Israel Journal of Chemistry最新文献

{"title":"Cover Picture: (Isr. J. Chem. 8-9/2024)","authors":"","doi":"10.1002/ijch.202480801","DOIUrl":"https://doi.org/10.1002/ijch.202480801","url":null,"abstract":"<p>The cover art depicts the RNA catalyst ‘flexizyme’ based on its three-dimensional structure. It attaches a yellow sphere representing a non-canonical amino acid onto a tRNA, which is shown as a classical two-dimensional ‘cloverleaf’ representation. The catalyst is aided by two structural magnesium ions represented by small, darker red circles. Surrounding the flexizyme is a pool of acylated tRNA molecules and numerous macrocyclic peptides incorporating the non-canonical amino acids shown as colored circles.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480801","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328480","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}

{"title":"Special Issue on RNA-Based Catalysts that Revolutionized the Discovery of Bioactive Peptides","authors":"Assoc. Prof. Seino A. K. Jongkees,&nbsp;Assoc. Prof. Joseph M. Rogers,&nbsp;Dr. Louise J. Walport","doi":"10.1002/ijch.202400064","DOIUrl":"https://doi.org/10.1002/ijch.202400064","url":null,"abstract":"&lt;p&gt;This special issue of the &lt;i&gt;Israel Journal of Chemistry&lt;/i&gt; is in celebration of the Wolf Prize awarded to Hiroaki Suga in 2023 &lt;i&gt;“for pioneering discoveries that illuminate the functions and pathological dysfunctions of RNA and proteins and for creating strategies to harness the capabilities of these biopolymers in new ways to ameliorate human diseases”&lt;/i&gt;. In this issue we collect contributions from former trainees, collaborators, and beyond to profile how his work has impacted the fields of bioorganic chemistry, synthetic biology, and drug discovery. Focusing on his development of RNA-based aminoacylation catalysts, his share of the prize &lt;i&gt;“For developing RNA-based catalysts that revolutionized the discovery of bioactive peptides&lt;/i&gt;” is emphasised here in a collection of nine review articles and one research article that span aspects of oligonucleotide acylation catalysis, reprogramming of the genetic code, and applications of this in peptide drug discovery.&lt;/p&gt;&lt;p&gt;The RNA-based catalysts developed by Suga are called flexizymes. These were initially developed using the oligonucleotide selection platform ‘SELEX’ (systematic evolution of ligands by exponential enrichment). The &lt;i&gt;in vitro&lt;/i&gt; selection scheme was designed to select for self-acylating activity by evolving a 5’ extension on tRNA, mimicking a key step in a potential transition between RNA-based life and modern protein-dominant life. RNA molecules that were able to attach a biotinylated amino acid to their own 3’ end were enriched by streptavidin pull-down, connecting survival to catalytic activity. After several more selection campaigns aiming to improve the level of activity and scope of the 5’ extension to independently aminoacylate added tRNA in &lt;i&gt;trans&lt;/i&gt;, the modern flexizymes eFx, dFx, and aFx were born (discussed in detail in several reviews elsewhere).&lt;span&gt;&lt;sup&gt;1, 2&lt;/sup&gt;&lt;/span&gt; While this work began in fundamental biochemistry, the practical applications of a catalyst that is largely agnostic about which amino acid it attaches to which tRNA soon became apparent. However, as outlined in the contribution by &lt;b&gt;Cho, Lee, and coworkers&lt;/b&gt;,&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; an understanding of the precise working of flexizymes at the molecular level is still lacking. While a crystal structure of the oligonucleotide has been available for some time,&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; the amino acid component is poorly resolved and so this leaves open questions about the positioning of the substrate ester and contributions of nucleotides in the catalytic pocket. They describe attempts to profile the rules for design of good flexizyme substrates, and how this has expanded research into novel bio-based polymers. One consequence of having relatively easy access to tRNA acylated with amino acid-like non-canonical building blocks is the ease with which translational space could be explored, and this fed back into further fundamental insights into the translation process itself.&lt;/p&gt;&lt;p&gt;Flexizy","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142328457","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}

{"title":"Hexagonal and Trigonal Quasiperiodic Tilings","authors":"Sam Coates, Akihisa Koga, Toranosuke Matsubara, Ryuji Tamura, Hem Raj Sharma, Ronan McGrath, Ron Lifshitz","doi":"10.1002/ijch.202300100","DOIUrl":"https://doi.org/10.1002/ijch.202300100","url":null,"abstract":"Exploring nonminimal‐rank quasicrystals, which have symmetries that can be found in both periodic and aperiodic crystals, often provides new insight into the physical nature of aperiodic long‐range order in models that are easier to treat. Motivated by the prevalence of experimental systems exhibiting aperiodic long‐range order with hexagonal and trigonal symmetry, we introduce a generic two‐parameter family of 2‐dimensional quasiperiodic tilings with such symmetries. We focus on the special case of trigonal and hexagonal Fibonacci, or golden‐mean, tilings, analogous to the well studied square Fibonacci tiling. We first generate the tilings using a generalized version of de Bruijn's dual grid method. We then discuss their interpretation in terms of projections of a hypercubic lattice from six dimensional superspace. We conclude by concentrating on two of the hexagonal members of the family, and examining a few of their properties more closely, while providing a set of substitution rules for their generation.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"9 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203511","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}

