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On the Fibonacci Tiling and its Modern Ramifications 关于斐波那契平铺及其现代意义
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-04-12 DOI: 10.1002/ijch.202300155
Michael Baake, Franz Gähler, Jan Mazáč
{"title":"On the Fibonacci Tiling and its Modern Ramifications","authors":"Michael Baake, Franz Gähler, Jan Mazáč","doi":"10.1002/ijch.202300155","DOIUrl":"https://doi.org/10.1002/ijch.202300155","url":null,"abstract":"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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"229 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Canonical‐Cell Tilings and their Atomic Decorations 典型单元倾斜及其原子装饰
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-26 DOI: 10.1002/ijch.202300130
Nobuhisa Fujita, Marek Mihalkovič, Christopher L. Henley
{"title":"Canonical‐Cell Tilings and their Atomic Decorations","authors":"Nobuhisa Fujita, Marek Mihalkovič, Christopher L. Henley","doi":"10.1002/ijch.202300130","DOIUrl":"https://doi.org/10.1002/ijch.202300130","url":null,"abstract":"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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"72 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Tsai vs. Bergman Cluster Stability in ZnMgSc 1/1 Periodic Approximant Crystal ZnMgSc 1/1 周期近似晶体中的蔡氏与伯格曼簇稳定性
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-26 DOI: 10.1002/ijch.202300139
Ireneusz Buganski, Radoslaw Strzalka, Janusz Wolny
{"title":"The Tsai vs. Bergman Cluster Stability in ZnMgSc 1/1 Periodic Approximant Crystal","authors":"Ireneusz Buganski, Radoslaw Strzalka, Janusz Wolny","doi":"10.1002/ijch.202300139","DOIUrl":"https://doi.org/10.1002/ijch.202300139","url":null,"abstract":"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<jats:sub>84.79</jats:sub>Mg<jats:sub>0.86</jats:sub>Sc<jats:sub>14.35</jats:sub> 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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"32 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140311064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Approximations of Symbolic Substitution Systems in One Dimension 一维符号替换系统的近似值
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-22 DOI: 10.1002/ijch.202300121
Lior Tenenbaum
{"title":"Approximations of Symbolic Substitution Systems in One Dimension","authors":"Lior Tenenbaum","doi":"10.1002/ijch.202300121","DOIUrl":"https://doi.org/10.1002/ijch.202300121","url":null,"abstract":"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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"368 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140203997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Non-Canonical Amino Acids for Engineering Peptides and Proteins with new Functions 用于制造具有新功能的多肽和蛋白质的非标准氨基酸
IF 2.3 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-21 DOI: 10.1002/ijch.202400006
Kelly Zhi Qi Zhou, Richard Obexer
{"title":"Non-Canonical Amino Acids for Engineering Peptides and Proteins with new Functions","authors":"Kelly Zhi Qi Zhou,&nbsp;Richard Obexer","doi":"10.1002/ijch.202400006","DOIUrl":"10.1002/ijch.202400006","url":null,"abstract":"<p>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 <i>in vivo</i> and <i>in vitro</i> 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 <i>in vivo</i> and <i>in vitro</i> systems and their subsequent use for engineering of peptides and proteins with new functions. <i>In vivo</i> 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. <i>In vitro</i> 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 <i>in vitro</i> selection techniques, have emerged as powerful tools for expanding the functional capabilities of peptides and proteins.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140204339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent Advances in Non-Standard Macrocyclic Peptide Ligand Discovery using mRNA Display 利用 mRNA 显示发现非标准大环肽配体的最新进展
IF 2.3 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-13 DOI: 10.1002/ijch.202300167
Yizhen Yin, Christopher John Hipolito
