Contributions from the IX Discussions in Structural Molecular Biology

Contributions from the IX Discussions in Structural Molecular Biology
Nove Hrady March 24 – 26 2011

V. Andrushchenko
Supramolecular Assemblies Formed by Diolein and Stearyl Alcohol

T. Baikova
Crystallization and structure-functional analysis of coupling of translocation to DNA cleavage in type I restriction enzyme EcoR124I

I. Barák
Lipid helices formation in Bacillus subtilis cell membrane

L. Bednářová
Antibacterial peptides in interaction with model membranes studied by various spectroscopic methods

I. Beššeová
How could flexibility of RNA three way junction from the GTP-ase associated center of 50S assist to the accommodation of the TRNA into the ribosome?

V. Bialevich
Helical-helicase 2 domains interactions in HsdR subunit of EcoR124I restriction-modification complex

L. Biedermannová
Investigation of ligand passage in proteins

J. Bílý
Localization of calmodulin and  PIP2 binding sites on the C-termini of the transient receptor potential cation channel TRPM5

J. Brynda
Crystal structure of the mouse galectin-4 N-terminal carbohydrate recognition domain

J. Burda
Reduction mechanism of the Pt(IV) Satraplatin derivates by guanosine monophosphate; quantum mechanical study

E. Dejmková
Thermodynamical analysis of the mutant CV-IIL lectins from Chromobacterium Violaceum

J. Dohnálek
The molecular puzzle of C-type lectin like natural killer cell receptors

R. Dopitová
Preparation of AHP proteins for structural analysis

R. Dvorský
Impact of Point Mutations on Protein Functions: Example Case of Ras GTPases

P. Dvořák
Engineering of biochemical pathway for degradation of anthropogenic environmental pollutant 1,2,3-trichloropropane

R. Ettrich
Functional coupling of DNA duplex translocation to its cleavage in a type I restriction enzyme

Z. Futera
Application of New QM/MM Interface to Study of Ru Drugs Interacting with DNA

S. Geidl
Predicting pKa values of substituted phenols from atomic charges

P. Hanč
Structural details of NKR-P1D : Clrb interaction elucidated by protein cross-linking and mass spectrometry

J. Hašek
Reliability and accuracy in protein structure determination

B. Holakovská
Comparison of C-terminal segments of  TRPV ion channel family members and their interactions with calmodulin

J. Houser
Aleuria aurantia lectin family – structural insight into differences of carbohydrate binding among related proteins

J. Hudecová
Conformational study of the cyclo(L-Trp-L-Trp)dipeptide

Z. Chval
Mechanism of the Oxaliplatin Binding to the Double-Stranded 1,2-ds(pGpG) Dinucleotide in Aqueous Solution

?. Melnicakova
The effect of Escherichia coli min proteins on Bacillus subtilis

Jawid Ahmad
Novel Ligands for IFNg derived from Streptococcal Protein G scaffold

M. Kacířová
Structural studies of 14-3-3/phosducin complex

I. Kishko
Kinetic analysis of E. coli WrbA redox activity

J. Kohoutová
Isolation of the extrinsic proteins from the oxygen-evolving complex of higher plants

P. Kolenko
Influence of RNA binding on the structure and functionality of Borna disease virus matrix protein

M. Kopecká
Preparation of regulatory domain of tyrosine hydroxylase for NMR studies

D. Kopečný
Biochemical characterization of a recombinant plant aldehyde dehydrogenase 7 from Pisum sativum (PsALDH7)

T. Koval
Structural analysis of a recombinant plant bifunctional nuclease TBN1

S. Kozmoň
Carbohydrate CH/p interactions – Theoretical investigation of the favourable regions in the carbohydrate surroundings

O. Kroutil
Structure and Conformatial Behavior of the DNA Oligonucleotide Attached to the Charged Surface: A Molecular Dynamics Study

