BrIdging Structural BiOlogy with Biological SyNthesis and Self Assembly to Reveal Key Processes in Living Systems

Risultati finali

Annual report on strategic events Year 1

Programmes and attendance records

Annual report on strategic events Year 3

Programmes and attendance records

Management knowledge transfer report

Summary of staff exchange and workshop

Final report on expert visits

Programme and attendance records

Communication, dissemination, and exploitation plan

Indicative schedule and guidelines for dissemination, communication and exploitation

Mid-term training report

Summary of training events and student progress

Mid-term communication, dissemination, and exploitation report

Summary of activities, update of plan

Final secondment report

Summary of implemented secondments

Annual report on strategic events Year 2

Programmes and attendance records

Mid-term report on expert visits

Programme and attendance records

Training plan

Preliminary schedule of training events

List of CEITEC MU publications for the last 3 years

Key Performance Indicators (KPI) baseline. In the reporting tool on the Participant Portal by month 2 all publications of the coordinator (CEITEC MU in the particular field of research) during the three years preceding the start date of the BISON project will be added. The deliverable D7.1 will be one-page statement that this task has been completed.

Final training report

Summary of training events and student progress

Secondment plan

Preliminary secondment schedule and supervisory arrangements

Mid-term secondment report

Summary of implemented secondments and update of Secondment plan

Final communication, dissemination, and exploitation report

Summary of activities

Pubblicazioni

Implementing efficient concerted rotations using Mathematica and C code⋆

Autori: Luca Tubiana, Miroslav Jurásek, Ivan Coluzza
Pubblicato in: The European Physical Journal E, Numero 41/7, 2018, ISSN 1292-8941
Editore: Springer Verlag
DOI: 10.1140/epje/i2018-11694-7

Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics

Autori: Kateřina Melková, Vojtěch Zapletal, Séverine Jansen, Erik Nomilner, Milan Zachrdla, Jozef Hritz, Jiří Nováček, Markus Zweckstetter, Malene R. Jensen, Martin Blackledge, Lukáš Žídek
Pubblicato in: Journal of Biological Chemistry, Numero 293/34, 2018, Pagina/e 13297-13309, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra118.001769

Label-free Voltammetric Detection of Products of Terminal Deoxynucleotidyl Transferase Tailing Reaction

Autori: Monika Hermanová, Pavlína Havranová-Vidláková, Anna Ondráčková, Swathi Senthil Kumar, Richard Bowater, Miroslav Fojta
Pubblicato in: Electroanalysis, Numero 31/2, 2019, Pagina/e 246-255, ISSN 1040-0397
Editore: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/elan.201800452

Asymmetric bifurcated halogen bonds

Autori: Martin Novák, Cina Foroutan-Nejad, Radek Marek
Pubblicato in: Phys. Chem. Chem. Phys., Numero 14639076, 2015, Pagina/e 6440-6450, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/c4cp05532b

DNA and RNA Quadruplex-Binding Proteins

Autori: Václav Brázda, Lucia Hároníková, Jack Liao, Miroslav Fojta
Pubblicato in: International Journal of Molecular Sciences, Numero 14220067, 2014, Pagina/e 17493-17517, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms151017493

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Autori: S. K. Mishra, M. Kara, M. Zacharias, J. Koca
Pubblicato in: Glycobiology, Numero 09596658, 2013, Pagina/e 70-84, ISSN 0959-6658
Editore: Oxford University Press
DOI: 10.1093/glycob/cwt093

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

Autori: Kateřina Němcová, Peter Šebest, Luděk Havran, Petr Orság, Miroslav Fojta, Hana Pivoňková
Pubblicato in: Analytical and Bioanalytical Chemistry, Numero 16182642, 2014, Pagina/e 5843-5852, ISSN 1618-2642
Editore: Springer Verlag
DOI: 10.1007/s00216-014-7996-0

Studying Weak and Dynamic Interactions of Posttranslationally Modified Proteins using Expressed Protein Ligation

Autori: Konstantinos Tripsianes, Nam K. Chu, Anders Friberg, Michael Sattler, Christian F. W. Becker
Pubblicato in: ACS Chemical Biology, Numero 15548929, 2014, Pagina/e 347-352, ISSN 1554-8929
Editore: American Chemical Society
DOI: 10.1021/cb400723j

Spectral density mapping protocols for analysis of molecular motions in disordered proteins

