XI Discussions 2013

Institute of Biotechnology AS CR
Institute of Microbiology AS CR
Institute of Nanobiology and Structural Biology, GCRC AS CR
South Bohemian University in České Budějovice
Czech Crystallographic Association
Czech Society for Structural Biology
proudly organize

XI Discussions in Structural Molecular Biology

Nové Hrady, Thursday March 14 – Saturday March 16 2013

Registration has been closed

Registered Participants

Abstracts of all contributions

Photos from the conference by Bohdan Schneider and by Radek Kuzel


Thursday, March 14

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

14:00 – 15:55 Session I: Chairperson Petr Novák

John Engen: Hydrogen exchange mass spectrometry to probe the conformation of proteins both in solution and in membranes (45′)
Alan Kádek: In-solution structure of cellobiose dehydrogenase probed by hydrogen / deuterium exchange mass spectrometry
Petr Novák: NKR-P1C Structural Model Revealed by Mass Spectrometry
Marek Šebela: Analysis of heterogeneous hinge-region O-glycosylation of human IgA1 using MALDI-TOF/TOF mass spectrometry (30′)

15:55 – 16:15 Coffee break

16:15 – 17:45  Session II: Chairperson Richard Štefl

Jaroslav Nunvář: Evolution of genetic diversity of repetitive extragenic palindromic elements
Babak Minofar: Structure and dynamics of biomolecules in non-aqueous ionic solutions
Sinha Dhiraj: Interdomain communication and interaction in the motor subunit of restriction modification system EcoR1241 from E.coli
Bohdan Schneider: Analysis of protein/DNA interactions by novel bioinformatic tools (30′)

17:45  Dinner

Friday , March 15

08:00  Breakfast

09:00 – 10:10 Session III: Chairperson Marek Šebela

Mike Williams: Protein characterisation using DLS – measurement principle and technology typical applications, limitations and troubleshooting, the new Zetasizer Nano (30′)
Lucie Bednárová: Antimicrobial peptides interacting with model membranes. Spectroscopic study
Irena Kratochvílová: Charge transport through DNA/DNA duplexes and DNA/RNA hybrids: complex mechanism study

10:10 – 10:30 Coffee break

10:30 – 12:10  Session IV: Chairperson Jiří Brynda

Jan Stránský: Plant nuclease TBN1 involved in apoptotic processes blocks its active site by a surface loop – sign of regulatory function?
Oksana Degtjarik: Preparation, Crystallization and Preliminary Structural Analysis of AHP2 Protein, the Signal Transmitter from Arabidopsis thaliana
Ľubomír Borko: Human cardiac ryanodine receptor: structural study of the N-terminal region
Petr Těšina: Structural study of LEDGF/p75 binding partners
Josef Houser: Power is in detail – structural analysis of an Aleuria aurantia lectin mutant

12:15 – 13:30  Lunch

13:45 – 15:05 Session V: Chairperson Cyril Bařinka

Vernon Smith: Bringing the Beamline Home: Increasing Productivity and Reducing Costs with the D8 VENTURE with METAJET X-Ray Source (30′)
Jan Dohnálek: Metals and ions in protein structures – from essential to marginal questions in identification of ions in enzymes and receptors (30′)
Ondrej Cehlár: Structural insight into the conformation of one of the microtubule binding motifs on the Alzheimer’s disease-associated protein tau

15:05 – 15:30 Coffee break

15:30 – 17:30 Session VI: Chairperson Tomáš Obšil

Petr Kolenko: Inhibitors of glutaminyl cyclases against Alzheimer’s disease (30′)
Jaroslav Burda: Reaction Mechanism of Ru(II) Piano-Stool Complexes; Umbrella Sampling QM/MM MD Study
Radek Matuska: CH-pi Interaction between Carbohydrates and Aromatic Moieties: Electron Density Issue
Žofie Sovová: Thylakoid membrane characterization and its interaction with PsbI protein from photosystem II
Kvido Stříšovský: Structural and mechanistic principles of intramembrane proteolysis – lessons from rhomboids (30′)

17:45 – 19:00  Dinner

19:00  General Assembly of the Czech Society for Structural Biology. Meeting will be held in the Czech and/or Slovak languages

Program Valného shromáždění ČSSB

1. Výroční zpráva Rady ČSSB o činnosti a hospodaření
2. Schválení výroční zprávy Rady ČSSB o činnosti a hospodaření
3. Zpráva revizní komise
4. Situace s budováním evropských infrastrukturních center
5. Členství naší společnosti v Radě vědeckých společností (RVS)
6. Reakce GA ČR na náš podnět o potřebě zřízení panelu specializovaného na strukturní biologii a bioinformatiku
7. Různé
8. Diskuse

20:15 – 22:45  Poster session

Saturday, March 16

08:00  Breakfast

09:00  – 10:40 Session VII: Chairperson Rudiger Ettrich

Evžen Bouřa: The crystal structure of the Phi6 major capsid protein (30′)
Daniel Němeček: Cryo-EM Reconstruction of the Bacteriophage ϕ6 Procapsid at Near-Atomic Resolution Shows Conformational Changes in dsRNA Virus Maturation
Mikalai Lapkouski: Complexes of HIV-1 RT and DNA/RNA hybrid reveal structure compatible with RNA degradation (30′)
Lukas Daniel: Role of the buried halide-binding site of haloalkane dehalogenase DbeA

