The Role of β-Glycosylated Wall Teichoic Acids in the Reduction of Vancomycin Susceptibility in Vancomycin-Intermediate Staphylococcus aureus.

Staphylococcus aureus is an opportunistic pathogen that causes a wide range of infections. Due to the rapid evolution of antibiotic resistance that leads to treatment failure, it is important to understand the underlying mechanisms. Here, the cell wall structures of several laboratory vancomycin-intermediate S.

High-affinity binding and catalytic activity of His/Tyr-based sequences: Extending heme-regulatory motifs beyond CP.

Background & Motivation: Peptides and proteins can interact with heme through His, Tyr, or Cys in heme-regulatory motifs (HRMs). The Cys-Pro dipeptide is a well investigated HRM, but for His and Tyr such a distinct motif is currently unknown. In addition, many heme-peptide complexes, such as heme-amyloid β, can display a peroxidase-like activity, albeit there is little understanding of how the local primary and secondary coordination environment influences catalytic activity.

Styrene Polymerization under Ambient Conditions by using a Transient 1,3,2-Diazaphospholane-2-oxyl Complex.

A combined theoretical and experimental study on the formation and reactivity of a P-OTEMP (P-bound TEMPO (TEMPO=2,2,6,6-tetramethyl-piperidin-1-oxyl)) substituted 1,3,2-diazaphospholane W(CO) complex is presented, including DFT-based mechanistic details. The complex possesses a thermally labile O-N bond that cleaves homolytically yielding the transient 1,3,2-diazaphospholane-2-oxyl complex [(CO) W(R PO )], which acts as a radical initiator for styrene polymerization under ambient conditions.

The 5'-AG CC-3' Fragment from the Human CPEB3 Ribozyme Forms an Ultrastable Parallel RNA G-Quadruplex.

An unusually thermostable G-quadruplex is formed by a sequence fragment of a naturally occurring ribozyme, the human CPEB3 ribozyme. Strong evidence is provided for the formation of a uniquely stable intermolecular G-quadruplex structure consisting of five tetrad layers, by using CD spectroscopy, UV melting curves, 2D NMR spectroscopy, and gel shift analysis. The cationic porphyrin TMPyP4 destabilizes the complex.

Synthesis and Rearrangement of P-Nitroxyl-Substituted P(III) and P(V) Phosphanes: A Combined Experimental and Theoretical Case Study.

Low-temperature generation of P-nitroxyl phosphane 2 (Ph2 POTEMP), which was obtained by the reaction of Ph2 PH (1) with two equivalents of TEMPO, is presented. Upon warming, phosphane 2 decomposed to give P-nitroxyl phosphane P-oxide 3 (Ph2 P(O)OTEMP) as one of the final products. This facile synthetic protocol also enabled access to P-sulfide and P-borane derivatives 7 and 13, respectively, by using Ph2 P(S)H (6) or Ph2 P(BH3 )H (11) and TEMPO.

Multiple conformational states of riboswitches fine-tune gene regulation.

Riboswitches are structured regions of mRNAs that modulate gene expression in response to specific binding of low molecular-weight ligands. They function by induced transitions between different functional conformations. The standard model assumed that the two functional states, the ligand-bound and ligand-free state, populated only two stable conformations.

The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain.

We report here an in-depth characterization of the aptamer domain of the transcriptional adenine-sensing riboswitch (pbuE) by NMR and fluorescence spectroscopy. By NMR studies, the structure of two aptamer sequences with different lengths of the helix P1, the central element involved in riboswitch conformational switching, was characterized. Hydrogen-bond interactions could be mapped at nucleotide resolution providing information about secondary and tertiary structure, structure homogeneity and dynamics.

Three-state mechanism couples ligand and temperature sensing in riboswitches.

Riboswitches are cis-acting gene-regulatory RNA elements that can function at the level of transcription, translation and RNA cleavage. The commonly accepted molecular mechanism for riboswitch function proposes a ligand-dependent conformational switch between two mutually exclusive states. According to this mechanism, ligand binding to an aptamer domain induces an allosteric conformational switch of an expression platform, leading to activation or repression of ligand-related gene expression.

Quantitative 2D and 3D Gamma-HCP experiments for the determination of the angles alpha and zeta in the phosphodiester backbone of oligonucleotides.

The quantitative Gamma-(HCP) experiment, a novel heteronuclear NMR pulse sequence for the determination of the RNA backbone angles alpha(O3'(i-1)-P(i)-O5'(i)-C5'(i)) and zeta(C3'(i)-O3'(i)-P(i+1)-O5'(i+1)) in (13)C-labeled RNA, is introduced. The experiment relies on the interaction between the CH bond vector dipole and the (31)P chemical shift anisotropy (CSA), which affects the relaxation of the (13)C,(31)P double- and zero-quantum coherence and thus the intensity of the detectable magnetization. With the new pulse sequence, five different cross-correlated relaxation rates along the phosphodiester backbone can be measured in a quantitative manner, allowing projection-angle and torsion-angle restraints for the two backbone angles alpha and zeta to be extracted.

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.

We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.

RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis.

We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample.