X Discussions 2012

Institute of Biotechnology AS CR
Institute of Microbiology AS CR
South Bohemian University in Ceske Budejovice
Czech Crystallographic Association
Czech Society for Structural Biology
proudly organize

X Discussions in Structural Molecular Biology

Nové Hrady, Thursday March 22 – Saturday March 24 2012

Registered Participants

Abstracts of all contributions

Photos from the conference


Thursday, March 22

12:00 – 13:15  Registration at Nový Zámek
13:15 – 13:45  Accommodation in hotels

14:00 Session I: Chairperson Vladimír Sklenář
Bohdan Schneider: Opening
Josef Houser: Protein oligomerization in Aleuria aurantia lectin family – importance and difficulties
Chojiro Kojima: Structure-based discovery of flowering hormone receptor
Radka Končitíková: Maize aldehyde dehydrogenases from family 10 and 7
Ivana Drienovská: Biochemical Characterization of Haloalkane Dehalogenase DpcA from Psychrobacter cryohalolentis K5: the First Extremophilic Member of the Family
Coffee break

15:50  Session II: Chairperson Marek Šebela
Petr Kolenko: BDV matrix protein: from mutation to function
Glenda Alquicer: High throughput screening of potential GCPII inhibitors by fluorescence polarization
Lada Biedermannová: Investigation of ligand passage in proteins
Artur Gora: Engineering Tunnels in Enzymes
Lukáš Pravda: Computational Methods for Detecting Ligand Accessible Pathways – Approaches and Benchmarking Study

18:00  Dinner


Friday , March 23

08:00  Breakfast

09:00 Session III: Chairperson Bohdan Schneider
Mark Benson: The BioSAXS-1000 and a new approach to combining visible and UV light imaging – the latest developments from Rigaku
Vernon Smith: Getting the best data from your crystal
Tomáš Polívka: ELI Beamlines facility as a new promising tool for structural studies of macromolecules
Miroslav Brumovský: Visualization of atomic charges in molecules: Comparison of available approaches and software tools
Coffee break

10:40  Session IV: Chairperson Jiří Vondrášek
Jiří Černý: Complete basis set extrapolation and hybrid schemes for geometry gradients and vibrational analysis of noncovalent complexes.
Boris Fačkovec: Universal Stability Model for Globular Proteins
Radek Matuška: Theoretical Description of Carbohydrate-Aromatic CH-π Interactions Additive Properties via DFT and Ab Initio Calculations
Žofie Sovová: Thylakoid membrane studied by the means of molecular dynamics
Jiří Vymětal: Computational study of retro Trp-cage

12:30  Lunch

14:00 Session V: Chairperson Vladimír Sychrovský
Yoshiyuki Tanaka: Isotope-assisted structural chemical analysis of nucleic acids (30 minutes)
Lukáš Žídek: Structural Biology without Structure – Delta Subunit of RNA Polymerase from Bacillus subtilis (30 minutes)
Jakub Šebera: Quantum chemistry study of repairing function of hOGG1 enzyme
Irena Kratochvilova: Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns
Coffee break

16:00  Session VI: Chairperson Lukáš Žídek
Tomáš Náhlík: Experiment based determination of fractal dimensionality of Belousov-Zhabotinsky reaction
Jan Prchal: Structure of Myristoylated Matrix Protein of Mason-Pfizer Monkey Virus and the Role of Phosphatidylinositol-(4,5)-bisphosphate in its Membrane Binding
Miroslava Kacířová: Structural basis of the 14-3-3 protein-dependent inhibition of phosducin function
Eva Macáková: Role of individual phosphorylation sites for the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1
Ondrej Cehlar: Complementary structural investigation of intrinsically disordered protein tau, involved in neurodegenerative diseases

18:00  Dinner

19:30  General Assembly of the Czech Society for Structural Biology. Meeting will be held in the Czech and/or Slovak languages
Program Valného shromáždění ČSSB
Výroční zpráva Rady ČSSB o činnosti
Schválení výroční zprávy Rady ČSSB o činnosti
Situace s budováním infrastrukturních center
Infrastruktura pro integrativni strukturni biologii INSTRUCT

20:30  Poster session

Saturday, March 24

08:00  Breakfast

09:00  Session VII: Chairperson Lada Biedermannová
Pavel Plevka: The structure of enterovirus 71 and its implications for the design of capsid binding anti-viral compounds
Jan Dohnálek: The C-type lectin-like fold in natural killer cell receptors
Vojtech Spiwok: Structural bioinformatics of CBS domain
Jindrich Hašek Intermolecular interactions displayed by X-ray diffraction
Coffee break

10:40  Session VIII: Chairperson Tomáš Obšil
Jana Melničáková: SpoIISA-SpoIISB proteins as suicide components of Bacillus subtilis
Ladislav Bumba: Analysis of biomolecular interactions by surface plasmon resonance
Bohdan Schneider: Increasing affinity between interferon gamma and its receptor by computer design of receptor mutations. I. Design of mutants
Pavel Mikulecký: Increasing affinity between interferon gamma and its receptor by computer design of receptor mutations. II. Affinity measurements

12:15  Lunch

  • All talks take 20 minutes including discussion if not stated otherwise.


