Correction: Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies.

Correction for 'Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies' by P. Bruzdziak et al., Phys. Chem. Chem. Phys., 2015, 17, 23155-23164.

Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies.

Interactions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes -l-proline and trimethylamine-N-oxide (TMAO) - belong to a group of stabilizing osmolytes, and according to the preferential exclusion/hydration hypothesis, both should be excluded from the vicinity of the protein backbone and surface. We provide experimental and computational evidence that although TMAO behaves according to the hypothesis, proline does not. Our results suggest that preferential exclusion is not a universal property of stabilizing osmolytes.

Interaction of cisplatin and two potential antitumoral platinum(II) complexes with a model lipid membrane: a combined NMR and MD study.

In this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, (31)P, (13)C and (2)H solid state NMR experiments were performed to obtain information on the phase structure, phase transitions and structural and dynamic changes in the phospholipid bilayer upon interaction with the platinum complexes. On the other hand, MD calculations yielded free energy profiles for the different complexes across the bilayer; the results were analysed to obtain MD predictions on complex distribution with respect to the bilayer, as well as to establish their effects on the conformational equilibrium of the DMPC acyl chains. The combination of NMR and MD approaches highlighted that, whereas the more hydrophilic cisplatin tends to remain in the polar head group region causing a decrease in flexibility of the bilayer, the two new complexes enter into the bilayer. In particular, complex 2 is preferentially located relatively close to the surface, only slightly affecting the bilayer structure and mobility, while complex 3 penetrates more deeply, strongly perturbing the bilayer and giving rise to lateral phase separation.

Chromosomal aberrations in peripheral blood lymphocytes exposed to a mixed beam of low energy neutrons and gamma radiation.

Cells exposed to thermal neutrons are simultaneously damaged by radiations with high and low linear energy transfer (LET). A question relevant for the assessment of risk of exposure to a mixed beam is whether the biological effect of both radiation types is additive or synergistic. The aim of the present investigation was to calculate whether the high and low LET components of a thermal neutron field interact when damaging cells. Human peripheral blood lymphocytes were exposed to neutrons from the HB11 beam at the Institute for Energy and Transport, Petten, Netherlands, in a 37 °C water phantom at varying depths, where the mix of high and low LET beam components differs. Chromosomal aberrations were analysed and the relative biological effectiveness (RBE) values as well as the expected contributions of protons and photons to the aberration yield were calculated based on a dose response of aberrations in lymphocytes exposed to (60)Co gamma radiation. The RBE for 10 dicentrics per 100 cells was 3 for mixed beam and 7.2 for protons. For 20 dicentrics per 100 cells the respective values were 2.4 and 5.8. Within the limitations of the experimental setup the results indicate that for this endpoint there is no synergism between the high and low LET radiations.

Phase diagram and dynamics of the liquid crystal isopentylcyanobiphenyl (5*CB).

From measurements of the specific volume as a function of temperature and pressure, the phase diagram for the liquid crystal forming isopentylcyanobiphenyl (5*CB) was determined. There are a number of phases (isotropic liquid, glass, cholesteric, and crystalline), and we show that the phase boundaries differ from previous reports, reflecting the slow crystallization kinetics of the system. Using dielectric spectroscopy at ambient and elevated pressure, we identify the relaxation processes in the isotropic and cholesteric phases. From application of density scaling to the dynamics, we obtain scaling exponents, which were found to vary with the type of motion. Moreover, unlike previous results for many other liquid crystals, the scaling exponent for the isotropic state differs from the thermodynamic potential parameter, and hence the relaxation time along the clearing line varies significantly with pressure. The distinctive properties of 5*CB reflect the very different volume dependences of the thermodynamics and the dynamics.

Orientational order of fluorinated mesogens containing the 1,3,2-dioxaborinane ring: a multidisciplinary approach.

Orientational order properties of two fluorinated liquid crystals containing the 1,3,2-dioxaborinane ring have been investigated by means of optical, dielectric, and (13)C and (19)F NMR spectroscopies. The optical birefringence and dielectric anisotropy values determined in the mesomorphic phases were analyzed in terms of well-established theoretical models to obtain the order parameters relative to the principal axis of the polarizability tensor and molecular dipole moment, respectively. A large set of data, including (13)C and (19)F chemical shift anisotropies and (13)C-(19)F and (1)H-(19)F couplings relative to nuclei on the aromatic rings, was acquired in the NMR experiments and analyzed to determine local order parameters (principal order parameter and biaxiality) for different rigid fragments of the mesogen aromatic core using advanced DFT methods for the calculation of geometrical parameters and chemical shift tensors. A critical analysis of the dependence of the order parameters on the data set employed and on the theoretical assumptions and approximations has also been performed. The orientational order parameters obtained using the different techniques are compared and discussed in relation to the reference frame associated with the anisotropic properties monitored.

Amphotericin B and its new derivatives - mode of action.

Amphotericin B (AmB) is a well known antifungal and antiprotozoal antibiotic used in the clinic for several decades. Clinical applications of AmB, however, are limited by its nephrotoxicity and many other acute side effects which are not acceptable by patients when their life is not threaten. In order to improve the therapeutic index of this drug, lipid formulations have been introduced and many efforts have been made to obtain less toxic AmB derivatives by chemical modifications of the parent drug. This review presents concise knowledge about this fascinating compound and a critical review of the data published within last few years about the mechanism of action of this antibiotic. In particular, in the present work we discuss: i) structure and properties of AmB and its recently synthesized new derivatives; ii) antifungal and antileishmanial activity and toxicity of these compounds; and iii) mode of action of AmB and its derivatives at cellular and molecular levels, with particular attention paid to interactions of AmB and different components of cellular membranes.

