BACKGROUND: Many prokaryotic genomes comprise Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) offering defense against foreign nucleic acids. These immune systems are conditioned by the production of small CRISPR-derived RNAs matured from long RNA precursors. This often requires a Csy4 endoribonuclease cleaving the RNA 3'-end. METHODS: We report extended explicit solvent molecular dynamic (MD) simulations of Csy4/RNA complex in precursor and product states, based on X-ray structures of product and inactivated precursor (55 simulations; ~3.7μs in total). RESULTS: The simulations identify double-protonated His29 and deprotonated terminal phosphate as the likely dominant protonation states consistent with the product structure. We revealed potential substates consistent with Ser148 and His29 acting as the general base and acid, respectively. The Ser148 could be straightforwardly deprotonated through solvent and could without further structural rearrangements deprotonate the nucleophile, contrasting similar studies investigating the general base role of nucleobases in ribozymes. We could not locate geometries consistent with His29 acting as general base. However, we caution that the X-ray structures do not always capture the catalytically active geometries and then the reactive structures may be unreachable by the simulation technique. CONCLUSIONS: We identified potential catalytic arrangement of the Csy4/RNA complex but we also report limitations of the simulation technique. Even for the dominant protonation state we could not achieve full agreement between the simulations and the structural data. GENERAL SIGNIFICANCE: Potential catalytic arrangement of the Csy4/RNA complex is found. Further, we provide unique insights into limitations of simulations of protein/RNA complexes, namely, the influence of the starting experimental structures and force field limitations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

• MeSH
• Cas proteiny chemie   metabolismus   MeSH
• časové faktory MeSH
• CRISPR-Cas systémy * MeSH
• endoribonukleasy chemie   metabolismus   MeSH
• katalytická doména MeSH
• krystalografie rentgenová MeSH
• sekvence CRISPR * MeSH
• simulace molekulární dynamiky * MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• elektrofyziologické techniky kardiologické metody   přístrojové vybavení   MeSH
• elektrokardiografie ambulantní MeSH
• katetrizační ablace metody   MeSH
• komorové extrasystoly diagnóza   terapie   MeSH
• lidé MeSH
• výsledek terapie MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH

The integration of complementary molecular methods (including X-ray crystallography, NMR spectroscopy, small angle X-ray/neutron scattering, and computational techniques) is frequently required to obtain a comprehensive understanding of dynamic macromolecular complexes. In particular, these techniques are critical for studying intrinsically disordered protein regions (IDRs) or intrinsically disordered proteins (IDPs) that are part of large protein:protein complexes. Here, we explain how to prepare IDP samples suitable for study using NMR spectroscopy, and describe a novel SAXS modeling method (ensemble refinement of SAXS; EROS) that integrates the results from complementary methods, including crystal structures and NMR chemical shift perturbations, among others, to accurately model SAXS data and describe ensemble structures of dynamic macromolecular complexes.

• MeSH
• endozomální třídící komplexy pro transport chemie   metabolismus   MeSH
• konformace proteinů MeSH
• krystalografie rentgenová metody   MeSH
• lidé MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• mitogenem aktivované proteinkinasy chemie   metabolismus   MeSH
• molekulární modely MeSH
• radiační rozptyl * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Fibrilace síní (FS) je nejčastější srdeční arytmií u dospělých a příčinou značné morbidity a mortality. Ve srovnání s běžnou populací zvyšuje FS riziko cévních mozkových příhod pětinásobně, přičemž základem prevence vzniku cévních mozkových příhod je perorální antikoagulační léčba. Aby bylo možno vyhledávat pacienty s vysokou pravděpodobností vzniku FS, je třeba zjistit faktory predikující vznik FS. Popisujeme případ 69letého pacienta s asymptomatickou palpitací, u něhož 24hodinové holterovské monitorování prokázalo několik nepřevedených předčasných síňových komplexů (non-conducted premature atrial complex, ncPAC) vedoucích ke vzniku FS.

Atrial fibrillation (AF) is the most common cardiac arrhythmia in adults with substantial morbidity and mortality. AF increases the risk of stroke 5-fold compared to the general population and oral anticoagulant therapy represents the cornerstone for stroke prevention. Therefore, it is necessary to identify predictive factors for the onset of AF in order to screen patients with a high probability of AF development. We report the case of a 69-year-old patient asymptomatic for palpitation with a 24-hour Holter ECG showing several ncPACs (non-conducted premature atrial complexes) leading to AF onset.