Autori: Pavel Kadeřávek, Vojtěch Zapletal, Alžbeta Rabatinová, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Pubblicato in: Journal of Biomolecular NMR, Numero 09252738, 2014, Pagina/e 193-207, ISSN 0925-2738
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10858-014-9816-4

Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins

Autori: Jitka Dadová, Petr Orság, Radek Pohl, Marie Brázdová, Miroslav Fojta, Michal Hocek
Pubblicato in: Angewandte Chemie International Edition, Numero 14337851, 2013, Pagina/e 10515-10518, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201303577

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ϕ6 Major Capsid Protein

Autori: Daniel Nemecek, Pavel Plevka, Evzen Boura
Pubblicato in: The Protein Journal, Numero 15723887, 2013, Pagina/e 635-640, ISSN 1572-3887
Editore: Springer Verlag
DOI: 10.1007/s10930-013-9526-x

A relativistic DFT methodology for calculating the structures and NMR chemical shifts of octahedral platinum and iridium complexes

Autori: Jan Vícha, Michael Patzschke, Radek Marek
Pubblicato in: Physical Chemistry Chemical Physics, Numero 14639076, 2013, Pagina/e 7740, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/c3cp44440f

Voltammetric Study of dsDNA Modified by Multi-redox Label Based on N-methyl-4-hydrazino-7-nitrobenzofurazan

Autori: Ales Danhel, Veronika Raindlova, Ludek Havran, Jiri Barek, Michal Hocek, Miroslav Fojta
Pubblicato in: Electrochimica Acta, Numero 00134686, 2014, Pagina/e 348-357, ISSN 0013-4686
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2014.02.137

Instability restricts signaling of multiple fibroblast growth factors

Autori: Marcela Buchtova, Radka Chaloupkova, Malgorzata Zakrzewska, Iva Vesela, Petra Cela, Jana Barathova, Iva Gudernova, Renata Zajickova, Lukas Trantirek, Jorge Martin, Michal Kostas, Jacek Otlewski, Jiri Damborsky, Alois Kozubik, Antoni Wiedlocha, Pavel Krejci
Pubblicato in: Cellular and Molecular Life Sciences, Numero 1420682X, 2015, Pagina/e 2445-2459, ISSN 1420-682X
Editore: Birkhauser Verlag
DOI: 10.1007/s00018-015-1856-8

A Novel Protein-Protein Interaction in the RES (REtention and Splicing) Complex

Autori: K. Tripsianes, A. Friberg, C. Barrandon, M. Brooks, H. van Tilbeurgh, B. Seraphin, M. Sattler
Pubblicato in: Journal of Biological Chemistry, Numero 00219258, 2014, Pagina/e 28640-28650, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M114.592311

How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids – A Computational Study

Autori: Zdeněk Kříž, Jiří Klusák, Zdena Krištofíková, Jaroslav Koča
Pubblicato in: PLoS ONE, Numero 19326203, 2013, Pagina/e e62914, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0062914

Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

Autori: Jiří Nováček, Lubomír Janda, Radka Dopitová, Lukáš Žídek, Vladimír Sklenář
Pubblicato in: Journal of Biomolecular NMR, Numero 09252738, 2013, Pagina/e 291-301, ISSN 0925-2738
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10858-013-9761-7

Electrochemical behaviour of 2,4-dinitrophenylhydrazi(o)ne as multi-redox centre DNA label at mercury meniscus modified silver solid amalgam electrode

Autori: Ales Danhel, Veronika Raindlova, Ludek Havran, Hana Pivonkova, Michal Hocek, Miroslav Fojta
Pubblicato in: Electrochimica Acta, Numero 00134686, 2014, Pagina/e 122-131, ISSN 0013-4686
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.electacta.2013.09.147

High-quality and universal empirical atomic charges for chemoinformatics applications

Autori: Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan, Jaroslav Koča
Pubblicato in: Journal of Cheminformatics, Numero 17582946, 2015, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-015-0107-1

Potential energy surface and binding energy in the presence of an external electric field: modulation of anion–π interactions for graphene-based receptors

Autori: Cina Foroutan-Nejad, Radek Marek
Pubblicato in: Phys. Chem. Chem. Phys., Numero 14639076, 2014, Pagina/e 2508-2514, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/c3cp52671b

Electrochemistry of closo-dodecaborate dianion and its simple exo-skeletal derivatives at carbon electrodes in aqueous phosphate buffers

