The Folding Mechanism of Barstar: Evidence for Multiple Pathways and Multiple Intermediates

The mechanism of folding of the small protein barstar in the pre-transition zone at pH 7, 25 degrees C has been characterized using rapid mixing techniques. Earlier studies had established the validity of the three-state U-S reversible arrow U-F reversible arrow N mechanism for folding and unfolding in the presence of guanidine hydrochloride (GdnHCl) at concentrations greater than 2.0 M, where U-S and U-F are the slow-refolding and fast-refolding unfolded forms, respectively, and N is the fully folded form. It is now shown that early intermediates, I-S1 and I-S2 as well as a late native-like intermediate, I-N, are present on the folding pathways of U-S, and an early intermediate I-F1 on the folding pathway of U-F, when bars tar is refolded in concentrations of GdnHCl below 2.0 M. The rates of formation and disappearance of I-N, and the rates of formation of N at three different concentrations of GdnHCl in the pre-transition zone have been measured. The data indicate that in 1.5 M GdnHCl, I-N is not fully populated on the U-S --> I-S1 --> I-N --> N pathway because the rate of its formation is so slow that the U-S reversible arrow U-F reversible arrow N pathway can effectively compete with that pathway. In 1.0 M GdnHCl, the U-S --> I-S1 --> I-N transition is so fast that I-N is fully populated. In 0.6 M GdnHCl, I-N appears not to be fully populated because an alternative folding pathway, U-S --> I-S2 --> N, becomes available for the folding of U-S, in addition to the U-S --> I-S1 --> I-N --> N pathway Measurement of the binding of the hydrophobic dye 1-anilino-8-naphthalenesulphonate (ANS) during folding indicates that ANS binds to two distinct intermediates, I-M1 and I-M2, that form within 2 ms on the U-S --> I-M1 --> I-S1 --> I-N --> N and U-S --> I-M2 --> I-S2 --> N pathways. There is no evidence for the accumulation of intermediates that can bind ANS on the folding pathway of U-F.

Is O-1(2) alone sufficient for DNA cleavage? Possible involvement of paramagnetic intermediates

It is proposed that singlet dioxygen reacting with guanosine or deoxyguanosine part of nucleotides does not, by itself, cause DNA cleavage. The strand break originates at the endoperoxide stage whenever this link evolves into a O-centered radical. The O-centered radical is then in a good spatial position to abstract an hydrogen intramolecularly from the ribose or desoxyribose part of the nucleotide. The carbon centered radical thus formed on the sugar part may lead to strand break either by a p-scission mechanism or by an homolytically induced solvolysis. High pH could also induce cleavage after the endoperoxide stage via a base catalyzed ring chain protomerism.

Photogenerated radical intermediates of vitamin K-1: a time-resolved resonance Raman study

Quinones play a vital role in the process of electron transfer in bacterial photosynthetic reaction centers. It is of interest to investigate the photochemical reactions involving quinones with a view to elucidating the structure-function relationships in the biological processes. Resonance Raman spectra of radical anions and the time-resolved resonance Raman spectra of vitamin K-1 (model compound for Q(A) in Rhodopseudomonas viridis, a bacterial photosynthetic reception center) are presented. The photochemical intermediates of vitamin K-1, viz. radical anion, ketyl radical and o-quinone methide have been identified. The vibrational assignments of all these intermediates are made on the basis of comparison with our earlier TR3 studies on radical anions of naphthoquinone and menaquinone. (C) 1999 Elsevier Science B.V. All rights reserved.

A method for the calculation of the adsorbed phase volume and pseudo-saturation pressure from adsorption isotherm data on activated carbon

We propose a new method for evaluating the adsorbed phase volume during physisorption of several gases on activated carbon specimens. We treat the adsorbed phase as another equilibrium phase which satisfies the Gibbs equation and hence assume that the law of rectilinear diameters is applicable. Since invariably the bulk gas phase densities are known along measured isotherms, the constants of the adsorbed phase volume can be regressed from the experimental data. We take the Dubinin-Astakhov isotherm as the model for verifying our hypothesis since it is one of the few equations that accounts for adsorbed phase volume changes. In addition, the pseudo-saturation pressure in the supercritical region is calculated by letting the index of the temperature term in Dubinin's equation to be temperature dependent. Based on over 50 combinations of activated carbons and adsorbates (nitrogen, oxygen, argon, carbon dioxide, hydrocarbons and halocarbon refrigerants) it is observed that the proposed changes fit experimental data quite well.

