Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Studies on the exchange of gramicidin in liposomes

The exchange of gramicidin between liposomes made of two different kinds of phospholipids has been studied using a fluorescent probe (pyranine). The experimentally observed rate of exchange is compared with that of nigericin, which is a simple carrier. Possible reasons for the difference in the rate of exchange are discussed and probable mechanisms suggested. It is proposed that gramicidin exchanges between vesicles by a contact mechanism.     

Palladium-catalyzed substitution reactions of 4-allylimidazole derivatives

In the context of synthetic studies toward the oroidin family of pyrrole-imidazole alkaloids, we required an efficient method for conducting substitution reactions of allylic alcohols derived from urocanic acid. While in some cases this could be accomplished quite readily by classical nucleophilic substitution, it was complicated by allylic transposition in others. Application of Pd-catalyzed π-allyl chemistry provided a convenient solution, giving substitution without allylic transposition. Herein we describe the scope of this reaction in imidazole-containing substrates, and the elaboration of one adduct into a homologated histidine derivative, and into a cyclic homohistidine derivative.     

Correlation analysis of reactivity in the reduction of Co(en)2Br2+ by Fe(CN)64– in water–methanol/1,4-dioxane media

The reduction of [Co(en)₂Br₂]⁺ by [Fe(CN)₆]^4– in H₂O–MeOH and H₂O–1,4-dioxane mixtures has been studied over a range of solvent compositions [5–30% (v/v)]. The reduction of [Co(en)₂Br₂]⁺ was monitored under second order conditions and was found to be rapid in the various solvent compositions investigated. The favoured mechanism is an outer-sphere electron-transfer process consisting of elementary steps, ion-pair formation (K _IP), electron-transfer (k _et) and successor dissociation. Therefore, the overall rate constant, k ₂ = K _IP k _et[Co(en)₂- Br₂ ⁺][Fe(CN)₆ ^4–]. The rates increase as the proportion of organic cosolvent increases. The rates correlate with solvent properties, such as relative permittivity (_r) and the Grunwald–Winstein parameter, Y _GW, which are used to explain the non-specific interaction upon solvation of mixture of solvents on the incipient reactants and on the ion-pair. In addition, they are also subjected to multiparametric analysis employing Swain's solvent vectors A and B also with Kamlet–Taft's solvatochromic parameters , and *. The reduction rates show an excellent correlation with multiparametric equations and are susceptible to both specific and non-specific solvation effects. A quantitative estimation of the latter components has been attempted.     

Elucidation of Binding Mechanism of Photodynamic Therapeutic Agent Toluidine Blue O with Chicken Egg White Lysozyme by Spectroscopic and Molecular Dynamics Studies

The nature of binding mechanism of toluidine blue O (TBO) with chicken egg white lysozyme was studied comprehensively by various spectroscopic and computational methods. Both steady state and time‐resolved fluorescence studies unambiguously point to the prevalence of static quenching mechanism in lysozyme–TBO system. Thermodynamic parameters revealed that the association of TBO with lysozyme was a spontaneous process in which hydrophobic and hydrogen bond interactions played a pivotal role in the binding process. The secondary and tertiary conformational changes of lysozyme in the presence of TBO were unraveled using absorption, Fourier transform infrared spectroscopy (FT‐IR) and circular dichroism (CD) techniques. Molecular docking studies of lysozyme–TBO system substantiated the findings of site marker experiment and revealed TBO adjacent to Trp‐63 and Trp‐108 residues of lysozyme. Molecular dynamics (MD) simulation studies of lysozyme–TBO system indicate a stable and effective complexation of TBO with lysozyme. It is hoped that the results presented here will enable further understanding of TBO toxicity.     

Enhanced photocatalytic activity of Cu-doped ZnO nanorods

Cu-doped ZnO nanorods with different Cu concentrations were synthesized through the vapor transport method. The synthesized nanorods were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM) and UV–vis spectroscopy. The XRD results revealed that Cu was successfully doped into ZnO lattice. The FE-SEM images showed that the undoped ZnO has needle like morphology whereas Cu-doped ZnO samples have rod like morphology with an average diameter and length of 60–90 nm and 1.5–3 μm respectively. The red shift in band edge absorption peak in UV-vis absorbance spectrum with increasing Cu content also confirm the doping of Cu in ZnO nanorods. The photocatalytic activity of pure and Cu-doped ZnO samples was studied by the photodegradation of resazurin (Rz) dye. Both pure ZnO and the Cu-doped ZnO nanorods effectively removed the Rz in a short time. This photodegradation of Rz followed the pseudo-first-order reaction kinetics. ZnO nanorods with increasing Cu doping exhibit enhanced photocatalytic activity. The pseudo-first-order reaction rate constant for 15 % Cu-doped ZnO is equal to 10.17×10^?2min^?1 about double of that with pure ZnO. The increased photocatalytic activity of Cu-doped ZnO is attributed to intrinsic oxygen vacancies due to high surface to volume ratio in nanorods and extrinsic defect due to Cu doping.     

Elimination of autofluorescence background from fluorescence tissue images by use of time-gated detection and the AzaDiOxaTriAngulenium (ADOTA) fluorophore

Sample autofluorescence (fluorescence of inherent components of tissue and fixative-induced fluorescence) is a significant problem in direct imaging of molecular processes in biological samples. A large variety of naturally occurring fluorescent components in tissue results in broad emission that overlaps the emission of typical fluorescent dyes used for tissue labeling. In addition, autofluorescence is characterized by complex fluorescence intensity decay composed of multiple components whose lifetimes range from sub-nanoseconds to a few nanoseconds. For these reasons, the real fluorescence signal of the probe is difficult to separate from the unwanted autofluorescence. Here we present a method for reducing the autofluorescence problem by utilizing an azadioxatriangulenium (ADOTA) dye with a fluorescence lifetime of approximately 15 ns, much longer than those of most of the components of autofluorescence. A probe with such a long lifetime enables us to use time-gated intensity imaging to separate the signal of the targeting dye from the autofluorescence. We have shown experimentally that by discarding photons detected within the first 20 ns of the excitation pulse, the signal-to-background ratio is improved fivefold. This time-gating eliminates over 96 % of autofluorescence. Analysis using a variable time-gate may enable quantitative determination of the bound probe without the contributions from the background.     

Frequency dependence of phase-synchronization time in nonlinear dynamical systems

It has been found recently that the averaged phase-synchronization time between the input and the output signals of a nonlinear dynamical system can exhibit an extremely high sensitivity to variations in the noise level. In real-world signal-processing applications, sensitivity to frequency variations may be of considerable interest. Here we investigate the dependence of the averaged phase-synchronization time on frequency of the input signal. Our finding is that, for typical nonlinear oscillator systems, there can be a frequency regime where the time exhibits significant sensitivity to frequency variations. We obtain an analytic formula to quantify the frequency dependence, provide numerical support, and present experimental evidence from a simple nonlinear circuit system.