Autori: Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
Pubblicato in: Journal of Electroanalytical Chemistry, Numero 15726657, 2013, Pagina/e 38-42, ISSN 1572-6657
Editore: Elsevier BV
DOI: 10.1016/j.jelechem.2013.08.016

Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159-Dyn2 Assembly

Autori: A. Nyarko, Y. Song, J. Novacek, L. Zidek, E. Barbar
Pubblicato in: Journal of Biological Chemistry, Numero 00219258, 2013, Pagina/e 2614-2622, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.M112.432831

Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex

Autori: Helena Konvalinová, Zuzana Dvořáková, Daniel Renčiuk, Klára Bednářová, Iva Kejnovská, Lukáš Trantírek, Michaela Vorlíčková, Janos Sagi
Pubblicato in: Biochimie, Numero 03009084, 2015, Pagina/e 15-25, ISSN 0300-9084
Editore: Elsevier BV
DOI: 10.1016/j.biochi.2015.07.013

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

Autori: Sophia Bazzi, Jan Novotný, Yevgen P. Yurenko, Radek Marek
Pubblicato in: Chemistry - A European Journal, Numero 09476539, 2015, Pagina/e 9414-9425, ISSN 0947-6539
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201500743

Expression of FGF19 in human embryonic stem cells

Autori: Pavel Krejci, Michaela Kunova, Iva Kubikova, Lukas Trantirek, Alois Kozubik, Petr Dvorak
Pubblicato in: STEM CELLS, Numero 10665099, 2013, Pagina/e 2582-2584, ISSN 1066-5099
Editore: AlphaMed Press Inc
DOI: 10.1002/stem.1493

Electrochemical behavior of anthraquinone- and nitrophenyl-labeled deoxynucleoside triphosphates: a contribution to development of multipotential redox labeling of DNA

Autori: Pavlína Vidláková, Hana Pivoňková, Miroslav Fojta, Luděk Havran
Pubblicato in: Monatshefte für Chemie - Chemical Monthly, Numero 00269247, 2015, Pagina/e 839-847, ISSN 0026-9247
Editore: Springer Verlag
DOI: 10.1007/s00706-015-1435-6

Biophysical and electrochemical studies of protein–nucleic acid interactions

Autori: Richard P. Bowater, Andrew M. Cobb, Hana Pivonkova, Ludek Havran, Miroslav Fojta
Pubblicato in: Monatshefte für Chemie - Chemical Monthly, Numero 00269247, 2015, Pagina/e 723-739, ISSN 0026-9247
Editore: Springer Verlag
DOI: 10.1007/s00706-014-1405-4

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

Autori: Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča
Pubblicato in: PLOS Computational Biology, Numero 1553734X, 2015, Pagina/e e1004061, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1004061

Understanding the Electronic Factors Responsible for Ligand Spin–Orbit NMR Shielding in Transition-Metal Complexes

Autori: Jan Vícha, Cina Foroutan-Nejad, Tomasz Pawlak, Markéta L. Munzarová, Michal Straka, Radek Marek
Pubblicato in: Journal of Chemical Theory and Computation, Numero 15499618, 2015, Pagina/e 1509-1517, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/ct501089z

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

Autori: Jiří Emmer, Andrea Vavrinská, Vladimír Sychrovský, Ladislav Benda, Zdeněk Kříž, Jaroslav Koča, Rolf Boelens, Vladimír Sklenář, Lukáš Trantírek
Pubblicato in: Journal of Biomolecular NMR, Numero 09252738, 2013, Pagina/e 59-70, ISSN 0925-2738
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10858-012-9686-6

Differential Salt-Induced Dissociation of the p53 Protein Complexes with Circular and Linear Plasmid DNA Substrates Suggest Involvement of a Sliding Mechanism

Autori: Peter Šebest, Marie Brázdová, Miroslav Fojta, Hana Pivoňková
Pubblicato in: International Journal of Molecular Sciences, Numero 14220067, 2015, Pagina/e 3163-3177, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms16023163

Polymerase synthesis of oligonucleotides containing a single chemically modified nucleobase for site-specific redox labelling

Autori: Petra Ménová, Hana Cahová, Medard Plucnara, Luděk Havran, Miroslav Fojta, Michal Hocek
Pubblicato in: Chemical Communications, Numero 13597345, 2013, Pagina/e 4652, ISSN 1359-7345
Editore: Royal Society of Chemistry
DOI: 10.1039/c3cc41438h

