In this work, the 3-D structure of the well-known opioid drug heroin in a solution was investigated. The goal was to provide a complete and detailed description of the stable conformers with their relative abundances. This knowledge is very important from the pharmaceutical and forensic point of view as it could help significantly with deeper understanding of heroin's metabolism and the development of antagonist medicines for the case of an overdose. As heroin is a chiral compound with five stereogenic centres, the methods of chiroptical spectroscopy supplemented by density functional theory (DFT) calculations were applied to study its conformations in chloroform solution. The selected chiroptical methods, namely, electronic circular dichroism (ECD) and vibrational circular dichroism (VCD), are inherently sensitive to the 3-D structure of small- to medium-sized chiral organic molecules. A thorough conformational analysis revealed four stable conformers of heroin in chloroform solution, where the conductor-like polarizable continuum model of the solvent was used for all the calculations. The simulated ultraviolet (UV), infrared (IR), ECD, and VCD spectra were compared with the experimental ones and very good agreement was found, which enabled a detailed structure description and interpretation of the spectra. Chiroptical spectroscopy in combination with DFT calculations proved to be a very sensitive tool for the analysis of the 3-D structure of heroin in a solution in contrast with conventional spectroscopic methods. Especially, the application of VCD seems to be a promising approach for monitoring structural changes, for instance, those caused by solvents or interactions with other agents.

• Klíčová slova
• 3-D structure, DFT calculations, chiroptical spectroscopy, circular dichroism, drugs, heroin,
• MeSH
• cirkulární dichroismus MeSH
• heroin chemie   MeSH
• molekulární struktura MeSH
• roztoky chemie   MeSH
• spektrální analýza MeSH
• stereoizomerie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• heroin MeSH
• roztoky MeSH

Structure and flexibility of natural compounds determine their biological activity. In the present study, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of cocaine hydrochloride in aqueous solutions were measured and related to the structure with the aid of density functional theory (DFT) computations. Additional measurements in deuterated environment made assignment of vibrational bands easier. The results suggest that the prevalent cocaine conformation in solution differs from that adopted in hydrochloride crystal. The spectroscopic results and computational analysis are consistent with X-ray structures of known cocaine-receptor complexes, in which the compound adopts a variety of conformations. All three kinds of chiroptical spectra exhibited significantly greater conformational sensitivity than unpolarized absorption or Raman scattering. The ROA technique provided the largest number of well-resolved bands, bearing rich structural information.

• Klíčová slova
• Raman spectroscopy, analytical methods, circular dichroism, density functional calculations, structure elucidation,
• MeSH
• cirkulární dichroismus MeSH
• kokain chemie   MeSH
• kvantová teorie * MeSH
• molekulární struktura MeSH
• Ramanova spektroskopie MeSH
• roztoky MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kokain MeSH
• roztoky MeSH

The formation and structure of the potassium complex with valinomycin in solution were studied by means of Raman and Raman optical activity (ROA) spectroscopy. The complexation caused significant spectral changes, particularly in the region 1200-1400 cm(-1). The experimental spectra were interpreted using first principles computations. A complete computational conformational search combined with the spectral analysis revealed the arrangement of the isopropyl side chains in the complex. From a total of 6579 unique conformers two predominant ones were confirmed in the solution by ROA. A third one was predicted theoretically, but its population in the experiment could be estimated only roughly. The most populated conformer does not exhibit C(3) symmetry, and is different from that present in the crystal and the NMR-derived structure. Molecular dynamics techniques were used to estimate the molecular flexibility and its effect on the spectra. Density functional computations and Cartesian coordinate transfer (CCT) techniques provided the ROA and Raman spectral shapes and intensities well comparable with the experiment. The polar solvent (methanol) environment modeled with a polarizable continuum model (PCM) leads to rather minor changes in the conformer populations and vibrational properties as compared to vacuum computations, due to the hydrophobic character of the complex. Additional computational experiments suggest that the vibrational interactions determining the ROA spectra are quite local, which contributes to the good spatial resolution of the method. A reduction of the noise in the experimental spectra as well as increased precision of the simulations is desirable for the further exploration of the potential of the ROA spectroscopy for biomolecular studies in the future.