{"title":"Recent Advances in Non-Standard Macrocyclic Peptide Ligand Discovery using mRNA Display","authors":"Yizhen Yin,&nbsp;Christopher John Hipolito","doi":"10.1002/ijch.202300167","DOIUrl":"10.1002/ijch.202300167","url":null,"abstract":"<p>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 <i>in vitro</i> 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.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modulating the Acceptor Preference of His-C-Geranyltransferase LimF 调节 His-C-Geranyl 转移酶 LimF 的受体偏好
IF 2.3 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-12 DOI: 10.1002/ijch.202300182
Yuchen Zhang, Yuki Goto, Hiroaki Suga
{"title":"Modulating the Acceptor Preference of His-C-Geranyltransferase LimF","authors":"Yuchen Zhang,&nbsp;Yuki Goto,&nbsp;Hiroaki Suga","doi":"10.1002/ijch.202300182","DOIUrl":"10.1002/ijch.202300182","url":null,"abstract":"<p>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-<i>C</i>-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.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140126971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Transthyretin Protein and Amyloidosis – an Extraordinary Chemical Biology Platform 转甲状腺素蛋白与淀粉样变性--非同寻常的化学生物学平台
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-06 DOI: 10.1002/ijch.202300164
Per Hammarström
{"title":"The Transthyretin Protein and Amyloidosis – an Extraordinary Chemical Biology Platform","authors":"Per Hammarström","doi":"10.1002/ijch.202300164","DOIUrl":"https://doi.org/10.1002/ijch.202300164","url":null,"abstract":"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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"274 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140057323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deamination- or N-Nitrosation-Based Methods for m6A Profiling 基于脱氨基或 N-亚硝基的 m6A 分析方法
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-03-04 DOI: 10.1002/ijch.202300180
Weiguo Shen, Jing Wang
{"title":"Deamination- or N-Nitrosation-Based Methods for m6A Profiling","authors":"Weiguo Shen,&nbsp;Jing Wang","doi":"10.1002/ijch.202300180","DOIUrl":"10.1002/ijch.202300180","url":null,"abstract":"<p>The addition of various chemical modifications to RNA introduces an additional layer of complexity to the regulation of gene expression. Among all RNA modifications, <i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A) has earned its status as the most abundant and well-studied post-transcriptional modification in mammalian mRNA. Nevertheless, understanding the role of m<sup>6</sup>A 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 m<sup>6</sup>A 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 m<sup>6</sup>A detection, GLORI showcases the promise of nitrite-based approaches. This review provides a comprehensive overview of m<sup>6</sup>A detection techniques based on deamination or nitrosation, evaluating their strengths and limitations. Furthermore, we offer insights into the future directions of innovative approaches in m<sup>6</sup>A profiling.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140033037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
RNA-Guided RNA Pseudouridylation and 2’-O-Methylation RNA 引导的 RNA 伪尿苷化和 2'-O 甲基化
IF 3.2 4区 化学
Israel Journal of Chemistry Pub Date : 2024-02-27 DOI: 10.1002/ijch.202400005
Hironori Adachi, Jonathan L. Chen, W.-Matthias Leeder, Pedro Morais, Yi-Tao Yu
{"title":"RNA-Guided RNA Pseudouridylation and 2’-O-Methylation","authors":"Hironori Adachi,&nbsp;Jonathan L. Chen,&nbsp;W.-Matthias Leeder,&nbsp;Pedro Morais,&nbsp;Yi-Tao Yu","doi":"10.1002/ijch.202400005","DOIUrl":"10.1002/ijch.202400005","url":null,"abstract":"<p>RNA-guided RNA modifications, including pseudouridylation and 2′-O-methylation, are naturally occurring processes that introduce pseudouridines (Ψ) and 2’-O-methylated residues (2’-O−Me) into various types of RNA. This modification is orchestrated by two distinct families of ribonucleoprotein complexes: Box H/ACA RNP and Box C/D RNP. Each complex comprises a unique guide (g)RNA (Box H/ACA gRNA or Box C/D gRNA) and a set of core proteins responsible for pseudouridylation and 2’-O-methylation, respectively. The specificity of these modifications is conferred by base-pairing of Box H/ACA gRNA and Box C/D gRNA with their RNA substrates. Here, we discuss the mechanism and function of RNA-guided pseudouridylation and 2’-O-methylation.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139987577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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