A novel variant of FGFR3 causes proportionate short stature

Autori: S. G. Kant, I. Cervenkova, L. Balek, L. Trantirek, G. W. E. Santen, M. C. de Vries, H. A. van Duyvenvoorde, M. J. R. van der Wielen, A. J. M. H. Verkerk, A. G. Uitterlinden, S. E. Hannema, J. M. Wit, W. Oostdijk, P. Krejci, M. Losekoot
Pubblicato in: European Journal of Endocrinology, Numero 08044643, 2015, Pagina/e 763-770, ISSN 0804-4643
Editore: BioScientifica Ltd.
DOI: 10.1530/EJE-14-0945

In-Cell NMR and EPR Spectroscopy of Biomacromolecules

Autori: Robert Hänsel, Laura M. Luh, Ivan Corbeski, Lukáš Trantirek, Volker Dötsch
Pubblicato in: Angewandte Chemie International Edition, Numero 14337851, 2014, Pagina/e 10300-10314, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201311320

Aqueous Heck Cross-Coupling Preparation of Acrylate-Modified Nucleotides and Nucleoside Triphosphates for Polymerase Synthesis of Acrylate-Labeled DNA

Autori: Jitka Dadová, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
Pubblicato in: The Journal of Organic Chemistry, Numero 00223263, 2013, Pagina/e 9627-9637, ISSN 0022-3263
Editore: American Chemical Society
DOI: 10.1021/jo4011574

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

Autori: Agnieszka Tudek, Odil Porrua, Tomasz Kabzinski, Michael Lidschreiber, Karel Kubicek, Andrea Fortova, François Lacroute, Stepanka Vanacova, Patrick Cramer, Richard Stefl, Domenico Libri
Pubblicato in: Molecular Cell, Numero 10972765, 2014, Pagina/e 467-481, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2014.05.031

Exploring Reaction Pathways for O -GlcNAc Transferase Catalysis. A String Method Study

Autori: Manju Kumari, Stanislav Kozmon, Petr Kulhánek, Jakub Štepán, Igor Tvaroška, Jaroslav Koča
Pubblicato in: The Journal of Physical Chemistry B, Numero 15206106, 2015, Pagina/e 4371-4381, ISSN 1520-6106
Editore: American Chemical Society
DOI: 10.1021/jp511235f

Autori: Pavel Kadeřávek, Sarina Grutsch, Nicola Salvi, Martin Tollinger, Lukáš Žídek, Geoffrey Bodenhausen, Fabien Ferrage
Pubblicato in: Journal of Biomolecular NMR, Numero 09252738, 2015, Pagina/e 353-365, ISSN 0925-2738
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10858-015-9994-8

Structural Study of the Partially Disordered Full-Length δ Subunit of RNA Polymerase from Bacillus subtilis

Autori: Veronika Papoušková, Pavel Kadeřávek, Olga Otrusinová, Alžbeta Rabatinová, Hana Šanderová, Jiří Nováček, Libor Krásný, Vladimír Sklenář, Lukáš Žídek
Pubblicato in: ChemBioChem, Numero 14394227, 2013, Pagina/e 1772-1779, ISSN 1439-4227
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201300226

Origin of the Conformational Modulation of the 13 C NMR Chemical Shift of Methoxy Groups in Aromatic Natural Compounds

Autori: Jaromír Toušek, Michal Straka, Vladimír Sklenář, Radek Marek
Pubblicato in: The Journal of Physical Chemistry A, Numero 10895639, 2013, Pagina/e 661-669, ISSN 1089-5639
Editore: American Chemical Society
DOI: 10.1021/jp310470f

High-Resolution Insight into G-Overhang Architecture

Autori: Robert Hänsel, Frank Löhr, Lukáš Trantirek, Volker Dötsch
Pubblicato in: Journal of the American Chemical Society, Numero 00027863, 2013, Pagina/e 2816-2824, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/ja312403b

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

Autori: R. S. Va ekova, D. Jaiswal, D. Sehnal, C.-M. Ionescu, S. Geidl, L. Pravda, V. Horsky, M. Wimmerova, J. Ko a
Pubblicato in: Nucleic Acids Research, Numero 03051048, 2014, Pagina/e W227-W233, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gku426

Structural insights into Aspergillus fumigatus lectin specificity: AFL binding sites are functionally non-equivalent