• MeSH
• draslík chemie   MeSH
• molekulární konformace MeSH
• organokovové sloučeniny chemie   MeSH
• Ramanova spektroskopie * MeSH
• roztoky MeSH
• simulace molekulární dynamiky MeSH
• valinomycin chemie   MeSH
• vibrace MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• draslík MeSH
• organokovové sloučeniny MeSH
• roztoky MeSH
• valinomycin MeSH

The interaction of the central magnesium atom of chlorophyll a (Chl a) with the carbon and nitrogen backbone was investigated by magnesium K near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in fluorescence detection mode. A crude extract of Chl a was measured as a 1 × 10-2 mol/L ethanol solution (which represents an upper limit of concentration without aggregation) and as dried droplets. For the first time, the investigation of Mg bound to Chl a in a liquid environment by means of X-ray absorption spectroscopy is demonstrated. A pre-edge feature in the dissolved as well as in dried Chl a NEXFAS spectra has been identified as a characteristic transition originating from Mg in the Chl a molecule. This result is confirmed by theoretical DFT calculations leading to molecular orbitals (MO) which are mainly situated on the magnesium atom and nitrogen and carbon atoms from the pyrrole rings. The description is the first referring to the MO distribution with respect to the central Mg ion of Chl a and the surrounding atoms. On this basis, new approaches for the investigations of dynamic processes of molecules in solution and structure-function relationships of photosynthetic pigments and pigment-protein complexes in their native environment can be developed.

• MeSH
• chlorofyl analogy a deriváty   chemie   MeSH
• ethanol chemie   MeSH
• hořčík chemie   MeSH
• rentgenová absorpční spektroskopie MeSH
• roztoky MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorofyl MeSH
• chlorophyll a' MeSH Prohlížeč
• ethanol MeSH
• hořčík MeSH
• roztoky MeSH

Mouse Nkrp1a receptor is a C-type lectin-like receptor expressed on the surface of natural killer cells that play an important role against virally infected and tumor cells. The recently solved crystal structure of Nkrp1a raises questions about a long loop region which was uniquely extended from the central region in the crystal. To understand the functional significance of the loop, the solution structure of Nkrp1a using nuclear magnetic resonance (NMR) spectroscopy was determined. A notable difference between the crystal and NMR structure of Nkrp1a appears in the conformation of the long loop region. While the extended loop points away from the central core and mediates formation of a domain swapped dimer in the crystal, the solution structure is monomeric with the loop tightly anchored to the central region. The findings described the first solution structure in the Nkrp1 family and revealed intriguing similarities and differences to the crystal structure. Proteins 2016; 84:1304-1311. © 2016 Wiley Periodicals, Inc.

• Klíčová slova
• CTLD, NK receptor, Nkrp1, Nkrp1a, domain-swapping, long loop region, nuclear magnetic resonance,
• MeSH
• aminokyselinové motivy MeSH
• Escherichia coli genetika   metabolismus   MeSH
• exprese genu MeSH
• klonování DNA MeSH
• krystalografie rentgenová MeSH
• lektinové receptory NK-buněk - podrodina B chemie   genetika   metabolismus   MeSH
• magnetická rezonanční spektroskopie MeSH
• myši MeSH
• proteinové domény MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• sekundární struktura proteinů MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• lektinové receptory NK-buněk - podrodina B MeSH
• rekombinantní proteiny MeSH

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found.

• Klíčová slova
• Spinacia oleracea, dynamic N-terminus, extrinsic photosynthetic protein, hydrogen bond dynamics, intrinsic disorder, solution structure,
• MeSH
• fotosystém II (proteinový komplex) chemie   genetika   metabolismus   MeSH
• krystalografie rentgenová MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• rekombinantní proteiny chemie   metabolismus   MeSH
• rostlinné proteiny chemie   genetika   metabolismus   MeSH
• roztoky MeSH
• sekundární struktura proteinů * MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky * MeSH
• Spinacia oleracea genetika   metabolismus   MeSH
• terciární struktura proteinů MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fotosystém II (proteinový komplex) MeSH
• rekombinantní proteiny MeSH
• rostlinné proteiny MeSH
• roztoky MeSH

Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.