{"title":"Breaking the Degeneracy of Sense Codons – How Far Can We Go?","authors":"Clark A. Jones,&nbsp;Matthew C. T. Hartman","doi":"10.1002/ijch.202400026","DOIUrl":"10.1002/ijch.202400026","url":null,"abstract":"<p>Genetic code expansion aims to incorporate non-canonical amino acids (ncAAs) into biological systems, enhancing protein functionality or enabling the <i>in vitro</i> selection of peptides from diverse mRNA displayed libraries. Typically, genetic code expansion has involved reassignment of stop codons to ncAAs through orthogonal translation systems. This review instead focuses on efforts to expand the genetic code by breaking the redundancy of sense codons <i>in vitro</i> and <i>in vivo. In vivo</i>, orthogonal aminoacyl-tRNA synthetase (AARS)/tRNA/AA systems are able to compete with endogenous machinery, enabling partial to full codon reassignment. Recent approaches, like genome recoding, offer potential solutions to reduce competition. <i>In vitro</i> studies utilize cell extract-based or reconstituted translation systems, allowing precise control of codon usage via gene design and tRNA addition, making breaking of sense degeneracy easier. In these systems several unsplit codon boxes have been successfully reassigned multiple to ncAAs. These efforts showcase both the successes and challenges in achieving orthogonality and selective codon decoding and point towards a future where the 64 codons can encode more than 30 monomers, enabling new advances in synthetic biology and drug discovery.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141939715","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}

{"title":"Cover Picture: (Isr. J. Chem. 6-7/2024)","authors":"","doi":"10.1002/ijch.202480601","DOIUrl":"10.1002/ijch.202480601","url":null,"abstract":"<p>The cover image shows amphiphilic calixarenes embedded in a phospholipid bilayer membrane. Anionic calixarenes facilitate counterion-mediated transport of positively charged peptides across said membranes highlighting the utility of amphiphilic calixarenes for peptide transport into liposome and for direct cytosolic delivery of charged molecules into cells, which still is a significant problem in the fields of biology and medicine. [the image refers to the article “Anionic Calixarenes in Biomembrane Transport of Peptides” by Justin Neumann and Andreas Hennig.]\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873446","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}

{"title":"Special Issue on Synthetic Host Molecules","authors":"Assist. Prof. Dr. Víctor García-López,&nbsp;Prof. Dr. Ofer Reany","doi":"10.1002/ijch.202400053","DOIUrl":"10.1002/ijch.202400053","url":null,"abstract":"&lt;p&gt;We are excited to introduce this special issue of the Israel Journal of Chemistry on &lt;i&gt;Synthetic Host Molecules&lt;/i&gt; to celebrate the remarkable progress of the field. Featuring eleven scientific reviews and research articles from leading scientists worldwide, the special issue on synthetic host molecules explores the latest advances in some of the host systems developed during the last decades.&lt;/p&gt;&lt;p&gt;This issue also commemorates the milestone of the Joint Conference on Calixarenes and Cucurbiturils (JCCC 2023), which merged the 17&lt;sup&gt;th&lt;/sup&gt; International Conference on Calixarenes (Calix 2023) and the 7&lt;sup&gt;th&lt;/sup&gt; International Conference on Cucurbiturils (ICCB 2023) in Tel Aviv in July 2023. This event offered a unique opportunity to unite experts from both subfields, fostering dialogues and collaborations. It was a particularly significant gathering after a hiatus caused by the COVID-19 pandemic, which had disrupted the individual meetings of each conference.&lt;/p&gt;&lt;p&gt;The field of synthetic host molecules originated in the ′60s when Charles J. Pedersen reported the first examples of crown ethers and their remarkable capabilities to bind alkali metal ions according to their cavity size and the metal radii. Shortly after, Jean-Marie Lehn developed cryptands, bicyclic crown ether compounds with higher selectivity. In 1979, Donald Cram introduced spherands, the first examples of synthetic hosts with complete preorganization, significantly reducing the energetic penalty associated with the reorganization and desolvation of crown ethers and cryptands. These groundbreaking contributions earned Pedersen, Lehn, and Cram the Nobel Prize in Chemistry in 1987, officially establishing the field of Supramolecular Chemistry.&lt;/p&gt;&lt;p&gt;Over the last four decades, the field has accelerated rapidly, developing numerous new classes of synthetic host molecules. These systems have evolved from molecules capable of binding organic and inorganic ions to advanced hosts with unique structural, catalytic, optoelectronic, magnetic, and transmembrane transport properties. They can selectively bind myriad organic and bioorganic molecules in diverse media, including water. As a result, these highly functional host molecules have found applications in various fields, including medicine, biotechnology, catalysis, chemical separation, data storage, polymer science, and nanotechnology. This progress has been made possible through interdisciplinary research that merges concepts from synthetic chemistry, physical organic chemistry, computational chemistry, biophysics, and state-of-the-art analytical techniques.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Prof. Pablo Ballester&lt;/b&gt; and &lt;b&gt;Dr. Gemma Aragay&lt;/b&gt; present an authoritative review on water-soluble aryl- and aryl-extended calix[4]pyrroles. They highlight their achievements over the last two decades to incorporate water-solubilizing groups, enhance the hydrophobic aromatic cavity, and reduce the conformational flexibility of calix[4]pyrroles, resulting in o","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873449","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}