Autori: Josef Houser, Jan Komarek, Gianluca Cioci, Annabelle Varrot, Anne Imberty, Michaela Wimmerova
Pubblicato in: Acta Crystallographica Section D Biological Crystallography, Numero 13990047, 2015, Pagina/e 442-453, ISSN 1399-0047
Editore: Wiley-Blackwell
DOI: 10.1107/S1399004714026595

The Subunit of RNA Polymerase Is Required for Rapid Changes in Gene Expression and Competitive Fitness of the Cell

Autori: A. Rabatinova, H. Sanderova, J. Jirat Matejckova, J. Korelusova, L. Sojka, I. Barvik, V. Papouskova, V. Sklenar, L. Zidek, L. Krasny
Pubblicato in: Journal of Bacteriology, Numero 00219193, 2013, Pagina/e 2603-2611, ISSN 0021-9193
Editore: American Society for Microbiology
DOI: 10.1128/JB.00188-13

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

Autori: Petr Stadlbauer, Petra Kührová, Pavel Banáš, Jaroslav Koča, Giovanni Bussi, Lukáš Trantírek, Michal Otyepka, Jiří Šponer
Pubblicato in: Nucleic Acids Research, Numero 03051048, 2015, Pagina/e gkv994, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkv994

Extended molecular dynamics of a c-kit promoter quadruplex

Autori: Barira Islam, Petr Stadlbauer, Miroslav Krepl, Jaroslav Koca, Stephen Neidle, Shozeb Haider, Jiri Sponer
Pubblicato in: Nucleic Acids Research, Numero 03051048, 2015, Pagina/e 8673-8693, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkv785

New sensitive detection method for lectin hemagglutination using microscopy

Autori: Lenka Adamová, Lenka Malinovská, Michaela Wimmerová
Pubblicato in: Microscopy Research and Technique, Numero 1059910X, 2014, Pagina/e 841-849, ISSN 1059-910X
Editore: John Wiley & Sons Inc.
DOI: 10.1002/jemt.22407

Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs

Autori: D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova, J. Pachernik, K. Cetkovska, S. Uldrijan, Z. Zdrahal, S. Vanacova
Pubblicato in: RNA, Numero 13558382, 2013, Pagina/e 1632-1638, ISSN 1355-8382
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.040055.113

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity

Autori: Zdeněk Kříž, Jan Adam, Jana Mrázková, Petros Zotos, Thomais Chatzipavlou, Michaela Wimmerová, Jaroslav Koča
Pubblicato in: Journal of Computer-Aided Molecular Design, Numero 0920654X, 2014, Pagina/e 951-960, ISSN 0920-654X
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10822-014-9774-7

Structure and NMR properties of 6-substituted-5,6-dihydrobenzo[ c ]phenanthridine alkaloids

Autori: Shivaji S. Kadam, Lukáš Maier, Tomáš Šolomek, Marek Nečas, Karel Šmejkal, Jiří Dostál, Vladimír Sklenář, Radek Marek
Pubblicato in: Journal of Physical Organic Chemistry, Numero 08943230, 2013, Pagina/e 814-821, ISSN 0894-3230
Editore: John Wiley & Sons Inc.
DOI: 10.1002/poc.3175

Conformational Dynamics and Antigenicity in the Disordered Malaria Antigen Merozoite Surface Protein 2

Autori: Christopher A. MacRaild, Milan Zachrdla, Dean Andrew, Bankala Krishnarjuna, Jiří Nováček, Lukáš Žídek, Vladimír Sklenář, Jack S. Richards, James G. Beeson, Robin F. Anders, Raymond S. Norton
Pubblicato in: PLOS ONE, Numero 19326203, 2015, Pagina/e e0119899, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0119899

Preferential Binding of Hot Spot Mutant p53 Proteins to Supercoiled DNA In Vitro and in Cells

Autori: Marie Brázdová, Lucie Navrátilová, Vlastimil Tichý, Kateřina Němcová, Matej Lexa, Roman Hrstka, Petr Pečinka, Matej Adámik, Borivoj Vojtesek, Emil Paleček, Wolfgang Deppert, Miroslav Fojta
Pubblicato in: PLoS ONE, Numero 19326203, 2013, Pagina/e e59567, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0059567

How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?