M. Krupička
Competing reactions of disulphides and hydroxyl anion – QM study

A. Křenek
CERIT-SC Centre: Looking for Synergies in Scientific Computing

Z. Kukačka
Structural assembly of β-N-acetylhexosaminidase complex

P. Kulhánek

M. Kutý
Thylakoid membrane and Photosystem II, structure and molecular dynamics simulations

M. Lahoda
Crystallization and structural analysis of DhaA31 protein from Rhodococcus rhodochrous

E. Macáková
Study of Structural Differences in H8-H9 Loop among 14-3-3 Protein Isoforms

J. Makroczyová
Functional and biochemical analysis of truncated SpoIISA toxin in Bacillus subtilis

P. Maloň
Vibrational and electronic optical activity of amide and disulfide groups in neurohypophyseal hormones and their models

P. Malý
Generation of artifical binders with affinity to human cytokines via computer-assisted mutagenesis of a stable protein scaffold and ribosome display selection

P. Man
Accessibility changes within diphtheria toxin T domain upon membrane penetration probed by hydrogen exchange and mass spectrometry

T. Náhlík
The state trajectory of cell

P. Pachl
Structure-based drug design of selective 5′-nucleotidases inhibitors

V. Papoušková
NMR study of RNA polymerase delta subunit unique for gram-positive bacteria

A. Pautsina
Biological systems state variable identification using joint analysis of biological and technical hypothesis in the time-lapse tissue culture development experiment

T. Pazderka
Raman and infrared spectroscopy of amino acids and its implication for improvement of the protein secondary structure determination

B. Pekárová
Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana

J. Písačková
Preparation, characterization and crystallization of recombinant fragment of anti-CD3 antibody MEM-57

J. Prchal
Expression and purification of myristoylated matrix protein of Mason-Pfizer monkey virus for Structural Studies

V. Profant
Experimental and theoretical study of formation of polyproline II helix by means of Raman optical activity

J. Přecechtělová
Torsion angle dependence of phosphorus chemcial shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations

D. Řeha
Biological Applications of QM/MM Calculations with MM Polarization

P. Řezáčová
Crystal structures of two protease inhibitors from tick saliva

L. Řežábková
Structure of the 14-3-3/RGS3 complex: New details on architecture of complexes formed by 14-3-3 proteins

D. Rozbeský
Chemical cross-linking and H/D exchange combined with mass spectrometry: a tool to validate and refine 3-D protein X–ray model

M. Ruda
MetaCentrum in e-Infrastructure era

J. Ryška
Docking study of matrix metalloproteinase inhibitors

K. Shamayeva
Identification of amino acid residues important for coupling ATPase and restriction activity in EcoR124I endonuclease

O. Schmidt
Higher plant photosystem II

T. Skálová
Structure of mouse CLRG – a ligand of NK cell receptor

O. Skřehota
QSPR modeling – algorithms, challenges and IT solutions

V. Spiwok
Molecular Simulation with Elastic Network Model Potential in Gromacs

P. Srb
Protein oligomerization and backbone flexibility

Z. Střelcová
Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism

A. Stsiapanava
Crystallization and preliminary crystallographic analysis of Rhodococcus rhodochrous wild-type DhaA protein and its variant DhaA13 complexed with different ligands

E. Sviridova
Neisseria Meningitidis iron-regulated protein FrpD: Crystallization and crystallographic characterization

V. Sychrovský
Proposal of alternative pathway of the glycosidic bond cleavage mechanism of 8-oxoguanosine catalyzed by the human DNA repair protein hOGG1

M. Šebela
Structural and functional study on the glycosylation in maize cytokinin oxidase/dehydrogenase1

J. Šebera
Proposal of alternative pathway of the glycosidic bond cleavage mechanism of 8-oxoguanosine catalyzed by the human DNA repair protein hOGG1

A. Štěpánková
Three-dimensional structure of binunctional anhydrolase

Yoshiuki Tanaka
NMR spectroscopic approaches to the mechanism of action of hammerhead ribozyme

J. Urban
Decomposition of cellular system via causal relations

L. Urbániková
Structural basis for substrate recognition by GH30 glucuronoxylanase from Erwinia Chrysanthemi

D. Veisová
The activity of NTH1 enzyme is mediated by yeast 14-3-3 isoforms