{"title":"Cover Picture: (Isr. J. Chem. 5/2024)","authors":"","doi":"10.1002/ijch.202480501","DOIUrl":"https://doi.org/10.1002/ijch.202480501","url":null,"abstract":"<p>Chemical Biology of Nucleic Acid Modifications II Issue editor: Chun-Xiao Song, Guifang Jia, Seraphine Wegner, and Chengqi Yi. The cover picture highlights Chuan He's wide-ranging research contributions across chemical biology, nucleic acid chemistry, biology, and epigenetics. His work focused on understanding DNA and RNA modifications in gene regulation. His groundbreaking discovery of reversible RNA modification revealed a new mode of gene regulation by RNA alongside DNA — and protein-based epigenetic mechanisms, leading to the emergence of the epitranscriptomics field.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480501","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141488218","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}

{"title":"The 87th Annual Meeting of the Israel Chemical Society: April 3, 2024, Smolarz Auditorium, Tel Aviv University","authors":"Ehud Keinan","doi":"10.1002/ijch.202400041","DOIUrl":"https://doi.org/10.1002/ijch.202400041","url":null,"abstract":"","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141488229","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}

{"title":"To what Extent could Solid‐State Chemistry and Nanotechnology Impact Sustainable Lifestyle of Human being on Earth in the Years to Come","authors":"Reshef Tenne","doi":"10.1002/ijch.202300069","DOIUrl":"https://doi.org/10.1002/ijch.202300069","url":null,"abstract":"The lifestyle of mankind has improved significantly since the start of the industrial revolution and the establishment of a science (engineering)‐based society, some 250 years ago. Notwithstanding, the outcome of these advances, a major threat is looming on the future of humanity due to the greenhouse effect produced by fossil fuel effluents and the degradation of the environment on earth. Chemistry and chemical engineering are key players in confronting these challenges and establishing sustainable lifestyle on earth. In particular, the interplay between materials research; solid‐state chemistry and nanoscience (nanotechnology) will be crucial for the future of sustainable life on earth. Education of the population‐at‐large to shift from a consumer‐based society into sustainability‐concerned lifestyle, is mandatory for realization of this paradigm shift. Harmonizing the interplay between entrepreneurs, financing bodies, public agencies, international organizations, legal bodies and research institutes should also play an integral part of this new equation.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"36 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141512431","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}

{"title":"Regulatory Role of RNA N6-Methyladenosine Modification in Plants","authors":"Subiding Tayier,&nbsp;Enlin Tian,&nbsp;Guifang Jia","doi":"10.1002/ijch.202400029","DOIUrl":"https://doi.org/10.1002/ijch.202400029","url":null,"abstract":"<p><i>N</i>⁶-methyladenosine (m⁶A), as the most abundant and well-studied RNA modification, can be reversibly added or removed by m⁶A methyltransferase and demethylase. The further molecular and biological function of m⁶A is achieved by the recognition of its binding protein. m⁶A functions in the diverse progress of RNA processing, including transcription regulation, splicing, nuclear export, stability, and translation, to regulate the fate of cells. Although been extensively studied in various animal cell systems, research on m⁶A's regulatory functions in plant cells lags. In recent years, with a deepening understanding of the functions of m⁶A and the development of various sequencing technologies, researches on m⁶A in plant cells have gradually increased. In this review, we focused on discussing the molecular functions of m⁶A in the nucleus and cytoplasm, aiming to elucidate the specific molecular mechanisms by which m⁶A regulates the fate of RNAs in plants. Finally, we provide some perspectives on future investigations of the detailed molecular mechanism of m⁶A-mediated regulation in plants, which might provide insights into future strategies for achieving multiple growth regulatory processes in crops.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 5","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141488138","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}