• Klíčová slova
• Biomolecular NMR, Integrated structural biology, Isotope labeling, NMR assignments, NMR structure determination, RNA-protein complex, RNA-protein interaction,
• MeSH
• izotopové značení metody   MeSH
• izotopy chemie   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• proteiny chemie   MeSH
• ribonukleoproteiny chemie   MeSH
• RNA chemie   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• izotopy MeSH
• proteiny MeSH
• ribonukleoproteiny MeSH
• RNA MeSH

Neutron diffraction with isotopic substitution (NDIS) experiments were done on both natural abundance potassium and isotopically labeled 41KCl heavy water solutions to characterize the solvent structuring around the potassium ion in water. Preliminary measurements suggested that the literature value for the coherent neutron scattering length (2.69 fm) for 41K was significantly in error. This value was remeasured using a neutron powder diffractometer and found to be 2.40 fm. This revision increases significantly the contrast between the natural abundance K and 41K by about 30% (from 1.0 to 1.3 fm). The experimentally determined structure factor of the potassium ion was then compared to that calculated from molecular dynamics (MD) simulations. Previous neutron scattering measurements of potassium gave a solvation number of 5.5 (see below). In this study, the NDIS and MD results are in good agreement and allowed us to derive a coordination number of 6.1 for water molecules and 0.8 for chloride ions around each K+ ion in 4 molal aqueous KCl solution.

• MeSH
• chlorid draselný chemie   MeSH
• molekulární konformace MeSH
• neutronová difrakce * MeSH
• roztoky MeSH
• simulace molekulární dynamiky * MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• chlorid draselný MeSH
• roztoky MeSH
• voda MeSH

Detailed analysis of the proton and carbon-13 NMR spectra of cyclo(L-prolyl-L-N-methylphenylalanyl) in chloroform and methanol in relation to its nonmethylated analog provided information on the conformation of the title compound in solution as well as on the effect of N-methylation and solvation. The X-ray structure of the title compound in the crystalline state showed the same conformational features as the solution structure. The phenyl group folds over the diketopiperazine ring which resembles a flattened half-chair. Both amide bonds are considerably nonplanar. The pyrrolidine ring of proline shows a strong pucker at the ring junction with the largest chi 5 value hitherto observed.

• MeSH
• cyklické peptidy chemie   MeSH
• difrakce rentgenového záření MeSH
• dipeptidy chemie   MeSH
• konformace proteinů MeSH
• magnetická rezonanční spektroskopie MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• roztoky MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cyclo(prolyl-N-methylphenylalanyl) MeSH Prohlížeč
• cyklické peptidy MeSH
• dipeptidy MeSH
• roztoky MeSH

Electrospray ionization mass spectrometry (ESI-MS) is used to probe the binding of small anions to the macrocycle of bambus[6]uril. For the halide ions, the experimental patterns suggest F(-) < Cl(-) < Br(-) < I(-), which is consistent with the order of anion binding found in the condensed phase. Parallel equilibrium studies in the condensed phase establish the association constants of halide anions and bambus[6]uril in mixed solvents. A detailed analysis of the mass spectrometric data is used to shed light on the correlations between the binding constants in the condensed phase and the ion abundances observed using ESI-MS. From the analysis it becomes apparent that ESI-MS can indeed represent the situation in solution to some extent, but the sampling in the gas-phase experiment is not 1:1 compared to that in solution.

• MeSH
• anionty chemie   MeSH
• hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
• imidazoly chemie   MeSH
• makrocyklické sloučeniny chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• plyny chemie   MeSH
• roztoky MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• anionty MeSH
• bambus(6)uril MeSH Prohlížeč
• imidazoly MeSH
• makrocyklické sloučeniny MeSH
• plyny MeSH
• roztoky MeSH