Thermodynamics and Kinetics of Ligand Photodissociation in Heme Proteins and Formation of DNA i-Motif

Heme proteins carry out a diverse array of functions in vivo while maintaining a well-conserved 3-over-3 α-helical structure. Human hemoglobin (Hb) is well-known for its oxygen transport function. Type 1 non-symbiotic hemoglobins (nsHb1) in plants and bacterial flavohemoglobins (fHb) from a variety of bacterial species have been predicted to carry out a nitric oxide dioxygenase function. In nsHb1 and fHb this function has been linked to protection from nitrosative stress. Herein, I combine photoacoustic calorimetry (PAC), transient absorption spectroscopy (TA), and classical molecular dynamics (cMD) simulations to characterize molecular mechanism of diatomic ligand interactions with a hexa-coordinate globin from plant (rice hemoglobin), bacterial flavohemoglobins and human hemoglobin. In rice type 1 non-symbiotic hemoglobin (rHb1), the dynamics and energetics of structural changes associated with ligand photodissociation is strongly impacted by solvent and temperature, namely CO escape from the protein matrix is slower at pH = 6.0 compare to neutral pH (ns) due to the CD loop reorganization which forms a pathway for ligand escape. In human hemoglobin, exogenous allosteric effectors modulate energetics of conformational changes associated with the CO and O2 escape although the effectors impact on rate constants for ligand association is small. The conformational dynamics associated with ligand photorelease from fHbs from Cupriavidus necator (FHP) and Staphylococcus aureus (HMPSa) are strongly modulated by the presence of azole drugs indicating that drug association modulates structural properties of the heme binding pocket. In addition, we carried out a study of the formation of the DNA intercalated motif (i-motif). The formation of the structure is strongly favored at acidic pH; therefore, PAC was combined with a 2-nitrobenzaldehyde pH-jump to probe formation of the i-motif on fast timescales. i-Motif folding is two-step process with the initial protonation of cytosine residues being endothermic with ΔHfast=8.5 ± 7.0 kcal mol-1 and ΔVfast=10.4 ± 1.6 mL mol-1 and subsequent nucleation/i-motif folding (τ = 140 ns) with ΔHslow=-51.5 ± 4.8 kcal mol-1 and ΔVslow=-6.6 ± 0.9 mL mol-1. The above results indicate that PAC can be employed to study diverse biochemical reactions such as DNA folding, drug binding and ligand photorelease from proteins

The Stargazin-Related Protein {gamma}7 Interacts with the mRNA-Binding Protein Heterogeneous Nuclear Ribonucleoprotein A2 and Regulates the Stability of Specific mRNAs, Including CaV2.2

The role(s) of the novel stargazin-like {gamma}-subunit proteins remain controversial. We have shown previously that the neuron-specific {gamma}7 suppresses the expression of certain calcium channels, particularly CaV2.2, and is therefore unlikely to operate as a calcium channel subunit. We now show that the effect of {gamma}7 on CaV2.2 expression is via an increase in the degradation rate of CaV2.2 mRNA and hence a reduction of CaV2.2 protein level. Furthermore, exogenous expression of {gamma}7 in PC12 cells also decreased the endogenous CaV2.2 mRNA level. Conversely, knockdown of endogenous {gamma}7 with short-hairpin RNAs produced a reciprocal enhancement of CaV2.2 mRNA stability and an increase in endogenous calcium currents in PC12 cells. Moreover, both endogenous and expressed {gamma}7 are present on intracellular membranes, rather than the plasma membrane. The cytoplasmic C terminus of {gamma}7 is essential for all its effects, and we show that {gamma}7 binds directly via its C terminus to a heterogeneous nuclear ribonucleoprotein (hnRNP A2), which also binds to a motif in CaV2.2 mRNA, and is associated with native CaV2.2 mRNA in PC12 cells. The expression of hnRNP A2 enhances CaV2.2 IBa, and this enhancement is prevented by a concentration of {gamma}7 that alone has no effect on IBa. The effect of {gamma}7 is selective for certain mRNAs because it had no effect on {alpha}2{delta}-2 mRNA stability, but it decreased the mRNA stability for the potassium-chloride cotransporter, KCC1, which contains a similar hnRNP A2 binding motif to that in CaV2.2 mRNA. Our results indicate that {gamma}7 plays a role in stabilizing CaV2.2 mRNA

Optically induced forces and torques:Interactions between nanoparticles in a laser beam

Distinctive optical forces and torques arise between nanoparticles irradiated by intense laser radiation. These forces, associated with a pairwise process of stimulated scattering, prove to enable the possibility of producing significant modifications to both the form and magnitude of interparticle forces, with additional contributions arising in the case of dipolar materials. Moreover, such forces have the capacity to generate unusual patterns of nanoscale response, entirely controlled by the input beam characteristics- principally the optical frequency, intensity, and polarization. Based on quantum electrodynamical theory, a general result is secured for the laser-induced force under arbitrary conditions, incorporating both static and dynamic coupling mechanisms. Specific features of the results are identified for pairs of particles with prolate cylindrical symmetry, e.g., carbon nanotubes, where it is shown that the laser-induced forces and torques are sensitive functions of the pair spacing and orientation, and the laser beam geometry; significantly, they can be either repulsive or attractive according to conditions. For nanoparticles trapped in a Laguerre-Gaussian laser beam the results also reveal additional and highly distinctive torques that suggest further possibilities for nanomanipulation with light. The paper concludes with a discussion on several potential applications of such forces. © 2005 The American Physical Society

Malarone treatment failure and in vitro confirmation of resistance of Plasmodium falciparum isolate from Lagos, Nigeria

