United States Department of Energy

About: United States Department of Energy is a government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topics: Catalysis & Coal. The organization has 13656 authors who have published 14177 publications receiving 556962 citations. The organization is also known as: DOE & Department of Energy.

Multiple native states reveal persistent ruggedness of an RNA folding landscape

Abstract: Just as the funnel hypothesis is used to describe protein folding, it has been suggested that the process of RNA folding involves a rugged energy terrain in which the molecule samples different valleys until it finds the single lowest-energy state — the global minimum. In this study, Solomatin et al. report the surprising finding that a group I intron RNA can stably exist in one of several catalytically active native states (representing local minima). These RNA conformations are able to interconvert, which promises interesting new avenues of study to determine how this occurs, and how the different native states vary at the molecular level. The 'thermodynamic hypothesis' proposes that the sequence of a biological macromolecule defines its folded, active structure as a global energy minimum in the folding landscape; however, it is not clear whether there is only one global minimum or several local minima corresponding to active conformations. Here, using single-molecule experiments, an RNA enzyme is shown to fold into multiple distinct native states that interconvert. According to the ‘thermodynamic hypothesis’, the sequence of a biological macromolecule defines its folded, active (or ‘native’) structure as a global energy minimum in the folding landscape1,2. However, the enormous complexity of folding landscapes of large macromolecules raises the question of whether there is in fact a unique global minimum corresponding to a unique native conformation or whether there are deep local minima corresponding to alternative active conformations3. The folding of many proteins is well described by two-state models, leading to highly simplified representations of protein folding landscapes with a single native conformation4,5. Nevertheless, accumulating experimental evidence suggests a more complex topology of folding landscapes with multiple active conformations that can take seconds or longer to interconvert6,7,8. Here we demonstrate, using single-molecule experiments, that an RNA enzyme folds into multiple distinct native states that interconvert on a timescale much longer than that of catalysis. These data demonstrate that severe ruggedness of RNA folding landscapes extends into conformational space occupied by native conformations.

Gene family encoding the major toxins of lethal Amanita mushrooms

Abstract: Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode alpha-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. alpha-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable "toxin" region capable of encoding a wide variety of peptides of 7-10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes.

Labeled gold nanoparticles immobilized at smooth metallic substrates: systematic investigation of surface plasmon resonance and surface-enhanced Raman scattering.

Abstract: This paper experimentally and theoretically investigates the influence of an underlying metallic substrate (ie, gold and silver) on the surface plasmon resonance (SPR) of labeled gold nanoparticles and the concomitant impact on the surface-enhanced Raman scattering (SERS) signal from the labels These experiments employ nanoparticles of varied sizes (30-100 nm) that are coated with a bifunctional Raman scatterer composed of (1) a disulfide for chemisorption to the nanoparticle surface, (2) a succinimidyl ester for formation of a covalent linkage to an amine-terminated self-assembled monolayer on the underlying substrate, and (3) an aryl nitro group with an intrinsically strong Raman active vibrational mode This approach allows facile systematic assessments of how variations in nanoparticle size, substrate composition, and the gap between the nanoparticle and substrate affect the SPR of the bound particles Both UV-vis transmission and reflection absorption (incident angle of 58 degrees ) spectroscopy are used to characterize the effect of each of these parameters on SPR These results are then correlated with SERS enhancement factors (EFs) that were determined by accounting for particle surface concentrations, which were measured by atomic force microscopy, and the absolute number of labels, which were calculated on the basis of the surface area of each of the different-sized particles All SERS spectra were collected at an incident angle of 58 degrees with respect to the surface normal As expected, the SPR for particles in solution red-shifts with increasing particle size More importantly, the SPR moves to even longer wavelengths as the size of immobilized particles increases and as the gap between the immobilized particle and substrate decreases The red shift is also greater for a gold nanoparticle tethered to a gold substrate compared to a silver substrate A theoretical model for the extinction of a particle above a flat substrate, corrected for surface scattering, radiation damping, and dynamic depolarization, is also briefly detailed SPR results calculated with the model are consistent with the shifts observed in the SPR position for each of the manipulated experimental variables The largest EFs are found for samples with an SPR maximum (lambda(max)) between the wavelengths for laser excitation (633 nm) and the Raman band for the symmetric nitro stretch of the particle coating (690 nm) As an example, an order of magnitude in the SERS enhancement factor is gained for a 60-nm particle immobilized 12 nm above a gold substrate (SPR lambda(max) = 657 nm) compared to that for a 30-nm particle (SPR lambda(max) = 596 nm)