Autori: Stanislav Geidl, Radka Svobodová Vařeková, Veronika Bendová, Lukáš Petrusek, Crina-Maria Ionescu, Zdeněk Jurka, Ruben Abagyan, Jaroslav Koča
Pubblicato in: Journal of Chemical Information and Modeling, Numero 15499596, 2015, Pagina/e 1088-1097, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/ci500758w

Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA-Protein Cross-Linking

Autori: Jitka Dadová, Milan Vrábel, Matej Adámik, Marie Brázdová, Radek Pohl, Miroslav Fojta, Michal Hocek
Pubblicato in: Chemistry - A European Journal, Numero 09476539, 2015, Pagina/e 16091-16102, ISSN 0947-6539
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201502209

A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 β1,6- N -Acetylglucosaminyltransferase

Autori: Igor Tvaroška, Stanislav Kozmon, Michaela Wimmerová, Jaroslav Koča
Pubblicato in: Chemistry - A European Journal, Numero 09476539, 2013, Pagina/e 8153-8162, ISSN 0947-6539
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201300383

Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications

Autori: Jan Novotný, Yevgen P. Yurenko, Petr Kulhánek, Radek Marek
Pubblicato in: Physical Chemistry Chemical Physics, Numero 14639076, 2014, Pagina/e 15241, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/c4cp00541d

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

Autori: Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukáš Pravda, Tomáš Bouchal, Radka Svobodová Vařeková, Stanislav Geidl, Jaroslav Koča
Pubblicato in: Journal of Cheminformatics, Numero 17582946, 2015, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-015-0099-x

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds, Interactions, and Bond/Line Paths

Autori: Cina Foroutan-Nejad, Shant Shahbazian, Radek Marek
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Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition

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Multi-center covalency: revisiting the nature of anion–π interactions

Autori: Cina Foroutan-Nejad, Zahra Badri, Radek Marek
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Dimeric Pd(II) and Pt(II) chloride organometallics with 2-phenylpyridine and their solvolysis in dimethylsulfoxide

Autori: Tomasz Pawlak, Daria Niedzielska, Jan Vícha, Radek Marek, Leszek Pazderski
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Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

Autori: Sushil K. Mishra, Gaetano Calabró, Hannes H. Loeffler, Julien Michel, Jaroslav Koča
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Synthesis and Tautomerism of Substituted Pyrazolo[4,3- c ]pyrazoles

Autori: Shivaji S. Kadam, Lukáš Maier, Ioannis Kostakis, Nicole Pouli, Jaromír Toušek, Marek Nečas, Panagiotis Marakos, Radek Marek
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Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and 13 C NMR Chemical Shift Tensors

Autori: Kateřina Bouzková, Martin Babinský, Lucie Novosadová, Radek Marek
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Adamantane-bearing benzylamines and benzylamides: novel building blocks for supramolecular systems with finely tuned binding properties towards β-cyclodextrin

Autori: Michal Rouchal, Alena Matelová, Fabiana Pires de Carvalho, Robert Bernat, Dragan Grbić, Ivo Kuřitka, Martin Babinský, Radek Marek, Richard Čmelík, Robert Vícha
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Benzofurazane as a New Redox Label for Electrochemical Detection of DNA: Towards Multipotential Redox Coding of DNA Bases

Autori: Jana Balintová, Medard Plucnara, Pavlína Vidláková, Radek Pohl, Luděk Havran, Miroslav Fojta, Michal Hocek
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Functional Analysis of Dishevelled-3 Phosphorylation Identifies Distinct Mechanisms Driven by Casein Kinase 1 and Frizzled5

Autori: O. Bernatik, K. edova, C. Schille, R. S. Ganji, I. ervenka, L. Trantirek, A. Schambony, Z. Zdrahal, V. Bryja
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Cloning, expression and purification of the human Islet Amyloid Polypeptide (hIAPP) from Escherichia coli

Autori: Diana C. Rodriguez Camargo, Konstantinos Tripsianes, Tobias G. Kapp, Joaquim Mendes, Jasmin Schubert, Burghard Cordes, Bernd Reif
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Electrochemistry of parent and exo-skeletally substituted icosahedral monocarba and dicarbaboranes and their derivatives at the graphite carbon electrode in aqueous phosphate buffers

Autori: Lukáš Fojt, Miroslav Fojta, Bohumír Grüner, Radim Vespalec
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Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger

Autori: Gabriel Demo, Barbora Fliedrová, Lenka Weignerová, Michaela Wimmerová
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Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding

Autori: M. Babinsky, R. Fiala, I. Kejnovska, K. Bedna ova, R. Marek, J. Sagi, V. Sklena , M. Vorli kova
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Editore: Oxford University Press
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Mechanism of Spin–Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR

Autori: Jan Vícha, Michal Straka, Markéta L. Munzarová, Radek Marek
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Stabilization of the β-hairpin in Mason-Pfizer monkey virus capsid protein- a critical step for infectivity

Autori: Martin Obr, Romana Hadravová, Michal Doležal, Ivana Křžová, Veronika Papoušková, Lukáš Žídek, Richard Hrabal, Tomáš Ruml, Michaela Rumlová
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Unwilling U–U bonding in U 2 @C 80 : cage-driven metal–metal bonds in di-uranium fullerenes

Autori: Cina Foroutan-Nejad, Jan Vícha, Radek Marek, Michael Patzschke, Michal Straka
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Editore: Royal Society of Chemistry
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129 Xe NMR chemical shift in Xe@C 60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent

Autori: Stanislav Standara, Petr Kulhánek, Radek Marek, Michal Straka
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Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43

Autori: Peter J Lukavsky, Dalia Daujotyte, James R Tollervey, Jernej Ule, Cristiana Stuani, Emanuele Buratti, Francisco E Baralle, Fred F Damberger, Frédéric H-T Allain
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Intermediate filament-associated cytolinker plectin 1c destabilizes microtubules in keratinocytes

Autori: R. G. Valencia, G. Walko, L. Janda, J. Novacek, E. Mihailovska, S. Reipert, K. Andra-Marobela, G. Wiche
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All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters

Autori: Zahra Badri, Shubhrodeep Pathak, Heike Fliegl, Parviz Rashidi-Ranjbar, Radovan Bast, Radek Marek, Cina Foroutan-Nejad, Kenneth Ruud
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Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta

Autori: Zaiyong Zhang, Justin Porter, Konstantinos Tripsianes, Oliver F. Lange
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Protein engineering study of -mannosidase to set up a potential chemically efficient biocatalyst

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X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase

Autori: Gabriel Demo, Veronika Papoušková, Jan Komárek, Pavel Kadeřávek, Olga Otrusinová, Pavel Srb, Alžbeta Rabatinová, Libor Krásný, Lukáš Žídek, Vladimír Sklenář, Michaela Wimmerová
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A Soluble Fucose-Specific Lectin from Aspergillus fumigatus Conidia - Structure, Specificity and Possible Role in Fungal Pathogenicity

Autori: Josef Houser, Jan Komarek, Nikola Kostlanova, Gianluca Cioci, Annabelle Varrot, Sheena C. Kerr, Martina Lahmann, Viviane Balloy, John V. Fahy, Michel Chignard, Anne Imberty, Michaela Wimmerova
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Electrochemical Activity of Wedelolactone and Probing its Interaction with DNA Using Voltammetry at a Carbon Electrode

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Enzyme-linked electrochemical detection of DNA fragments amplified by PCR in the presence of a biotinylated deoxynucleoside triphosphate using disposable pencil graphite electrodes

Autori: Lucia Hároníková, Jan Špaček, Medard Plucnara, Petra Horáková, Hana Pivoňková, Luděk Havran, Arzum Erdem, Miroslav Fojta
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Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana

Autori: Oksana Degtjarik, Radka Dopitova, Sandra Puehringer, Eliska Nejedla, Michal Kuty, Manfred S. Weiss, Jan Hejatko, Lubomir Janda, Ivana Kuta Smatanova
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Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

Autori: Konstantinos Gkionis, Holger Kruse, James A. Platts, Arnošt Mládek, Jaroslav Koča, Jiří Šponer
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Editore: American Chemical Society
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Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems

Autori: Yevgen P. Yurenko, Jan Novotný, Mariusz P. Mitoraj, Vladimir Sklenář, Artur Michalak, Radek Marek
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Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA

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Origin of the Thermodynamic Stability of the Polymorph IV of Crystalline Barbituric Acid: Evidence from Solid-State NMR and Electron Density Analyses

Autori: Zahra Badri, Kateřina Bouzková, Cina Foroutan-Nejad, Radek Marek
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Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach

Autori: Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
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G-quadruplex-based structural transitions in 15-mer DNA oligonucleotides varying in lengths of internal oligo(dG) stretches detected by voltammetric techniques

