Nature Of Preferences Research Articles

Exploring a unique class of flavoenzymes: Identification and biochemical characterization of ribosomal RNA dihydrouridine synthase

Dihydrouridine (D), a prevalent and evolutionarily conserved base in the transcriptome, primarily resides in tRNAs and, to a lesser extent, in mRNAs. Notably, this modification is found at position 2449 in the Escherichia coli 23S rRNA, strategically positioned near the ribosome's peptidyl transferase site. Despite the prior identification, in E. coli genome, of three dihydrouridine synthases (DUS), a set of NADPH and FMN-dependent enzymes known for introducing D in tRNAs and mRNAs, characterization of the enzyme responsible for D2449 deposition has remained elusive. This study introduces a rapid method for detecting D in rRNA, involving reverse transcriptase-blockage at the rhodamine-labeled D2449 site, followed by PCR amplification (RhoRT-PCR). Through analysis of rRNA from diverse E. coli strains, harboring chromosomal or single-gene deletions, we pinpoint the yhiN gene as the ribosomal dihydrouridine synthase, now designated as RdsA. Biochemical characterizations uncovered RdsA as a unique class of flavoenzymes, dependent on FAD and NADH, with a complex structural topology. In vitro assays demonstrated that RdsA dihydrouridylates a short rRNA transcript mimicking the local structure of the peptidyl transferase site. This suggests an early introduction of this modification before ribosome assembly. Phylogenetic studies unveiled the widespread distribution of the yhiN gene in the bacterial kingdom, emphasizing the conservation of rRNA dihydrouridylation. In a broader context, these findings underscore nature's preference for utilizing reduced flavin in the reduction of uridines and their derivatives.

A Highly Reactive Oxoiron(IV) Complex Supported by a Bioinspired N3 O Macrocyclic Ligand.

The sluggish oxidants [FeIV (O)(TMC)(CH3 CN)]2+ (TMC=1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) and [FeIV (O)(TMCN-d12 )(OTf)]+ (TMCN-d12 =1,4,7,11-tetra(methyl-d3 )-1,4,7,11-tetraazacyclotetradecane) are transformed into the highly reactive oxidant [FeIV (O)(TMCO)(OTf)]+ (1; TMCO=4,8,12-trimethyl-1-oxa-4,8,12-triazacyclotetradecane) upon replacement of an NMe donor in the TMC and TMCN ligands by an O atom. A rate enhancement of five to six orders of magnitude in both H atom and O atom transfer reactions was observed upon oxygen incorporation into the macrocyclic ligand. This finding was explained in terms of the higher electrophilicity of the iron center and the higher availability of the more reactive S=2 state in 1. This rationalizes nature's preference for using O-rich ligand environments for the hydroxylation of strong C-H bonds in enzymatic reactions.

A Highly Reactive Oxoiron(IV) Complex Supported by a Bioinspired N3O Macrocyclic Ligand

AbstractThe sluggish oxidants [FeIV(O)(TMC)(CH3CN)]2+ (TMC=1,4,8,11‐tetramethyl‐1,4,8,11‐tetraazacyclotetradecane) and [FeIV(O)(TMCN‐d12)(OTf)]+ (TMCN‐d12=1,4,7,11‐tetra(methyl‐d3)‐1,4,7,11‐tetraazacyclotetradecane) are transformed into the highly reactive oxidant [FeIV(O)(TMCO)(OTf)]+ (1; TMCO=4,8,12‐trimethyl‐1‐oxa‐4,8,12‐triazacyclotetradecane) upon replacement of an NMe donor in the TMC and TMCN ligands by an O atom. A rate enhancement of five to six orders of magnitude in both H atom and O atom transfer reactions was observed upon oxygen incorporation into the macrocyclic ligand. This finding was explained in terms of the higher electrophilicity of the iron center and the higher availability of the more reactive S=2 state in 1. This rationalizes nature's preference for using O‐rich ligand environments for the hydroxylation of strong C−H bonds in enzymatic reactions.

Understanding information and computation: from Einstein to Web science

Contents: Foreword, Yorick Wilks Foreword. L.J. Rich Preface Introduction Dot-to-dots point the way Hitler, Turing and quantum mechanics A different perspective on numbers, straight lines and other such mathematical curiosities Twists, turns and nature's preference for curves Curves of curves To process or not? Information and computation as a field Why are conic sections important? The gifts that Newton gave, Turing opened and which no chapter one has really appreciated yet Einstein's torch bearers Special relativity General relativity Beyond the fourth dimension Time to reformulate with a little help from information retrieval research Supporting evidence Where does this get us? References Index.

X‐Ray Structures of Copper(II) and Nickel(II) Radical Salen Complexes: The Preference of Galactose Oxidase for Copper(II)

Copper or nickel? The depicted CuII salen complex, an active-site model of galactose oxidase (GO), is a localized radical in the solid state with a quinoid distribution of bond lengths in one ring. While the ligand-radical structure is not metal-dependent, the composition of the radical SOMO is. This feature may explain the much lower reactivity of the Ni complex and nature's preference for a CuII center in GO.

Cation−π Interactions with a Model for the Side Chain of Tryptophan: Structures and Absolute Binding Energies of Alkali Metal Cation−Indole Complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.