Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.

Reactivation of mutant p53 by a dietary-related compound phenethyl isothiocyanate inhibits tumor growth.

Mutations in the p53 tumor-suppressor gene are prevalent in human cancers. The majority of p53 mutations are missense, which can be classified into contact mutations (that directly disrupts the DNA-binding activity of p53) and structural mutations (that disrupts the conformation of p53). Both of the mutations can disable the normal wild-type (WT) p53 activities. Nevertheless, it has been amply documented that small molecules can rescue activity from mutant p53 by restoring WT tumor-suppressive functions. These compounds hold promise for cancer therapy and have now entered clinical trials. In this study, we show that cruciferous-vegetable-derived phenethyl isothiocyanate (PEITC) can reactivate p53 mutant under in vitro and in vivo conditions, revealing a new mechanism of action for a dietary-related compound. PEITC exhibits growth-inhibitory activity in cells expressing p53 mutants with preferential activity toward p53(R175), one of the most frequent 'hotspot' mutations within the p53 sequence. Mechanistic studies revealed that PEITC induces apoptosis in a p53(R175) mutant-dependent manner by restoring p53 WT conformation and transactivation functions. Accordingly, in PEITC-treated cells the reactivated p53(R175) mutant induces apoptosis by activating canonical WT p53 targets, inducing a delay in S and G2/M phase, and by phosphorylating ATM/CHK2. Interestingly, the growth-inhibitory effects of PEITC depend on the redox state of the cell. Further, PEITC treatments render the p53(R175) mutant sensitive to degradation by the proteasome and autophagy in a concentration-dependent manner. PEITC-induced reactivation of p53(R175) and its subsequent sensitivity to the degradation pathways likely contribute to its anticancer activities. We further show that dietary supplementation of PEITC is able to reactivate WT activity in vivo as well, inhibiting tumor growth in xenograft mouse model. These findings provide the first example of mutant p53 reactivation by a dietary compound and have important implications for cancer prevention and therapy.

[Niemann-Pick disease--a rare disease in children's hepatology (a clinical case)].

The aim is to acquaint medical society with literature data and specific details of clinical incidents of Niemann-Pick disease among 14 year old children. The article gives a brief review of literature on the problem of diagnostics, symptoms and treatment of Niemann-Pick disease in children. A clinical case of a forteen-year-old girl with type C Niemann-Pick disease is presented, the peculiarity of which is a combination of symptoms typical of the disease with a low level of ceruloplasmin in serum.

Differential zinc and DNA binding by partial peptides of human protamine HP2.

The Zn(II) binding by partial peptides of human protamine HP2: HP2(1-15); HP2(1-25), HP2(26-40), HP2(37-47), and HP2(43-57) was studied by circular dichroism (CD). Precipitation of a 20-mer DNA by these partial peptides and the effects of Zn(II) thereon were investigated using polyacrylamide gel electrophoresis (GE). The results of this study suggest that reduced HP2 (thiol groups intact) can bind Zn(II) at various parts of the molecule. In the absence of DNA, the primary Zn(II) binding site in reduced HP2 is located in the 37-47 sequence (involving Cys-37, His-39, His-43, and Cys-47), while in the presence of DNA, the strongest Zn(II) binding is provided by sequences 12-22 (by His-12, Cys-13, His-19, and His-22) and 43-57 (His-43, Cys-47, Cys-53, and His-57). In its oxidized form, HP2 can bind zinc through His residues of the 7-22 sequence. Zn(II) markedly enhances DNA binding by all partial peptides. These findings suggest that Zn(II) ions may be a regulatory factor for sperm chromatin condensation processes.

Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission.

The diffraction barrier responsible for a finite focal spot size and limited resolution in far-field fluorescence microscopy has been fundamentally broken. This is accomplished by quenching excited organic molecules at the rim of the focal spot through stimulated emission. Along the optic axis, the spot size was reduced by up to 6 times beyond the diffraction barrier. The simultaneous 2-fold improvement in the radial direction rendered a nearly spherical fluorescence spot with a diameter of 90-110 nm. The spot volume of down to 0.67 attoliters is 18 times smaller than that of confocal microscopy, thus making our results also relevant to three-dimensional photochemistry and single molecule spectroscopy. Images of live cells reveal greater details.