Cell survival and chromosomal aberrations in CHO-K1 cells irradiated by carbon ions.

Chinese hamster ovary CHO-K1 cells were exposed to high LET (12)C-beam (LET: 830 keV/microm) in the dose range of 0-6 Gy and to (60)Co irradiation and the RBE value was obtained. Effects of (12)C-beam exposure on cell survival and chromosomal aberrations were calculated. The chromosomal aberration data were fitted with linear equation. The distribution of aberration in cells was examined with a standard u-test and used to evaluate the data according to Poisson probabilities. The variance to the mean ratio sigma(2)/Y and the dispersion index (u) were determined. Overdispersion was significant (p<0.05) when the value of u exceeded 1.96.

Orientational order of difluorinated liquid crystals: a comparative 13C-NMR, Optical, and dielectric study in nematic and smectic B phases.

Structural and orientational order properties of 3Cy2CyBF2 and of 5CyCy2BF2 have been investigated by means of (13)C-NMR, optical, and dielectric spectroscopy methods. In the case of NMR, order parameters have been independently obtained from the analysis of either (13)C-(19)F dipolar couplings or (13)C chemical shift anisotropies, both measured from (13)C-{(1)H} NMR static spectra. The assignment of the (13)C resonances has been carried out thanks to the comparison with solution state spectra and DFT calculations, and the relevant geometrical parameters and (13)C chemical shift tensors needed to derive orientational order parameters have been calculated by DFT methods. In the analysis of (13)C-(19)F dipolar couplings, empirical corrections for vibrations and anisotropic scalar couplings have been included. Dielectric measurements have been performed over a broad frequency range for two orientations of the nematic director with respect to the measuring field. At low frequencies (static case) a positive dielectric anisotropy has been determined, which has enabled the calculation of the order parameters according to a well-tested procedure. At high frequencies the dielectric anisotropy changes its sign, a property which can be useful in designing a dual addressing display. The nematic order parameter determined from optical, dielectric, and NMR methods have been compared: their trends with temperature are very similar, apart from some slight shifts, and were analyzed by Haller and Chirtoc models. The differences among the results obtained by the four methods have been discussed in detail, also with reference to the assumptions and approximations used in each case, and to the results recently reported for similar fluorinated nematogens. The presence of a non-negligible order biaxiality has been related to the presence of a CH2CH2 bridging group, linking one cyclohexylic unit with either the other cyclohexyl or the phenyl ring.

Interaction potential in nematogenic 6CHBT.

Pressure-volume-temperature (PVT) measurements were carried out on the nematic liquid crystal 4(trans-4'-n-hexylcyclohexyl)isothiocyanatobenzene (6CHBT). In combination with previous dielectric relaxation measurements at elevated pressure and new measurements extending to GHz frequencies, the characteristics of the anisotropic interaction potential were determined. The thermodynamic potential parameter, gamma, which measures the variation of the interaction energy with volume, equals 5.03 +/- 0.06, with a barrier height equal to approximately 7 kJ/mol. Thus, there is a low potential barrier to reorientations of the 6CHBT molecule about its short axis; however, the retarding potential is strongly volume-dependent. The longitudinal reorientational times determined for various thermodynamic conditions superpose using a scaling exponent equal to gamma within the experimental error. It then follows, as found recently for other liquid crystals, that this relaxation time must be constant along the pressure-dependent clearing line. Thus, the control parameter (e.g., Gibbs free energy) governing the competition between the anisotropic energy and the entropy must also govern the rotational dynamics in the ordered phase of this liquid crystal.

Thermodynamic analysis of the low frequency relaxation time in the smectic A and C phases of a liquid crystal.

Pressure-temperature-volume (pVT) measurements were carried out on 2-(4-hexyloxyphenyl)-5-octyl-pyrimidine, a substance exhibiting nematic and smectic A and C polymorphism. Analysis of the longitudinal relaxation times obtained recently for elevated pressures [Czub et al., Z. Naturforsch. A: Phys. Sci. 58, 333 (2003)] was performed for isobaric, isothermal, and isochoric conditions within the two smectic phases. Several relationships linking the dynamical and thermodynamical quantities, derived recently for isotropic glass formers [Roland et al. Rep. Prog. Phys. 68, 1405 (2005)], were found to hold for the liquid crystal, revealing a striking similarity of behaviors for these two types of materials. The parameter gamma characterizing the steepness of the interaction potential was derived in different ways. It is interesting that the liquid crystal gives relaxation time versus TV(-gamma) plots that are linear, unlike results for glass formers, implying that the dynamics of the former is thermally activated.

An irradiation facility with a horizontal beam for radiobiological studies.

A facility with a horizontal beam for radiobiological experiments with heavy ions has been designed and constructed at the Heavy Ion Laboratory in Warsaw University. The facility is optimal to investigate the radiobiological effects of charged heavy particles on a cellular or molecular level as in the region of the Bragg peak.