Time-Resolved Resonance Raman Spectroscopy: Exploring Reactive Intermediates

The study of reaction mechanisms involves systematic investigations of the correlation between structure, reactivity, and time. The challenge is to be able to observe the chemical changes undergone by reactants as they change into products via one or several intermediates such as electronic excited states (singlet and triplet), radicals, radical ions, carbocations, carbanions, carbenes, nitrenes, nitrinium ions, etc. The vast array of intermediates and timescales means there is no single ``do-it-all'' technique. The simultaneous advances in contemporary time-resolved Raman spectroscopic techniques and computational methods have done much towards visualizing molecular fingerprint snapshots of the reactive intermediates in the microsecond to femtosecond time domain. Raman spectroscopy and its sensitive counterpart resonance Raman spectroscopy have been well proven as means for determining molecular structure, chemical bonding, reactivity, and dynamics of short-lived intermediates in solution phase and are advantageous in comparison to commonly used time-resolved absorption and emission spectroscopy. Today time-resolved Raman spectroscopy is a mature technique; its development owes much to the advent of pulsed tunable lasers, highly efficient spectrometers, and high speed, highly sensitive multichannel detectors able to collect a complete spectrum. This review article will provide a brief chronological development of the experimental setup and demonstrate how experimentalists have conquered numerous challenges to obtain background-free (removing fluorescence), intense, and highly spectrally resolved Raman spectra in the nanosecond to microsecond (ns-mu s) and picosecond (ps) time domains and, perhaps surprisingly, laid the foundations for new techniques such as spatially offset Raman spectroscopy.

Filling Characteristics for an Activated Carbon Based Adsorbed Natural Gas Storage System

The storage capacity of an activated carbon bed is studied using a 2D transport model with constant inlet flow conditions. The predicted filling times and variation in bed pressure and temperature are in good agreement with experimental observations obtained using a 1.82 L prototype ANG storage cylinder. Storage efficiencies based on the maximum achievable V/V (volume of gas/volume of container) and filling times are used to quantify the performance of the charging process. For the high permeability beds used in the experiments, storage efficiencies are controlled by the rate of heat removal. Filling times, defined as the time at which the bed pressure reaches 3.5 MPa, range from 120 to 3.4 min for inlet flow rates of 1.0 L min(-1) and 30.0 L min(-1), respectively. The corresponding storage efficiencies, eta(s), vary from 90% to 76%, respectively. Simulations with L/D ratios ranging from 0.35 to 7.8 indicate that the storage efficiencies can be improved with an increase in the LID ratios and/or with water cooled convection. Thus for an inlet flow rate of 30.0 L min(-1), an eta(s) value of 90% can be obtained with water cooling for an L/D ratio of 7.8 and a filling time of a few minutes. In the absence of water cooling the eta(s) value reduces to 83% at the same L/D ratio. Our study suggests that with an appropriate choice of cylinder dimensions, solutions based on convective cooling during adsorptive storage are possible with some compromise in the storage capacity.

Enhanced Raman Spectroscopy of Molecules Adsorbed on Carbon-Doped TiO2 Obtained from Titanium Carbide: A Visible-Light-Assisted Renewable Substrate

Titanium carbide (TiC) is an electrically conducting material with favorable electrochemical properties. In the present studies, carbon-doped TiO2 (C-TiO2) has been synthesized from TiC particles, as well as TiC films coated on stainless steel substrate via thermal annealing under various conditions. Several C-TiO2 substrates are synthesized by varying experimental, conditions and characterized by UV-visible spectroscopy, photoluminescence, X-ray diffraction and X-ray photoelectron spectroscopic techniques. C-TiO2 in the dry state (in powder form as well as in film form) is subsequently used as a substrate for enhancing Raman signals corresponding to 4-mercaptobenzoic acid and 4-nitrothiophenol by utilizing chemical enhancement based on charge-transfer interactions. Carbon, a nonmetal dopant in TiO2, improves the intensities of Raman signals, compared, to undoped TiO2. Significant dependence of Raman intensity on carbon doping is observed. Ameliorated performance obtained using C-TiO2 is attributed to the presence of surface defects that originate due to carbon as a dopant, which, in turn,, triggers charge transfer between TiO2 and analyte. The C-TiO2 substrates are subsequently regenerated for repetitive use by illuminating an analyte-adsorbed substrate with visible light for a period of 5 h.

