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Multimerization rules for G-quadruplexes

Sofia Kolesnikova, Martin Hubálek, Lucie Bednárová, Josef Cvačka, Edward A. Curtis
2017 Nucleic Acids Research  
G-quadruplexes can multimerize under certain conditions, but the sequence requirements of such structures are not well understood. In this study, we investigated the ability of all possible variants of the central tetrad in a monomeric, parallel-strand G-quadruplex to form higher-order structures. Although most of these 256 variants existed primarily as monomers under the conditions of our screen, ∼10% formed dimers or tetramers. These structures could form in a wide range of monovalent and
more » ... lent metal ions, and folding was highly cooperative in both KCl and MgCl 2 . As was previously shown for G-quadruplexes that bind GTP and promote peroxidase reactions, G-quadruplexes that form dimers and tetramers have distinct sequence requirements. Some mutants could also form heteromultimers, and a second screen was performed to characterize the sequence requirements of these structures. Taken together, these experiments provide new insights into the sequence requirements and structures of both homomultimeric and heteromultimeric G-quadruplexes.
doi:10.1093/nar/gkx637 pmid:28911118 pmcid:PMC5587800 fatcat:gf3yrs3vcfcwxgm23rmny3jceq

Spectroscopic properties of the nonplanar amide group: A computational study

Lucie Bednárová, Petr Maloň, Petr Bouř
2007 Chirality  
Experimental studies suggest that amide bond may significantly deviate from planar arrangement even in linear peptides and proteins. In order to find out the extent to which such deviation may influence principal amide spectroscopic properties, we conducted a computational study of nonplanar N-methylacetamide (NMA) conformers. Vibrational absorption, Raman, and electronic spectra including optical activity were simulated with ab initio and density functional theory (DFT) methods. According to
more » ... e results, small nonplanarity deviations may be detectable by nonpolarized spectroscopic techniques, albeit as subtle spectral changes. The optical activity methods, such as the vibrational circular dichroism (VCD), Raman optical activity (ROA), and electronic circular dichroism (CD, ECD), provide enhanced information about the amide nonplanarity, because planar amide is not optically active (chiral). For VCD, however, the inherently chiral contribution in most peptides and proteins most probably provides very weak signal in comparison with other contributions, such as the dipolar coupling. For the electronic CD, the nonplanarity contribution is relatively big and causes a strong CD couplet in the n-p* absorption region accompanied by a red frequency shift. The p-p* CD region is relatively unaffected. The ROA spectroscopy appears most promising for the nonplanarity detection and the inherent chiral signal may dominate entire spectral parts. The amide I and III vibrational ROA bands are most challenging experimentally because of their relatively weak coupling to other peptide vibrations. Chirality 19:775-786, 2007. V V C 2007 Wiley-Liss, Inc. Fig. 12. Calculated (B3LYP/PCM/6-31G**) VCD intensities of the helical acetyl-L-alanylmethylamide segment simulated with planar and nonplanar amide groups. 784 BEDNÁ ROVÁ ET AL.
doi:10.1002/chir.20462 pmid:17687760 fatcat:vv25f7agjrczraqki6b6s5hqbe

Raman Microspectroscopy of the Yeast Vacuoles

Lucie Bednárová, Jan Palacký, Václava Bauerová, Olga Hrušková-Heidingsfeldová, Iva Pichová, Peter Mojzeš
2012 Spectroscopy (Ottawa)  
In the present work, real ability of a confocal Raman microspectroscopy to monitor chemical composition of the vacuoles within living yeast cells was investigated and critically assessed. Simple, economical, and practical protocols of the yeast immobilization suitable for less laborious, high-throughput, and spatially resolved Raman measurements were tested for their possible impacts on physiological states and viability of the cells. We have demonstrated that, acquiring Raman spectra from
more » ... stically sound sets of immobilized cells and employing advanced multivariate methods for spectral analysis, the chemical composition of the yeast vacuoles can be reliably studied. The most easily and accurately quantifiable seems to be the concentration of polyphosphates which can be unambiguously identified due to unmistakable Raman features. Our approach can be useful for routine, label-free, and noninvasive monitoring of the chemical composition of the vacuoles of living yeasts exposed to various stress factors, the information important in biomedical research of pathogens.
doi:10.1155/2012/746597 fatcat:dt6sdwjp6nh3ziqrvtuvbhydye