Autori: Pavlína Vidláková, Hana Pivoňková, Iva Kejnovská, Libuše Trnková, Michaela Vorlíčková, Miroslav Fojta, Luděk Havran
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NMR Determines Transient Structure and Dynamics in the Disordered C-Terminal Domain of WASp Interacting Protein

Autori: Noam Y. Haba, Renana Gross, Jiri Novacek, Hadassa Shaked, Lukas Zidek, Mira Barda-Saad, Jordan H. Chill
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Detection of p53 Gene by Using Genomagnetic Assay Combined with Carbon Nanotube Modified Disposable Sensor Technology

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Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA–protein interactions

Autori: Jana Balintová, Jan Špaček, Radek Pohl, Marie Brázdová, Luděk Havran, Miroslav Fojta, Michal Hocek
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MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Autori: David Sehnal, Radka Svobodová Vařeková, Karel Berka, Lukáš Pravda, Veronika Navrátilová, Pavel Banáš, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koča
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Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Autori: Petr Stadlbauer, Lukáš Trantírek, Thomas E. Cheatham, Jaroslav Koča, Jiří Šponer
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Anatomy of enzyme channels

Autori: Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka
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Antibodies against CKI1RD, a receiver domain of the sensor histidine kinase in Arabidopsis thaliana: From antigen preparation to in planta immunolocalization

Autori: Petra Borkovcová, Blanka Pekárová, Martina Válková, Radka Dopitová, Břetislav Brzobohatý, Lubomír Janda, Jan Hejátko
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The activation of N-glycosidic bond cleavage performed by base-excision repair enzyme hOGG1; theoretical study of the role of Lys 249 residue in activation of G, OxoG and FapyG

Autori: Jakub Šebera, Lukáš Trantírek, Yoshiyuki Tanaka, Radim Nencka, Jiří Fukal, Vladimír Sychrovský
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NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis

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Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches

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Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein

Autori: Y. Liu, H. K. Salter, A. N. Holding, C. M. Johnson, E. Stephens, P. J. Lukavsky, J. Walshaw, S. L. Bullock
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Interpretation of Crystal Effects on NMR Chemical Shift Tensors: Electron and Shielding Deformation Densities

Autori: Martin Babinský, Kateřina Bouzková, Matej Pipíška, Lucie Novosadová, Radek Marek
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Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

Autori: Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vařeková, Jaroslav Koča
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Fluorescent Cellular Assay for Screening Agents Inhibiting Pseudomonas aeruginosa Adherence

Autori: Libuše Nosková, Božena Kubíčková, Lucie Vašková, Barbora Bláhová, Michaela Wimmerová, Marie Stiborová, Petr Hodek
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Methoxyphenol and Dihydrobenzofuran as Oxidizable Labels for Electrochemical Detection of DNA

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PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

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ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

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Toward optimal-resolution NMR of intrinsically disordered proteins

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Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

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RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3'-end extended forms of snRNAs

Autori: D. Hrossova, T. Sikorsky, D. Potesil, M. Bartosovic, J. Pasulka, Z. Zdrahal, R. Stefl, S. Vanacova
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Design of Stereoelectronically Promoted Super Lewis Acids and Unprecedented Chemistry of Their Complexes

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Substituting CF 2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Autori: Yevgen P. Yurenko, Jan Novotný, Vladimir Sklenář, Radek Marek
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Catalytic oxidation of aromatic hydrocarbons by mono-oxido-alkoxidovanadium(V) complexes of ONNO donor ethylenediamine-bis(phenolate) ligands

Autori: Mainak Debnath, Arpan Dutta, Surajit Biswas, Kalyan Kumar Das, Hon Man Lee, Jan Vícha, Radek Marek, Jaromir Marek, Mahammad Ali
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Targeted In Vivo Inhibition of Specific Protein–Protein Interactions Using Recombinant Antibodies

Autori: Matej Zábrady, Vendula Hrdinová, Bruno Müller, Udo Conrad, Jan Hejátko, Lubomír Janda
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Predicting p Ka values from EEM atomic charges

Autori: Radka Vařeková, Stanislav Geidl, Crina-Maria Ionescu, Ondřej Skřehota, Tomáš Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koča
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Editore: Royal Society of Chemistry
DOI: 10.1039/c5cp04489h

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DOI: 10.1007/s00216-014-7811-y

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