pažický (Charles University in Prague)

Václav Profant (Charles University in Prague)
ROA study of chondroitin sulphate

Tatyana Prudnikova (Jihoceska Univerzita)
Structure-functional characterization of haloalkane dehalogenases

Katarína Pšenáková (UK Praha)
Role of Cys residues on the stability of the complex between proteinkinase ASK1 and thioredoxin

Jakub Ptáček (Institute of Biotechnology, Academy of Sciences)
Calcium ion is required for proper folding, dimerization and enzymatic activity of human glutamate carboxypeptidase II

David Řeha (Institute of Microbiology of the CAS, v.v.i.)
Theoretical study of crystal structure of WrbA from E. coli in complex with benzoquinone using QM calculations of charge transfer rates

Ondřej Skořepa (Charles University in Prague)

Vojtěch Spiwok (University of Chemistry and Technology, Prague)
Moving Hills Method

Jaroslav Srp (ÚOCHB AV ČR)
Crystal structure of plant defense protein in complex with serine protease

Jan Stránský (Institute of Biotechnology, CAS)
A parameter of diffraction experiment with low attention: exposure

Ekaterina Sviridova (Jihoceska Univerzita v Ceskych Budejovicich)
Integrated structural biology study of the FrpD protein from Neisseria meningitidis

Marek Šebela (Palacky University in Olomouc)
Oligonucleotide analysis and sequencing using MALDI-TOF mass spectrometry

Jan Šlhan (IOCB)
Structural study of the reaction mechanism of 3′ DNA phosphatase from Neisseria meningitidis

Katsiaryna Tratsiak (University of South Bohemia in Budweis)
Structure-functional analysis of the α/β-hydrolase fold superfamily member

Zuzana Trošanová (Masaryk University)
Solvation of engrailed homeodomain mutant K52E

Ondřej Vaněk (Charles University in Prague)

Jiří Zahradník (Charles University in Prague)
Crystal structure of a glycerol trinitrate reductase XdpB from Agrobacterium sp. R89-1 revealed Inhibition by reversible aggregation

Vojtěch Zapletal (Masaryk University)
Comparison of computational and experimental results for intrinsically disordered proteins (IDPs)

Nina Zemanova (Institute of Neuroimmunology, Slovak Academy of Sciences)
Structural and biophysical characterization of the projection domain of neuronal tau protein

Hana Zigová (Masaryk University)
Improved interpretation of 14-3-3ζ fluorescence measurements by molecular dynamics simulations

Lucie Zímová (Institute of Physiology CAS)
The role of the S1-S4 sensor domain in the activation and modulation of the TRPA1 ion channel

Poster dimensions: A0

Organizers of the meeting Bohdan SchneiderRadek KuželIvana Kutá-SmatanováRudiger EttrichJan Dohnálek