nuclear dynamics
Dotaz
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2nd ed. xxv, 714 s., [7] s. příl. : il. (některé barev.) ; 26 cm
xxiv, 686 s. : il. ; 26 cm
- MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- Publikační typ
- příručky MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- radiologie, nukleární medicína a zobrazovací metody
Methods in enzymology ; Vol. 176
530 s. : obr., tab.
To investigate the temporal regulation of the DNA damage response, we applied quantitative mass spectrometry-based proteomics to measure site-specific phosphorylation changes of nuclear proteins after ionizing radiation. We profiled 5204 phosphorylation sites at five time points following DNA damage of which 594 sites on 209 proteins were observed to be regulated more than 2-fold. Of the 594 sites, 372 are novel phosphorylation sites primarily of nuclear origin. The 594 sites could be classified to distinct temporal profiles. Sites regulated shortly after radiation were enriched in the ataxia telangiectasia mutated (ATM) kinase SQ consensus sequence motif and a novel SXXQ motif. Importantly, in addition to induced phosphorylation, we identified a considerable group of sites that undergo DNA damage-induced dephosphorylation. Together, our data extend the number of known phosphorylation sites regulated by DNA damage, provides so far unprecedented temporal dissection of DNA damage-modified phosphorylation events, and elucidate the cross-talk between different types of post-translational modifications in the dynamic regulation of a multifaceted DNA damage response.
- MeSH
- aminokyselinové motivy MeSH
- buněčné jádro * metabolismus MeSH
- buněčné linie MeSH
- časové faktory MeSH
- chromatografie MeSH
- fosforylace MeSH
- jaderné proteiny * chemie metabolismus MeSH
- konsenzuální sekvence MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- poškození DNA * MeSH
- posttranslační úpravy proteinů MeSH
- proteinkinasy chemie metabolismus MeSH
- proteom * chemie metabolismus MeSH
- reprodukovatelnost výsledků MeSH
- sekvence aminokyselin MeSH
- shluková analýza MeSH
- signální transdukce MeSH
- Check Tag
- lidé MeSH
... Kidney (Excluding Transplant) -- Unilateral decrease or absence of renal perfusion in first-pass dynamic ...
A publication of the Society of nuclear medicine
250 stran ; 26 cm
- MeSH
- diferenciální diagnóza MeSH
- nukleární lékařství MeSH
- radiografie MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Lékařské vědy. Lékařství
- NLK Obory
- radiologie, nukleární medicína a zobrazovací metody
The isotropic (129)Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129)Xe NMR CS. The (129)Xe shielding constant was obtained by averaging the (129)Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C60 system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit-Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C60 system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated (129)Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental (129)Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of (129)Xe NMR parameters in different Xe atom guest-host systems.
Clusters of a solute and a few solvent molecules obtained from molecular dynamics (MD) are a powerful tool to study solvation effects by advanced quantum chemical (QC) methods. For spectroscopic properties strongly dependent on the solvation, however, a large number of clusters are needed for a good convergence. In this work, a parallel variable selection (PVS) method is proposed that in some cases efficiently reduces the number of clusters needed for the averaging. The mass, charge, or atomic density MD distributions are used as a secondary variable to preselect the most probable cluster geometries used for averaging of solute spectral properties. When applied to nuclear magnetic resonance chemical shift of a model alcohol, the method allowed one to significantly reduce the total computational time, by a factor of 10. Even larger savings were achieved for the modeling of Raman and Raman optical activity spectra of (S)-lactamide molecule dissolved in water. The results thus suggest that the PVS method can be generally used for simulations of spectroscopic properties of solvated molecules and makes multiscale MD/QC computations more affordable.
Mitochondria, the powerhouse and the vital signaling hub of the cell, participate in a variety of biological processes, such as apoptosis, redox responses, cell senescence, autophagy, and iron homeostasis. Mitochondria form a mostly tubular network, made up of an outer and a cristeae-forming inner membrane. The network undergoes dynamic fusion and fission that change its morphological structure according to the functional needs. Approximately 1500 mitochondrial proteins encoded by nuclear genome plus over 10 proteins encoded by mitochondrial DNA are folded and assembled in the mitochondria under a high-fidelity control system. These proteins are involved in oxidative phosphorylation, metabolism, network and cristae dynamics, mitophagy, import machinery, ion channels, and mitochondrial DNA maintenance. This Collection gathers original research that advances our understanding of the monitoring techniques and pathophysiological significance of mitochondrial dynamics in health and disease.
- MeSH
- lidé MeSH
- mitochondriální dynamika * MeSH
- mitochondrie * metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- práce podpořená grantem MeSH
- úvodníky MeSH
Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.
- MeSH
- hořčík chemie MeSH
- izotopy dusíku chemie MeSH
- izotopy uhlíku chemie MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- proteinkinasy chemie MeSH
- proteinové domény MeSH
- proteiny huseníčku chemie MeSH
- simulace molekulární dynamiky MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop-a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids.
- MeSH
- cytosin chemie MeSH
- draslík MeSH
- hořčík MeSH
- ionty chemie MeSH
- kationty chemie MeSH
- konformace nukleové kyseliny MeSH
- ligandy MeSH
- mutace MeSH
- neomycin MeSH
- nukleární magnetická rezonance biomolekulární MeSH
- párování bází MeSH
- riboswitch * MeSH
- simulace molekulární dynamiky MeSH
- uracil chemie MeSH
- vazebná místa MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