We report the first in vitro and genetic confirmation of Malarone(®) (GlaxoSmithKline; atovaquone and proguanil hydrochloride) resistance in Plasmodium falciparum acquired in Africa. On presenting with malaria two weeks after returning from a 4-week visit to Lagos, Nigeria without prophylaxis, a male patient was given a standard 3-day treatment course of Malarone(®). Twenty-eight days later the parasitaemia recrudesced. Parasites were cultured from the blood and the isolate (NGATV01) was shown to be resistant to atovaquone and the antifolate pyrimethamine. The cytochrome b gene of isolate NGATV01 showed a single mutation, Tyr268Asn which has not been seen previously

A photonic basis for deriving nonlinear optical response

Nonlinear optics is generally first presented as an extension of conventional optics. Typically the subject is introduced with reference to a classical oscillatory electric polarization, accommodating correction terms that become significant at high intensities. The material parameters that quantify the extent of the nonlinear response are cast as coefficients in a power series - nonlinear optical susceptibilities signifying a propensity to generate optical harmonics, for example. Taking the subject to a deeper level requires a more detailed knowledge of the structure and properties of each nonlinear susceptibility tensor, the latter differing in form according to the process under investigation. Typically, the derivations involve intricate development based on time-dependent perturbation theory, assisted by recourse to a set of Feynman diagrams. This paper presents a more direct route to the required results, based on photonic rather than semiclassical principles, and offers a significantly clearer perspective on the photophysics underlying nonlinear optical response. The method, here illustrated by specific application to harmonic generation and down-conversion processes, is simple, intuitive and readily amenable for processes of arbitrary photonic order. © 2009 IOP Publishing Ltd

Electromagnetic trapping of chiral molecules: orientational effects of the irradiating beam

The photonic interaction generally responsible for the electromagnetic trapping of molecules is forward-Rayleigh scattering, a process that is mediated by transition electric dipoles connecting the ground electronic state and virtual excited states. Higher order electric and magnetic multipole contributions to the scattering amplitude are usually negligible. However, on consideration of chiral discrimination effects (in which an input light of left-handed circular polarization can present different observables compared to right-handed polarization, or molecules of opposite enantiomeric form respond differently to a set circular polarization), the mechanism must be extended to specifically accommodate transition magnetic dipoles. Moreover, it is important to account for the fact that chiral molecules are necessarily non-spherical, so that their interactions with a laser beam will have an orientational dependence. Using quantum electrodynamics, this article quantifies the extent of the energetic discrimination that arises when chiral molecules are optically trapped, placing particular emphasis on the orientational effects of the trapping beam. An in-depth description of the intricate ensemble-weighted method used to incorporate the latter is presented. It is thus shown that, when a mixture of molecular enantiomers is irradiated by a continuous beam of circularly polarized light, a difference arises in the relative rates of migration of each enantiomer in and out of the most intense regions of the beam. In consequence, optical trapping can be used as a means of achieving enantiomer separation

Variable X-ray Absorption in the Seyfert 2 Galaxy Mrk 348

We present RXTE monitoring observations of the Seyfert 2 galaxy Mrk 348 spanning a 6 month period. The time-averaged spectrum in the 3-20 keV band shows many features characteristic of a Compton-thin Seyfert 2 galaxy, namely a hard underlying power-law continuum (photon index = 1.8) with heavy soft X-ray absorption (N_h ~ 10^23 cm^-2) plus measureable iron line emission (equivalent width ~ 100 eV) and, at high energy, evidence for a reflection component (R < 1). During the first half of the monitoring period the X-ray continuum flux from Mrk 348 remained relatively steady. However this was followed by a significant brightening of the source (by roughly a factor of 4) with the fastest change corresponding to a doubling of its X-ray flux on a timescale of about 20 days. The flux increase was accompanied by a marked softening of X-ray spectrum most likely attributable to a factor 3 decline in the intrinsic line-of-sight column density. In contrast the iron line and the reflection components showed no evidence of variability. These observations suggest a scenario in which the central X-ray source is surrounded by a patchy distribution of absorbing material located within about a light-week of the nucleus of Mrk 348. The random movement of individual clouds within the absorbing screen, across our line of sight, produces substantial temporal variations in the measured column density on timescales of weeks to months and gives rise to the observed X-ray spectral variability. However, as viewed from the nucleus the global coverage and typical thickness of the cloud layer remains relatively constant.Comment: 19 pages, 3 figures Accepted for publication in the Astrophysical Journa

Southern GEMS groups II: HI distribution, mass functions and HI deficient galaxies

We investigate the neutral hydrogen (HI) content of sixteen groups for which we have multi-wavelength data including X-ray observations. Wide-field imaging of the groups was obtained with the 20-cm multibeam system on the 64-m Parkes telescope. We have detected ten previously uncatalogued HI sources, one of which has no visible optical counterpart. We examine the HI properties of the groups, compared to their X-ray characteristics, finding that those groups with a higher X-ray temperature and luminosity contain less HI per galaxy. The HI content of a group depends on its morphological make-up, with those groups dominated by early-type galaxies containing the least total HI. We determined the expected HI for the spiral galaxies in the groups, and found that a number of the galaxies were HI deficient. The HI deficient spirals were found both in groups with and without a hot intra-group medium. The HI deficient galaxies were not necessarily found at the centre of the groups, however, we did find that two thirds of HI deficient galaxies were found within about 1 Mpc from the group centre, indicating that the group environment is affecting the gas-loss from these galaxies. We determined the HI mass function for a composite sample of 15 groups, and found that it is significantly flatter than the field HI mass function. We also find a lack of high HI-mass galaxies in groups. One possible cause of this effect is the tidal stripping of HI gas from spiral galaxies as they are pre-processed in groups.Comment: accepted for publication in MNRAS, 26 pages, 13 Figures, 2 Appendice