Israel Journal of Chemistry最新文献

N⁶-methyladenosine (m⁶A) is the most abundant internal modification in mammalian messenger RNA (mRNA), constituting 0.1 %–0.4 % of total adenosine residues in the transcriptome. m⁶A regulates mRNA stability and translation, pre-mRNA splicing, miRNA biogenesis, lncRNA binding, and many other physiological and pathological processes. While the majority of m⁶As occur in a consensus motif of DRm⁶ACH (D=A/G/U, R=A/G, H=U/A/C), the presence of such a motif does not guarantee methylation. Different RNA copies transcribed from the same gene may be methylated to varying levels. Within a single transcript, m⁶As are not evenly distributed, showing an enrichment in long internal and terminal exons. These characteristics of m⁶A deposition call for sequencing methods that not only pinpoint m⁶A sites at base resolution, but also quantitate the abundance of methylation across different RNA copies. In this review, we summarize existing m⁶A profiling methods, with an emphasis on next generation sequencing-(NGS−)based, site-specific, and quantitative methods, as well as several emerging single-cell methods.

In the last 30 years, the mathematical theory of aperiodic order has developed enormously. Many new tilings and properties have been discovered, few of which are covered or anticipated by the early papers and books. Here, we start from the well-known Fibonacci chain to explain some of them, with pointers to various generalisations as well as to higher-dimensional phenomena and results. This should give some entry points to the modern literature on the subject.

The canonical cell tiling is a geometrical framework that uses four kinds of basic polyhedra, called the canonical cells, to model the packing of atoms and clusters in icosahedral quasicrystals and related periodic approximants. Over the past three decades, it has become increasingly clear that this framework is the most sensible approach to describe related structures, albeit technically much less tractable than the Ammann-Kramer-Neri tiling, which is the simplest icosahedral tiling geometry based on the two Ammann rhombohedra. Geometrical arrangements of cells pose a number of combinatorial problems that cannot be handled using simple linear algebra, making it infeasible to determine structures using the standard six-dimensional scheme. This up-to-date review begins with the motivation, definition, and mathematical facts about the canonical cell tiling. Then the reader is taken through the zoo of concrete structures, from smaller periodic approximants to larger ones, along with an overview of the techniques and heuristics used to study them. The recent discovery of a quasiperiodic canonical cell tiling is also briefly illustrated. The latter half of this review surveys the atomistic modeling of real atomic structures in all the three existing structural families based on the decoration concept of the canonical cell tiling.

Quasicrystals with icosahedral symmetry can be classified into two main groups: Bergman-type and Tsai-type. While these are considered as distinct phases, they share a common feature of being constructed from atomic clusters, either Tsai or Bergman. In this study, we employ Density Functional Theory to perform electronic structure calculations on the Zn_84.79Mg_0.86Sc_14.35 periodic approximant crystal phase. Our investigation involves systematically displacing atoms from Tsai cluster sites to Bergman cluster sites, allowing us to explore modifications in the electronic structure. Our findings reveal that the stability of the phase is influenced by the interaction between Zn-4p and Sc-3d orbitals. We observe that the sp-d hybridization effect may play a more crucial role rather than Hume-Rothery stabilization, as this observation holds true regardless of the presence or absence of periodic boundary conditions. Notably, the additional atom present in the Tsai structure serves as a significant electron acceptor in low-energy orbitals. Its absence in Bergman structures results in a composition with fewer atoms possessing high-energy d orbitals. This discovery provides a rationale for the frequent occurrence of Bergman phases with transition metals or rare earth elements, which occupy less than 10 % of the sites in the structure.

Periodic approximations of quasicrystals are a powerful tool in analyzing spectra of Schrödinger operators arising from quasicrystals, given the known theory for periodic crystals. Namely, we seek periodic operators whose spectra approximate the spectrum of the limiting operator (of the quasicrystal). This naturally leads to study the convergence of the underlying dynamical systems.

We treat dynamical systems which are based on one-dimensional substitutions. We first find natural candidates of dynamical subsystems to approximate the substitution dynamical system. Subsequently, we offer a characterization of their convergence and provide estimates for the rate of convergence. We apply the proposed theory to some guiding examples.