• MeSH
• cévní mozková příhoda prevence a kontrola   MeSH
• elektrokardiografie ambulantní metody   MeSH
• fibrilace síní diagnóza   etiologie   prevence a kontrola   MeSH
• lidé MeSH
• rizikové faktory kardiovaskulárních chorob MeSH
• senioři MeSH
• síňové extrasystoly * diagnostické zobrazování   prevence a kontrola   MeSH
• srdeční arytmie diagnostické zobrazování   prevence a kontrola   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• Publikační typ
• kazuistiky MeSH

• MeSH
• centrální nervový systém fyziologie   MeSH
• elektroencefalografie MeSH
• epilepsie MeSH
• mozek fyziologie   MeSH
• mozková kůra MeSH
• Publikační typ
• monografie MeSH

• Konspekt
• Patologie. Klinická medicína
• NLK Obory
• neurologie
• neurovědy

Energy relaxation in light-harvesting complexes has been extensively studied by various ultrafast spectroscopic techniques, the fastest processes being in the sub-100-fs range. At the same time, much slower dynamics have been observed in individual complexes by single-molecule fluorescence spectroscopy (SMS). In this work, we use a pump-probe-type SMS technique to observe the ultrafast energy relaxation in single light-harvesting complexes LH2 of purple bacteria. After excitation at 800 nm, the measured relaxation time distribution of multiple complexes has a peak at 95 fs and is asymmetric, with a tail at slower relaxation times. When tuning the excitation wavelength, the distribution changes in both its shape and position. The observed behavior agrees with what is to be expected from the LH2 excited states structure. As we show by a Redfield theory calculation of the relaxation times, the distribution shape corresponds to the expected effect of Gaussian disorder of the pigment transition energies. By repeatedly measuring few individual complexes for minutes, we find that complexes sample the relaxation time distribution on a timescale of seconds. Furthermore, by comparing the distribution from a single long-lived complex with the whole ensemble, we demonstrate that, regarding the relaxation times, the ensemble can be considered ergodic. Our findings thus agree with the commonly used notion of an ensemble of identical LH2 complexes experiencing slow random fluctuations.

• MeSH
• bakteriochlorofyly chemie   účinky záření   MeSH
• čas MeSH
• fluorescenční spektrometrie metody   MeSH
• konfokální mikroskopie MeSH
• lasery MeSH
• neparametrická statistika MeSH
• normální rozdělení MeSH
• přenos energie * MeSH
• Rhodopseudomonas chemie   MeSH
• světlo MeSH
• světlosběrné proteinové komplexy chemie   účinky záření   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• srovnávací studie MeSH

• MeSH
• buňky MeSH

• Konspekt
• Buněčná biologie. Cytologie
• NLK Obory
• cytologie, klinická cytologie

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website.

• MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• proteiny vázající RNA chemie   metabolismus   MeSH
• RNA chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

RNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than 50 μs of simulations and show that the MD method is robust enough to reliably describe the structural dynamics of the RRM-RNA complexes. The simulations predict unanticipated specific participation of Arg142 at the protein-RNA interface of the SRFS1 complex, which is subsequently confirmed by NMR and ITC measurements. Several segments of the protein-RNA interface may involve competition between dynamical local substates rather than firmly formed interactions, which is indirectly consistent with the primary NMR data. We demonstrate that the simulations can be used to interpret the NMR atomistic models and can provide qualified predictions. Finally, we propose a protocol for 'MD-adapted structure ensemble' as a way to integrate the simulation predictions and expand upon the deposited NMR structures. Unbiased μs-scale atomistic MD could become a technique routinely complementing the NMR measurements of protein-RNA complexes.

• MeSH
• konformace proteinů MeSH
• lidé MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární modely MeSH
• motiv rozpoznávající RNA genetika   MeSH
• multiproteinové komplexy chemie   genetika   MeSH
• RNA chemie   genetika   MeSH
• sekvence aminokyselin genetika   MeSH
• serin-arginin sestřihové faktory chemie   genetika   MeSH
• sestřihové faktory chemie   genetika   MeSH
• simulace molekulární dynamiky MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Currently, mental disorders are usually conceptualized as a hidden causal factor, manifested by its symptoms. This notion rests upon the reflective latent model, which is implicitly at work every time complex symptomatology gets summarized by a single number or a categorical state. The present paper reflects on the quantitative, testable implications of this psychometric model and shows how its restraints are untenable for most mental disorders. The observed data are instead consistent with mental disorders being complex dynamic systems. Instead of being treated as interchangeable measures of the same latent factor, symptoms likely act as independent causal entities, directly affecting each other. In recent years, this shift in ontological stance toward psychopathology has laid a basis for adapting the network theory. Under this theory, a mental disorder is a relatively stable emergent state, which arises due to a pronounced and recurrent interaction of causally linked symptoms. It is discussed how models embedded within the network theory can help provide insight into the etiopathogenesis of mental disorders and address clinical intervention. In conclusion, limits and future challenges to the network theory are discussed.

• MeSH
• duševní zdraví * MeSH
• kauzalita MeSH
• lidé MeSH
• psychometrie metody   MeSH
• psychopatologie * metody   MeSH
• teoretické modely MeSH
• Check Tag
• lidé MeSH