Effect of Interfacial Microstructure of Adsorbed Poly(ethylene glycol) Monooleate on Steel Substrate on Sliding Friction in Oil in Water Emulsion

The concentration of a nonionic surfactant and water pH were varied in an oil-in-water emulsion to minimize the friction coefficient between a steel ball sliding on a steel flat. At a surfactant concentration near the CMC (critical micelle concentration) the oil droplet size was found to be minimum. In this paper we study the microstructure of the surfactant molecules self-assembled on the steel substrate in water to comment on the ability of the surfactant aggregate to attract and retain oil. We find that a near semicylindrical hemimiceller microstructure with hydrocarbon tails projecting into bulk water as obtained at CMC in near neutral water is best able to capture and retain oil in yielding a low coefficient of friction.

Improvement in Bone Properties by Using Risedronate Adsorbed Hydroxyapatite Novel Nanoparticle Based Formulation in a Rat Model of Osteoporosis

A superior drug formulation capable of achieving efficient osteogenesis is in imperative demand for the treatment of osteoporosis. In the present study we investigated the potential of using novel risedronate-hydroxyapatite (HA) nanoparticle based formulation in an animal model of established osteoporosis. Nanoparticles of HA loaded with risedronate (NHLR) of various sizes (80-130 nm) were generated for bone targeted drug delivery. Three months after ovariectomy, 36 ovariectomized (OVX) rats were divided into 6 equal groups and treated with various doses of NHLR (500,350 and 250 mu g/kg intravenous single dose) and sodium risedronate (500 mu g/kg, intravenous single dose). Untreated OVX and sham OVX served as controls. One month after drug administration, the left tibia and femur were tested for bone mechanical properties and histology, respectively. In the right femur, bone density was measured by method based on Archimedes principle and bone porosity analyses were performed using X-ray imaging. NHLR (250 mu g/kg) showed a significant increase in bone density and reduced bone porosity when compared with OVX control. Moreover, NHLR (250 mu g/kg) significantly increased bone mechanical properties and bone quality when compared with OVX control. The results strongly suggest that the NHLR, which is a novel nanoparticle based formulation, has a therapeutic advantage over risedronate sodium monotherapy for the treatment of osteoporosis in a rat model of postmenopausal osteoporosis.

Processing of DNA double-stranded breaks and intermediates of recombination and repair by saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single-over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.

Selenium adsorption on Au(111) and Ag(111) surfaces: adsorbed selenium and selenide films

Results of a high resolution photoemission and electrochemistry study of Se adsorption Au(111) and Ag(111) surfaces performed by immersion of pristine samples into an aqeuous solution of Na2Se are presented. Cyclic voltammetry on Au shows formation of selenium adsorbed species and the structures observed in reductive desorption are to the atomic and polymeric species observed in XPS. In the case of Au(111) XPS spectra in the Se(3d) region indeed show two main features attributed to Se chemisorbed atomically and polymeric Se-8 features.' Smaller structures due to other types of Se conformations were also observed. The Au(4f) peak line, shape does not show core level, shifts: indicative of Au selenide formation the case of silver, XPS spectra for the Ag(3d) show a broadening of the peak and a deconvolution into Ag-B bulk like Ag-Se components shows that the Ag-Se is located at a lower binding energy, an effect similar to oxidation and sulfidation of Ag. The Se(3d) XPS spectrum is found to be substantially different from the Au case and dominated by atomic type Se due to the selenide, though a smaller intensity Se structure at an energy similar to the Se-8 structure for Au is also observed. Changes in the valence band region. related to Se adsorption are reported.

Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.