Sam Coates, Akihisa Koga, Toranosuke Matsubara, Ryuji Tamura, Hem Raj Sharma, Ronan McGrath, Ron Lifshitz
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.
{"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":null,"pages":null},"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}
Genetic code expansion aims to incorporate non‐canonical amino acids (ncAAs) into biological systems, enhancing protein functionality or enabling the in vitro 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 in vitro and in vivo. In vivo, 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. In vitro 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.
{"title":"Breaking the Degeneracy of Sense Codons – How Far Can We Go?","authors":"Clark A. Jones, Matthew C. T. Hartman","doi":"10.1002/ijch.202400026","DOIUrl":"https://doi.org/10.1002/ijch.202400026","url":null,"abstract":"Genetic code expansion aims to incorporate non‐canonical amino acids (ncAAs) into biological systems, enhancing protein functionality or enabling the in vitro 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 in vitro and in vivo. In vivo, 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. In vitro 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.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.]