Poster session, Friday March 23, starts at 20:30

Jan Bílý: Transient receptor protein C6 and S100A1 protein as binding partners
Ľubomír  Borko: The study of human Ryanodine Receptor 2 N-terminal region responsible for heart disfunction
Zuzana Chromíková: SpoIIE links asymmetric cell division to compartmentalization of gene expression during sporulation of Bacillus subtilis
Radka Dopitová: Preparation and crystallization of AHP2 protein, the signal transmitter from Arabidopsis thaliana
Jiří Heller: Photosynthetic PsbR protein from higher plants
Vladena Bauerova: Characterization of N-terminal and central part of human ryanodine receptor 2
Vitali Bialevich: The influence of the C-terminal helical domain on ATPase activity in the restriction-modification complex EcoR124I
Katsiaryna Shamayeva: How can stalling of translocation activate the endonuclease in the type I restriction-modification system EcoR124I
Rudiger Ettrich: Charybdotoxin unbinding from the mKv1.3 potassium channel: A combined computational and experimental study
David Kopecny: Structure-function study on plant S-nitrosoglutathione reductase from tomato
Dalibor Košek: Preparation of the 14-3-3:ASK1 kinase complex for structural studies.
Tomáš Kovaľ: Reaction mechanism principles of the bifunctional plant nuclease TBN1
Milan Kuchař: Protein variants of ABD domain targeting human IL-23 receptor
Daryna Kulik: Preparation of the construct recombinant PsbO protein from higher plants
Jakub Ptáček: Structural and Biochemical Characterization of the Folyl-poly-γ-L-glutamate Hydrolysing Activity of Human Glutamate Carboxypeptidase II
Karina Romanova: Cell states on the basis of manual detection
Lucie Surá: The cluster of acidic residues in the C terminus of TRPA1 contributes to calcium sensing
Martina Tylichova: Structure-function study on maize nucleoside N-ribohydrolase family
David Bednar: Design of non-enantioselective enzyme for biodegradation of toxic environmental pollutant 1,2,3-trichloropropane
Lukáš Chrást: Characterization of novel haloalkane dehalogenase isolated from psychrophilic bacterium Marinobacter sp. ELB17
Lukas Daniel: Discovery of Inhibitors of Haloalkane Dehalogenase DmbA by Virtual Screening
Veronika Stepankova: Molecular mechanisms of activation and inhibition of haloalkane dehalogenases by organic cosolvents
Katsiaryna Tratsiak:  Crystallization results and X-ray diffraction of haloalkane dehalogenase DpcA, isolated  from Psychrobacter cryohalolentis K5 and   co-crystallized with it’s substrate

Valery Andrushchenko: Vibrational Circular Dichroism Study of Isotropic and Liquid Crystalline Phases Formed by Guanine Quadruplexes
Michaela Jirků: SPR studies on the interactions of TRP channels and their activity modulators
Tana Koudelakova: Engineering enzyme resistance to organic co-solvent and elevated temperature
Ondřej Kroutil: Behavior Of Water, Ions And Small Organic Molecules Near Quatz (101) Surfaces
Petr Kulhanek: Ion Transfer in G4-wires
Petr Novak: Chemical cross-linking and high resolution mass spectrometry for mNKR-P1C protein structure modeling
Václav Profant: ROA study of chondroitin sulphate and its building blocks
Barbora Rezacova: Spectroscopic study of the MADS box
Anna Zhyrova: State trajectory of the Belousov-Zhabotinsky reaction
Eva Chovancová: CAVER 3.0: A tool for analysis of transport pathways in dynamic protein structures
Tomáš Bouchal: QSPR models predicting pKa from atomic charges
Petr Jeřábek: Utilization of molecular dynamics methods for identification of stable CYP1A2-cytochrome B5 binary complexes
Michal Kutý: Photosystem II reaction center, QM study of charge distribution and transfer
David Reha: Application of QM/MM Calculations with Novel Polarized Embedding to Detail Investigation of the Flavoprotein WrbA
Dhiraj Sinha: In silico charecterization of HsdR
Jakub Štěpán: Reaction Mechanism of MutH Enzyme – Quantum Mechanics/Molecular Mechanics Study
Tomáš Trnka: Quantum-chemical insight into the reaction mechanism of polypeptide UDP-GalNAc transferase 2, a retaining glycosyltransferase
Vlastimil Zíma: Computational modeling of TRPA1 C-terminus
Vladimir Sychrovsky: Metalophillic Attraction in the Consecutive T-HgII-T DNA base pairs
Iva Zuskova: The role of weak non-covalent interactions in FOXO4 binding to the target DNA
Miroslava Kopecka: NMR studies of the regulatory domain of tyrosine hydroxylase
Tomas Kroupa: Preparation and structure determination of T41I/T78I mutant of M-PMV matrix protein
Pavel Srb: Plasma-membrane permeability of S. cerevisiae by PGSE NMR
Milan Zachrdla: Importance of NMR data validation prior to structure calculation
Ivana Kuta: Smatanova Protein crystallization studies – complex overview
Volha Shmidt: Improvement of the PSII purification procedure for crystallization
Tereza Skálová: Structural studies of NK receptors and ligands
Rostislav Skrabana: Non-robotic high-throughput setup yielding diffraction-quality crystals in nanoliter drops manually assembled by motorized pipette
Ekaterina Sviridova: Crystal structure of the iron-regulated outer membrane lipoprotein FrpD (NMB0584) from Neisseria Meningitidis


All deadlines have passed

Please, send questions, requests to Bohdan Schneider