J. Šponer, G. Bussi, M. Krepl, P. Banáš, S. Bottaro, R. A. Cunha, A. Gil-Ley, G. Pinamonti, S. Poblete, P. Jurečka, N. G. Walter, M. Otyepka: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview, CHEMICAL REVIEWS, Article in press, 2018.
DOI: 10.1021/acs.chemrev.7b00427, IF = 47.928
Abstract: With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
C. C. Mayorga-Martinez, Z. Sofer, J. Luxa, Š. Huber, D. Sedmidubský, P. Brázda, L. Palatinus, M. Mikulics, P. Lazar, R. Medlín, M. Pumera: TaS3 Nanofibers: Layered Trichalcogenide for High-Performance Electronic and Sensing Devices, ACS NANO, Artical in press, 2018.
DOI: 10.1021/acsnano.7b06853, IF = 13.942
Abstract: Layered materials, like transition metal dichalcogenides, exhibit broad spectra with outstanding properties with huge application potential, whereas another group of related materials, layered transition metal trichalcogenides, remains unexplored. Here, we show the broad application potential of this interesting structural type of layered tantalum trisulfide prepared in a form of nanofibers. This material shows tailorable attractive electronic properties dependent on the tensile strain applied to it. Structure of this so-called orthorhombic phase of TaS3 grown in a form of long nanofibers has been solved and refined. Taking advantage of these capabilities, we demonstrate a highly specific impedimetric NO gas sensor based on TaS3 nanofibers as well as construction of photodetectors with excellent responsivity and field-effect transistors. Various flexible substrates were used for the construction of a NO gas sensor. Such a device exhibits a low limit of detection of 0.48 ppb, well under the allowed value set by environmental agencies for NOx (50 ppb). Moreover, this NO gas sensor also showed excellent selectivity in the presence of common interferences formed during fuel combustion. TaS3 nanofibers produced in large scale exhibited excellent broad application potential for various types of devices covering nanoelectronic, optoelectronic, and gas-sensing applications.
O. Stetsovych, P. Mutombo, M. Švec, M. Šámal, J. Nejedly, I. Cisarova, H. Vazquez, M. Moro-Lagares, J. Berger, J. Vacek, I. G. Stará, I. Stary, P. Jelinek: Large converse piezoelectric effect measured on a single molecule on a metallic surface, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Article in press, 2017.
DOI: 10.1021/jacs.7b08729, IF = 13.858
Abstract: The converse piezoelectric effect is a phenomenon in which the mechanical strain is generated in a material due to an applied electrical field. In this work, we demonstrate the converse piezoelectric effect in single heptahelicene-derived molecules on the Ag(111) surface using atomic force microscopy (AFM) and total energy density functional (DFT) calculations. The force-distance spectroscopy acquired over a wide range of bias voltages reveals a linear shift of the tip-sample distance at which the contact between the molecule and tip apex is established. We demonstrate that this effect is caused by the bias-induced de-formation of the spring-like scaffold of the helical polyaromatic molecules. We attribute this effect to coupling of a soft vibrational mode of the molecular helix with a vertical electric dipole induced by molecule-substrate charge transfer. In addi-tion, we also performed the same spectroscopic measurements on a more rigid o-carborane dithiol molecule on the Ag(111) surface. In this case, we identify a weaker linear electromechanical response, which underpins the importance of the helical scaffold on the observed piezoelectric response.
J. Peng, J. Guo, P. Hapala, D. Cao, R. Ma, B. Cheng, L. Xu, M. Ondráček, P. Jelínek, E. Wang, Y. Jiang: Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy, NATURE COMMUNICATIONS vol. 9, iss. 1, 2018.
DOI: 10.1038/s41467-017-02635-5, IF = 12.124
Abstract: Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.
L. Pravda, D. Sehnal, R. Svobodová Vařeková, V. Navrátilová, D. Toušek, K. Berka, M. Otyepka, J. Koča: ChannelsDB: database of biomacromolecular tunnels and pores, NUCLEIC ACIDS RESEARCH vol. 46, iss. D1, pp. D399-D405, 2018.
DOI: 10.1093/nar/gkx868, IF = 10.162
Abstract: ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.
A. Halder, M. Kilianová, B. Yang, E. C. Tyo, S. Seifert, R. Prucek, A. Panáček, P. Suchomel, O. Tomanec, D. J. Gosztola, D. Milde, H. Wang, L. Kvítek, R. Zbořil, S. Vajda: Highly efficient Cu-decorated iron oxide nanocatalyst for low pressure CO 2 conversion, APPLIED CATALYSIS B: ENVIRONMENTAL vol. 225, pp. 128-138, 2017.
DOI: 10.1016/j.apcatb.2017.11.047, IF = 9.446
Abstract: We report a nanoparticulate iron oxide based catalyst for CO2 conversion with high efficiency at low pressures and on the effect of the presence of copper on the catalyst’s restructuring and its catalytic performance. In situ X-ray scattering reveals the restructuring of the catalyst at the nanometer scale. In situ X-ray absorption near edge structure (XANES) shows the evolution of the composition and oxidation state of the iron and copper components under reaction conditions along with the promotional effect of copper on the chemical transformation of the iron component. X-ray diffraction (XRD), XANES and Raman spectroscopy proved that the starting nanocatalyst is composed of iron oxides differing in chemical nature (α-Fe2O3, Fe3O4, FeO(OH)) and dimensionality, while the catalyst after CO2 conversion was identified as a mixture of α-Fe, Fe3C, and traces of Fe5C2. The significant increase of the rate CO2 is turned over in the presence of copper nanoparticles indicates that Cu nanoparticles activate hydrogen, which after spilling over to the neighbouring iron sites, facilitate a more efficient conversion of carbon dioxide.
M. Zgarbová, P. Jurečka, J. Šponer, M. Otyepka: A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker, JOURNAL OF CHEMICAL THEORY AND COMPUTATION vol. 14, iss. 1, pp. 319-328, 2018.
DOI: 10.1021/acs.jctc.7b00926, IF = 5.245
Abstract: The A/B transition is a basic element of DNA conformational change. Because of its involvement in the sensing of the ionic conditions by DNA and in specific protein–DNA interactions, this transition is important for biological functions of DNA. Therefore, accurate modeling of the A/B equilibrium by means of empirical force fields is of utmost interest. In this work, we examine the A/B equilibrium in three AMBER force fields, including the recent bsc1 and OL15 modifications, using much longer MD simulations than attempted before. Special attention is paid to the coupling of the A/B equilibrium with the south/north (S/N) transition of the sugar pucker. We found that none of the tested force fields provided a satisfactory description of the A/B equilibrium because the B-form was predicted to be much too stable and the A-form was predicted to be almost absent even in concentrated trifluoroethanol solutions. Based on comparison with NMR data for duplexes and single nucleosides, we hypothesize that this problem arose from the incorrect description of the S/N equilibrium of sugar pucker, where the south conformation is much too stable, thus stabilizing the B-form. Because neither the A/B equilibrium in duplexes nor the S/N equilibrium in nucleosides was described accurately, further refinements of the AMBER DNA force fields are needed.