10:40 – 11:00 Coffee break

11:00 – 12:10  Session VIII: Chairperson Richard Hrabal

Jan Frömmel: Aminoaldehyde dehydrogenase 1 from tomato – enzyme structure and possible use for the detection of aldehydes in beverages
Tomas Kroupa: Interaction of the myristoylated M-PMV matrix protein and his mutants with phospholipids
Lukáš Žídek: Molecular motions monitored by NMR relaxation – a conservative approach (30′)

12:10 – 12:12 Closing remarks

12:15  Lunch

  • All talks labeled (30′) take 30 minutes, all others take 20 minutes. These times will be observed and include discussion, leave at least 5 minutes to your colleagegues!

Posters (alphabetically)

Poster session starts on Friday March 15 at 20:15

Petr Ashcheulov: Influence of specific boron defects on boron-doped diamond conductivity
Hana Barvíková: Computational study of interactions of organic matter and biomolecules with mineral surfaces
Vitali Bialevich: Proposed translocation cycle of the restriction-modification system EcoR124I
Jarmila Dušková: Extracellular chitinolytic enzymes of Clostridium Paraputrificum J4; separation and characterization.
Rudiger Ettrich: Biphasic kinetic behavior of FMN-dependent NAD(P)H:quinone oxidoreductase WrbA from E. coli: A molecular understanding
Katarína Hlat-Glembová: Prediction and structural studies of active site of selected glycosyl hydrolases from Paenibacillus thiaminolyticus
Tatsiana Holubeva: Isolation and crystallization of the recombinant PsbR protein of higher-plant photosystem II
Petr Hošek: Combination of alchemical free energy simulation and metadynamics in the simulation package GROMACS
Dominik Hrebík: Magnesium binding to the receiver domain of cytokinin receptor CKI1RD from Arabidopsis thaliana
Michaela Jirků: Ca2+ binding proteins interact with the N-terminal region of TRPM1
Ivo Kabelka: Study of bsobi endonuclease by molecular dynamics
Miroslava Kacířová: Mapping of the interaction surface of phosducin using HDX-MS
Alina Kevorkova: Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme
Petr Kolenko: Yfid from E.coli as a Pfl repair protein
Radka Končitíková: Structural characterization of two maize aldehyde dehydrogenases from family 2
Miroslava Kopecká: How calcium and Bmh1 activate yeast neutral trehalase Nth1?
Dalibor Kosek: Biophysical study of the complex between the 14-3-3 protein and the kinase domain of ASK1
Tomas Koval: Structure of multifunctional plant nuclease TBN1
Natallia Kulik: Homology modeling of fungal hexosaminidase from T.flavus with high substrate promiscuity
Ivana Kutá Smatanová: Practical aspects of protein crystallography
Michal Kutý: Towards a structure of green plant Photosystem II
Lucie Marečková: Novel binders derived from an albumin-binding domain scaffold targeting Prostate Secretory Protein-94
Petra Matunová: Thermodynamic and kinetic parameters for interaction of selected Pt(II) complexes with guanine
Pavel Mikulecký: Rational design of high-affinity variants of interferon-gamma receptor 1
Pavel Oborský: Digital metadynamics: New biased simulation concept and its testing on the conformational equilibrium of Ac-Ala-NHMe
Saurabh Pandey: Computational simulation of trimer rotation in hexameric Argine repressor from e.coli
Jiří Pavlíček: Gateway-based system for optimization of recombinant protein expression in K. lactis
Jakub Ptáček: Selection and characterization of Anticalin-based binders targeting human glutamate carboxypeptidase II
David Reha: Biological Applications of QM/MM Calculations with Polarized Embedding
Jakub Šebera: Theoretical Study of Metal Ion Binding in Modified and Natural Cytosine-Cytosine Base Pairs
Tereza Skálová: Structural properties of NK receptors and ligands with C-type lectine-like fold
Rostislav Škrabana: Validation of a high-throughput setup for manual assembly of nanolitre vapour-diffusion protein crystallization screens
Katsiaryna Tratsiak: Characterization of the selected haloalkane dehalogenases crystals specific activity towards to their substrates
Lucie Vaňková: Human IL-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells
Milan Zachrdla: NMR Investigation of Unstructured Malaria Surface Protein MSP2, Isoform 3D7
Vojtěch Zapletal: Motions of biomoleculs monitored by spectral density mapping
Jitka Žídková: Glycoproteins and Protein Glycations Identified in Barley Grain and Malt by 2D-HPLC and MS/MS

The whole program takes place at Nový zámek.

Organizers of the meeting Bohdan Schneider, Radek Kužel, Ivana Kutá-Smatanová, Rudiger Ettrich, Anita Zupčanová, Petr Novák, Jindřich Hašek, Jan Dohnálek

 (c) Bohdan Schneider 2013