Organic nanotubes created from mesogenic derivatives [article]

Vladimira Novotna, Vera Hamplova, Lubor Lejcek, Damian Pociecha, Martin Cigl, Ladislav Fekete, Milada Glogarova, Lucie Bednarova, Pawel W. Majewski, Ewa Gorecka
2019 arXiv   pre-print
A facile route to prepare the nanotubes from rod-like mesogens dissolved in typical organic solvents is reported. For selected types of chiral rod-like molecules, both enantiomers as well as the racemic mixtures formed the nanotubes by slow evaporation from a solution, regardless of the solvent, concentration or deposition type. Obtained supramolecular assemblies were studied using AFM and SEM techniques. Additional methods (IR, UV-Vis spectroscopy and x-ray diffraction) were applied to
more » ... rize the observed nanotubes. The difference in the surface tension at opposite crystallite surfaces is suggested as a possible mechanism for the nanotube nucleation.
arXiv:1901.10712v1 fatcat:sqi2rqbvpfdhxnfb7yz3i5ecuy

Anharmonic Force Field of Formamide. A Computational Study

Petr Bour, Lucie Bednarova
1995 The Journal of Physical Chemistry  
Vibrational energies of HCONH2 and DCONH2 molecules are calculated and compared to experiment. Rotational constants of formamide and water molecules are calculated for several vibrational states. The anharmonic force fields are calculated ab initio on HF and MP2 levels and using local and nonlocal density functional theory. Possible applications of DFT anharmonic force field in a prediction of vibrational properties are discussed. Dipolar derivatives are calculated to second order on the HF
more » ... l. The phase integral quantum concept is introduced as a tool for an efficient diagonalization of the vibrational Hamiltonian.
doi:10.1021/j100016a035 fatcat:xddyay5eg5evhmxwi57b4aze7e

Altered biochemical specificity of G-quadruplexes with mutated tetrads

Kateřina Švehlová, Michael S. Lawrence, Lucie Bednárová, Edward A. Curtis
2016 Nucleic Acids Research  
A fundamental motif in canonical nucleic acid structure is the base pair. Mutations that disrupt base pairs are typically destabilizing, but stability can often be restored by a second mutation that replaces the original base pair with an isosteric variant. Such concerted changes are a way to identify helical regions in secondary structures and to identify new functional motifs in sequenced genomes. In principle, such analysis can be extended to non-canonical nucleic acid structures, but this
more » ... proach has not been utilized because the sequence requirements of such structures are not well understood. Here we investigate the sequence requirements of a Gquadruplex that can both bind GTP and promote peroxidase reactions. Characterization of all 256 variants of the central tetrad in this structure indicates that certain mutations can compensate for canonical G-G-G-G tetrads in the context of both GTPbinding and peroxidase activity. Furthermore, the sequence requirements of these two motifs are significantly different, indicating that tetrad sequence plays a role in determining the biochemical specificity of Gquadruplex activity. Our results provide insight into the sequence requirements of G-quadruplexes, and should facilitate the analysis of such motifs in sequenced genomes.
doi:10.1093/nar/gkw987 pmid:27789695 pmcid:PMC5159562 fatcat:neqbktxlnjbwxapv2is6vy7loa

Organic nanotubes created from mesogenic derivatives

Vladimira Novotna, Vera Hamplova, Lubor Lejcek, Damian Pociecha, Martin Cigl, Ladislav Fekete, Milada Glogarova, Lucie Bednárová, Pawel W. Majewski, Ewa Gorecka
2019 Nanoscale Advances  
A facile route to prepare the nanotubes from rod-like mesogens dissolved in typical organic solvents is reported. For selected types of chiral rod-like molecules, both enantiomers as well as the...
doi:10.1039/c9na00175a fatcat:r5nwqvqiljeklmhufc7rxgel7y

In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations [article]

Valerio Guido Giacobelli, Kosuke Fujishima, Martin Lepsik, Vyacheslav Tretyachenko, Tereza Kadava, Lucie Bednarova, Petr Novak, Klara Hlouchova
2021 bioRxiv   pre-print
RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal
more » ... C-terminal domain was selected from a ~10^10 library of partially randomized sequences, all composed of 10 prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with MD simulations uncover qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant L11 domain uses bridging ion (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues was compensated by acidic residues plus metal ions.
doi:10.1101/2021.08.01.454623 fatcat:cycpu5b7bnh3nh34uko2wekfbi

Antimicrobial Peptide from the Eusocial BeeHalictus sexcinctusInteracting with Model Membranes

Markéta Pazderková, Eva Kočišová, Tomáš Pazderka, Petr Maloň, Vladimír Kopecký Jr., Lenka Monincová, Václav Čeřovský, Lucie Bednárová
2012 Spectroscopy (Ottawa)  
Halictine-1 (Hal-1)—a linear antibacterial dodecapeptide isolated from the venom of the eusocial beeHalictus sexcinctus—has been subjected to a detailed spectroscopic study including circular dichroism, fluorescence, and vibrational spectroscopy. We investigated Hal-1 ability to adopt an amphipathicα-helical structure upon interaction with model lipid-based bacterial membranes (phosphatidylcholine/phosphatidylglycerol-based large unilamellar vesicles and sodium dodecylsulfate micelles) and
more » ... inducing components (trifluoroethanol). It was found that Hal-1 responds sensitively to the composition of the membrane model and to the peptide/lipid ratio. The amphipathic nature of the helical Hal-1 seems to favour flat charged surfaces of the model lipid particles over the nondirectional interaction with trifluoroethanol. Increasing fraction of polyproline II type conformation was detected at low peptide/lipid ratios.
doi:10.1155/2012/840956 fatcat:dj7t3vuopvbf7hmyuja3jcczka

Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases

Anežka Tichá, Stancho Stanchev, Jan Škerle, Jakub Began, Marek Ingr, Kateřina Švehlová, Lucie Polovinkin, Martin Růžička, Lucie Bednárová, Romana Hadravová, Edita Poláchová, Petra Rampírová (+4 others)
2017 Journal of Biological Chemistry  
Edited by George N. DeMartino Rhomboid proteases are increasingly being explored as potential drug targets, but their potent and specific inhibitors are not available, and strategies for inhibitor development are hampered by the lack of widely usable and easily modifiable in vitro activity assays. Here we address this bottleneck and report on the development of new fluorogenic transmembrane peptide substrates, which are cleaved by several unrelated rhomboid proteases, can be used both in
more » ... nt micelles and in liposomes, and contain red-shifted fluorophores that are suitable for high-throughput screening of compound libraries. We show that nearly the entire transmembrane domain of the substrate is important for efficient cleavage, implying that it extensively interacts with the enzyme. Importantly, we demonstrate that in the detergent micelle system, commonly used for the enzymatic analyses of intramembrane proteolysis, the cleavage rate strongly depends on detergent concentration, because the reaction proceeds only in the micelles. Furthermore, we show that the catalytic efficiency and selectivity toward a rhomboid substrate can be dramatically improved by targeted modification of the sequence of its P5 to P1 region. The fluorogenic substrates that we describe and their sequence variants should find wide use in the detection of activity and development of inhibitors of rhomboid proteases.
doi:10.1074/jbc.m116.762849 pmid:28069810 pmcid:PMC5314168 fatcat:qujdz34smnbqlprl44qdqpyy4y

Enzyme catalysis prior to aromatic residues: reverse engineering of a dephosphoCoA kinase [article]