The universal genetic code, which specifies the 20 standard amino acids (AAs), forms the basis for all natural proteins. Researchers have developed efficient and robust in vivo and in vitro strategies to overcome the constraints of the genetic code to expand the repertoire of AA building blocks that can be ribosomally incorporated into proteins. This review summarizes the development of these in vivo and in vitro systems and their subsequent use for engineering of peptides and proteins with new functions. In vivo genetic code expansion employing engineered othogonal tRNA/aaRS pairs has led to the development of proteins that selectively bind small molecules, cleave nucleic acids and catalyze non-natural chemical transformations. In vitro genetic code reprogramming using Flexizymes coupled with mRNA display has resulted in potent macrocyclic peptides that selectively bind to therapeutically important proteins. Through these examples, we hope to illustrate how genetic code expansion and reprogramming, especially when coupled with directed evolution or in vitro selection techniques, have emerged as powerful tools for expanding the functional capabilities of peptides and proteins.

Advancements in platform technologies have facilitated the production of libraries consisting of macrocyclic peptides composed of natural and non-canonical amino acids for more drug-like characteristics. Identification of macrocyclic peptide ligands against targets of interest can be accomplished using mRNA display. Despite numerous successful in vitro selections for macrocyclic peptide ligands against extracellular targets, identifying macrocyclic peptide hits that can reach intracellular targets continue to be a challenge. Breakthroughs in defining the features of a macrocyclic peptide that promote cell permeability have recently been disclosed. Here, we review the successful selections of non-standard macrocyclic peptide ligands using mRNA display in the last five years and chemical optimization of a drug-like macrocyclic peptide ligand for targeting intracellular KRAS.

Lipidation stands as a pivotal strategy for enhancing the metabolic stability of target peptides. Prenyltransferases in cyanobactin biosynthesis have garnered significant attention as potential peptide lipidation biocatalysts because of their exceptional regio- and chemoselectivity. However, these enzymes often exhibit a biased preference for certain acceptor substrates, requiring specific amino acids adjacent to the modifying residue. In this study, we demonstrate the structure-guided engineering of LimF, a His-C-geranyltransferase, to broaden its peptide substrate tolerance. By altering key residues in the peptide-binding pocket, we created a LimF variant capable of modifying sequence motifs previously inaccessible to the wildtype enzyme. The variant successfully modified some previously unfavored sequence motifs in artificial peptide substrates and bioactive peptide agents, validating the engineered substrate scope. With the discovery of novel peptide prenyltransferases, this approach would lead to a more comprehensive toolbox of peptide prenylation biocatalysts.

The amyloidoses are diseases caused by accumulation of amyloid fibrils from over 40 different human misfolded proteins in various organs of the body depending on precursor protein. Amyloidogenesis is a self-perpetuating reaction with deleterious consequences causing degeneration in cells and organs where depositions occur. Transthyretin, TTR, is an amyloidogenic protein causing sporadic disease from the wild-type protein during aging and from numerous different autosomal dominant familial mutations at earlier ages depending on the sequence of the hereditary variant. Until recently the disease process was poorly understood, and therapies were scarce. Over the past decades, spurred by clinical data, using chemical biology research, the mechanisms of TTR production and misfolding have been elucidated affording almost complete coverage of the TTR amyloidogenesis pathway to be targeted. This translational science success has provided a plethora of therapeutic options for the TTR amyloidoses providing an inspiring example for success in previously intractable diseases.

The addition of various chemical modifications to RNA introduces an additional layer of complexity to the regulation of gene expression. Among all RNA modifications, N⁶-methyladenosine (m⁶A) has earned its status as the most abundant and well-studied post-transcriptional modification in mammalian mRNA. Nevertheless, understanding the role of m⁶A in shaping the fate of RNA molecules and its influence on gene expression heavily depends on the development and application of detection technologies. Among all m⁶A detection methods, chemical-based sequencing methods show unique advantages. Our group recently developed an absolute quantification method named GLORI, which employs nitrite and glyoxal to convert adenosine to inosine efficiently. With its potential to emerge as the gold standard for m⁶A detection, GLORI showcases the promise of nitrite-based approaches. This review provides a comprehensive overview of m⁶A detection techniques based on deamination or nitrosation, evaluating their strengths and limitations. Furthermore, we offer insights into the future directions of innovative approaches in m⁶A profiling.