New conformationally restricted analog of the immunosuppressory mini-domain of HLA-DQ and its biological properties.

Our previous studies revealed that the nonapeptide fragment of HLA-DQ located in the beta 164-172 loop of the Thr-Pro-Gln-Arg-Gly-Asp-Val-Tyr-Thr sequence suppresses the immune humoral and cellular responses [30]. Based on the crystal structure of HLA-class II molecules we designed and synthesized a cyclic analog with restricted conformation, cyclo(Suc-Thr-Pro-Gln-Arg-Gly-Asp-Val-Lys)-Thr-OH (Suc = succinyl) by reacting a Lys side chain with a succinylated N-terminus. The cyclization product more potently suppresses the cellular immune response than its linear counterparts and is efficiently cleaved by trypsin. The results indicate that the beta 164-172 loop may serve as a functional epitope on the HLA class II surface for intermolecular binding.

Specific interactions of bovine and human beta-casomorphin-7 with Cu(II) ions.

Complex formation between Cu(II) and human and bovine beta-casomorphin heptapeptides, Tyr-Pro-Phe-Val-Glu-Pro-Ile and Tyr-Pro-Phe-Pro-Gly-Pro-Ile, respectively, was investigated by pH potentiometry and spectroscopic (CD, EPR and electronic absorption) techniques. The results showed the critical impact of Pro residues on the complex equilibria formed. The presence of the Pro residue at the second position leads to formation of very stable dimeric species in which two metal ions co-ordinate to N-terminal ¿NH2, C=O¿ binding sites of one peptide molecule and the deprotonated phenolic oxygen of the second ligand molecule. The presence of two additional hydrophobic residues on the C-terminal makes heptapeptide molecule much more effective ligand than its pentapeptide N-terminal fragment.

Binding ability of Cu2+ ions by opiate-like fragments of bovine casein.

The coordination modes of Cu(II) to alpha-casein (90-95) and alpha-casein (90-96) peptides with opioid activity isolated from pepsin hydrolisates of alpha-casein were investigated by means of electron paramagnetic resonance, absorption, and circular dichroism spectroscopy and potentiometry. The results allow the identification of the complex species involved and the attribution of the spectral data set to the various complex structures. According to the spectroscopic data, a phenolate side-chain of Tyr residue belonging to the Gly-Tyr-Leu or Gly-Tyr-Leu-Gln fragment of the peptides is involved in the metal coordination in a complex which is a minor species at neutral pH range.

The impact of the amino-acid sequence on the specificity of copper(II) interactions with peptides having nonco-ordinating side-chains.

The review presents specific interactions that occur in complexes of Cu(II) ions with peptides composed only of amino acids with nonco-ordinating side chains. Three classes of such peptides are discussed. The first type (NSFRY analogues) is characterised by the presence of a specific combination of bulky and aromatic residues, leading to a formation of multiple weak interactions around Cu(II) that result in an extremely high stability of complexes. The second class is composed of complexes of vasopressins and oxytocins, achieving superstability through a pre-conformation in the peptide molecule. The third group are oligopeptides containing one or two proline residues. These peptides form exotic macrochelate loops with Cu(II) in a result of the break-point effect of Pro residues. Particular emphasis in the review was given to stability constants of complexes, compared to oligoglycine or oligoalanine peptides.

Specific interactions of Cu2+ ions with fragments of envelope protein of hepatitis B virus.

Potentionmetric and spectroscopic (EPR, CD and absorption spectra) data have shown that a fragment of envelope proteins of the hepatitis B virus could be very specific bind molecules for Cu2+ ions using arginine lateral NH2 donor sites. The presence of Pro and Asp residues makes Arg binding not only very specific, but also very efficient.