Ligand requirements for glmS ribozyme self-cleavage

Natural RNA catalysts (ribozymes) perform essential reactions in biological RNA processing and protein synthesis, whereby catalysis is intrinsic to RNA structure alone or in combination with metal ion cofactors. The recently discovered glmS ribozyme is unique in that it functions as a glucosamine-6-phosphate (GlcN6P)-dependent catalyst believed to enable "riboswitch" regulation of amino-sugar biosynthesis in certain prokaryotes. However, it is unclear whether GlcN6P functions as an effector or coenzyme to promote ribozyme self-cleavage. Herein, we demonstrate that ligand is absolutely requisite for glmS ribozyme self-cleavage activity. Furthermore, catalysis both requires and is dependent upon the acid dissociation constant (pKa) of the amine functionality of GlcN6P and related compounds. The data demonstrate that ligand is integral to catalysis, consistent with a coenzyme role for GlcN6P and illustrating an expanded capacity for biological RNA catalysis.     

Simple efficient synthesis of LTB4 and 12-epi-LTB4

Using L-and D-arabinose respectively as the source of chirality at C-12 in LTB₄, efficient new syntheses of LTB₄ and 12-epi-LTB₄ have been realized.     

Proton affinity of β-oxalylaminoalanine (BOAA): Incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.     

Structure of a de novo designed protein model of radical enzymes

The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.     

Electron and nuclear dynamics of molecular clusters in ultraintense laser fields. I. Extreme multielectron ionization

In this paper we present a theoretical and computational study of extreme multielectron ionization (involving the stripping of all the electrons from light, first-row atoms, and the production of heavily charged ions, e.g., Xe(+q) (q< or =36) from heavy atoms) in elemental and molecular clusters of Xe(n),(D(2))(n), and (CD(4))(n) (n=55-1061) in ultraintense (intensity I=10(15)-10(19) W cm(-2)) laser fields. Single atom or molecule multielectron ionization can be adequately described by the semiclassical barrier suppression ionization (BSI) mechanism. Extreme cluster multielectron ionization is distinct from that of a single atomic or molecular species in terms of the mechanisms, the ionization level and the time scales for electron dynamics and for nuclear motion. The novel compound mechanism of cluster multielectron ionization, which applies when the cluster size (radius R(0)) considerably exceeds the barrier distance for the BSI of a single constituent, involves a sequential-parallel, inner-outer ionization. The cluster inner ionization driven by the BSI for the constituents is induced by a composite field consisting of the laser field and inner fields. The energetics and dynamics of the system consisting of high energy (< or =3 keV) electrons and of less, similar 100 keV ions in the laser field was treated by molecular dynamics simulations, which incorporate electron-electron, electron-ion, ion-ion, and charge-laser interactions. High-energy electron dynamics also incorporates relativistic effects and includes magnetic field effects. We treat inner ionization considering inner field ignition, screening and fluctuation contributions as well as small [(< or =13%)] impact ionization contributions. Subsequent to inner ionization a charged nanoplasma is contained within the cluster, whose response to the composite (laser+inner) field results in outer ionization, which can be approximately described by an entire cluster barrier suppression ionization mechanism.     

Studies on the substrate specificity of Escherichia coli galactokinase

In vitro glycorandomization (IVG) technology is dependent upon the ability to rapidly synthesize sugar phosphates. Compared with chemical synthesis, enzymatic (kinase) routes to sugar phosphates would be attractive for this application. This work focuses upon the development of a high-throughput colorimetric galactokinase (GalK) assay and its application toward probing the substrate specificity and kinetic parameters of Escherichia coli GalK. The demonstrated dinitrosalicylic assay should also be generally applicable to a variety of sugar-processing enzymes. [reaction: see text]     

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.     

Electron transfer dissociation of peptide anions

Ion/ion reactions of multiply deprotonated peptide anions with xenon radical cations result in electron abstraction to generate charge-reduced peptide anions containing a free-radical site. Peptide backbone cleavage then occurs by hydrogen radical abstraction from a backbone amide N to facilitate cleavage of the adjacent C-C bond, thereby producing a- and x-type product ions. Introduction of free-radical sites to multiply charged peptides allows access to new fragmentation pathways that are otherwise too costly (e. g., lowers activation energies). Further, ion/ion chemistry, namely electron transfer reactions, presents a rapid and efficient means of generating odd-electron multiply charged peptides; these reactions can be used for studying gas-phase chemistries and for peptide sequence analysis.     

Directly visualizing carrier transport and recombination at individual defects within 2D semiconductors

Two-dimensional semiconductors (2DSCs) are promising materials for a wide range of optoelectronic applications. While the fabrication of 2DSCs with thicknesses down to the monolayer limit has been demonstrated through a variety of routes, a robust understanding of carrier transport within these materials is needed to guide the rational design of improved practical devices. In particular, the influence of different types of structural defects on transport is critical, but difficult to interrogate experimentally. Here, a new approach to visualizing carrier transport within 2DSCs, Carrier Generation-Tip Collection Scanning Electrochemical Cell Microscopy (CG-TC SECCM), is described which is capable of providing information at the single-defect level. In this approach, carriers are locally generated within a material using a focused light source and detected as they drive photoelectrochemical reactions at a spatially-offset electrolyte interface created through contact with a pipet-based probe, allowing carrier transport across well-defined, µm-scale paths within a material to be directly interrogated. The efficacy of this approach is demonstrated through studies of minority carrier transport within mechanically-exfoliated n-type WSe₂ nanosheets. CG-TC SECCM imaging experiments carried out within pristine basal planes revealed highly anisotropic hole transport, with in-plane and out-of-plane hole diffusion lengths of 2.8 µm and 5.8 nm, respectively. Experiments were also carried out to probe recombination across individual step edge defects within n-WSe₂ which suggest a significant surface charge (∼5 mC m⁻²) exists at these defects, significantly influencing carrier transport. Together, these studies demonstrate a powerful new approach to visualizing carrier transport and recombination within 2DSCs, down to the single-defect level.

Probe-based electrochemical techniques can be used to map carrier transport and recombination within two-dimensional semiconductors.