Mikhail Makarov, Jingwei Meng, Vyacheslav Tretyachenko, Pavel Srb, Anna Brezinova, Valerio Guido Giacobelli, Lucie Bednarova, Jiri Vondrasek, A. Keith Dunker, Klara Hlouchova
2020 bioRxiv   pre-print
It is well-known that the large diversity of protein functions and structures is derived from the broad spectrum of physicochemical properties of the 20 canonical amino acids. According to the generally accepted hypothesis, protein evolution was continuously associated with enrichment of this alphabet, increasing stability, specificity and spectrum of catalytic functions. Aromatic amino acids are considered the latest addition to genetic code. The main objective of this study was to test
more » ... enzymatic catalysis can spare the aromatic amino acids (aromatics) by determining the effect of amino acid alphabet reduction on structure and function of dephospho-CoA kinase (DPCK). We designed two mutant variants of a putative DPCK from Aquifex aeolicus by substituting (i) Tyr, Phe and Trp or (ii) all aromatics (including His), i.e. ~10% of the total sequence. Their structural characterization indicates that removal of aromatic amino acids may support rich secondary structure content although inevitably impairs a firm globular arrangement. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate is however heavily uncoupled and only one of the variants is still able to perform the reaction. Here we provide support to the hypothesis that proteins in the early stages of life could support at least some enzymatic activities, despite lower efficiencies resulting from the lack of a firm hydrophobic core. Based on the presented data we hypothesize that further protein scaffolding role may be provided by ligands upon binding.
doi:10.1101/2020.11.11.377994 fatcat:4s5p7ikndbduribh73we2zlbae

Analysis of the Nse3/MAGE-Binding Domain of the Nse4/EID Family Proteins

Marc Guerineau, Zdenek Kriz, Lucie Kozakova, Katerina Bednarova, Pavel Janos, Jan Palecek, Bin Xue
2012 PLoS ONE  
Citation: Guerineau M, Kriz Z, Kozakova L, Bednarova K, Janos P, et al. (2012) Analysis of the Nse3/MAGE-Binding Domain of the Nse4/EID Family Proteins. PLoS ONE 7(4): e35813.  ... 
doi:10.1371/journal.pone.0035813 pmid:22536443 pmcid:PMC3335016 fatcat:e4l65irhfzefxbvvxwae7czuj4

Additive transport in DNA molecular circuits

Táňa Sebechlebská, Viliam Kolivoška, Jakub Šebera, Jiří Fukal, David Řeha, Miloš Buděšínský, Ivan Rosenberg, Lucie Bednárová, Jindřich Gasior, Gábor Mészáros, Magdaléna Hromadová, Vladimír Sychrovský
2022 Journal of Materials Chemistry C  
parametrization of molecular dynamics simulations of gold surface and DNA linkers, Milos ˇBude ˇs ˇı ´nsky ´: data curation and analysis, NMR measurement, Ivan Rosenberg: data curation and analysis, Lucie  ... 
doi:10.1039/d2tc01219g fatcat:kf74qp3lhfe4tfjtsth4p2pggm

cis–transIsomerization of silybins A and B

Michaela Novotná, Radek Gažák, David Biedermann, Florent Di Meo, Petr Marhol, Marek Kuzma, Lucie Bednárová, Kateřina Fuksová, Patrick Trouillas, Vladimír Křen
2014 Beilstein Journal of Organic Chemistry  
Methods were developed and optimized for the preparation of the 2,3-cis-and the 10,11-cis-isomers of silybin by the Lewis acid catalyzed (BF 3 •OEt 2 ) isomerization of silybins A (1a) and B (1b) (trans-isomers). The absolute configuration of all optically pure compounds was determined by using NMR and comparing their electronic circular dichroism data with model compounds of known absolute configurations. Mechanisms for cis-trans-isomerization of silybin are proposed and supported by quantum mechanical calculations. 1047
doi:10.3762/bjoc.10.105 pmid:24991256 pmcid:PMC4077359 fatcat:rb5wnnrcv5c2fouunlkr5dphoy

A phenological study on European larch (Larix decidua Mill.) in the Drahanská vrchovina highlands

Emilie Bednářová, Lucie Merklová
2008 Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis  
Emilie Bednářová, CSc., Ing. Lucie Merklová, Ústav ekologie lesa, Mendelova zemědělská a lesnická univerzita v Brně, Zemědělská 1, 613 00 Brno, Česká republika  ...  BEDNÁŘOVÁ, E., MERKLOVÁ, L.: A phenological study on European larch (Larix decidua Mill.) in the Drahanská vrchovina highlands. Acta univ. agric. et silvic. Mendel.  ...  , KUČERA, 2002; MERKLOVÁ, BEDNÁŘOVÁ, 2005) .  ... 
doi:10.11118/actaun200856020013 fatcat:u2opxyrpvnfvjksivqa37vlrcm
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