Article
Biochemical Research Methods
Daniela S. Strugach, Dagan Hadar, Miriam Amiram
Summary: This study found a photoswitch with suitable light-responsive properties that can be incorporated into proteins, enabling light-responsive behavior. The method allows for multisite incorporation of the photoswitch at the polypeptide level, providing a general approach for designing proteins and polymers with robust light-responsive behavior.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Genetics & Heredity
Ruifang Li, Hong Li, Xue Feng, Ruifeng Zhao, Yongxia Cheng
Summary: The study analyzed the relationship between the vocabulary and phraseology parameters of mRNA sequences and protein folding rates, finding that D-2 and GC content values are negatively correlated with protein folding rates, while D-1 values are positively correlated. The relationships between genetic language parameters and protein folding rates are different for different protein groups, providing new insights for predicting protein folding rates.
FRONTIERS IN GENETICS
(2021)
Article
Polymer Science
Winnie H. Shi, Rohan S. Adhikari, Dilipkumar N. Asthagiri, Amanda B. Marciel
Summary: We studied the influence of charge block length on the structure and behavior of polyampholyte chains using SAXS and molecular simulations. By synthesizing polyampholytes with different lengths of glutamic acid and lysine blocks, we found that longer blocks tend to induce phase separation. The addition of NaCl affected the phase behavior in a manner dependent on the charge block length. Our findings suggest the importance of electrostatic interactions and hydrogen bonding in phase separation and offer insights for intracellular condensates and material design.
Article
Polymer Science
Winnie H. Shi, Rohan S. Adhikari, Dilipkumar N. Asthagiri, Amanda B. Marciel
Summary: In this study, the effect of charge block length on the conformation and phase behavior of polyampholyte chains was investigated using small-angle X-ray scattering (SAXS) and molecular simulations. The results showed that as the block size increased, the polyampholyte chains tended to phase separate. The addition of NaCl resulted in a salting-in effect in the phase separated polyampholytes, which was dependent on the charge block length. Fourier-transform infrared (FTIR) spectroscopy revealed the disruption of intramolecular hydrogen bonds upon the addition of NaCl, indicating the involvement of electrostatic interactions and hydrogen bonding in the phase behavior. SAXS spectra showed minimal dependence of charge block length on the radius of gyration (Rg) for soluble polyampholytes under no-added salt conditions, but local chain stiffening was found to be dependent on charge block length. With increasing NaCl, all polyampholytes expanded and behaved as neutral or swollen chains in good solvent conditions, consistent with electrostatic screening. Molecular simulations were in qualitative agreement with the experiments. The implications of this study for understanding intracellular condensates and material design were also highlighted.
Review
Chemistry, Multidisciplinary
Andreas Kirschning
Summary: This report focuses on the prebiotic and metabolic aspects of amino acids and proteins, as well as the major biosynthetic pathways. Coenzymes play a key role in amino acid metabolism, being linked to glycolysis and the tricarboxylic acid cycle. Thus, the report provides additional insights into the molecular evolution of primary metabolism.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Multidisciplinary Sciences
Wesley E. Robertson, Louise F. H. Funke, Daniel de la Torre, Julius Fredens, Thomas S. Elliott, Martin Spinck, Yonka Christova, Daniele Cervettini, Franz L. Boge, Kim C. Liu, Salvador Buse, Sarah Maslen, George P. C. Salmond, Jason W. Chin
Summary: By deleting tRNAs in cells through experimental compression and evolution, these cells became completely resistant to viruses and were unable to read the canonical genetic code. By reassigning codons, the cells were able to efficiently synthesize proteins containing different noncanonical amino acids. Additionally, the cells were successfully reprogrammed to translate diverse noncanonical heteropolymers and macrocycles.
Editorial Material
Chemistry, Multidisciplinary
Mirren F. M. White, Stephen Wallace
Summary: The discovery and engineering of new plastic degrading enzymes is crucial for the transition to a more sustainable and circular plastics economy. Recent research has reported the discovery of a novel PET hydrolase from human saliva metagenome, which shows improved properties and performance over previous PETases. The study also demonstrates the incorporation of a photocaged unnatural amino acid, enabling covalent binding to the PET surface, highlighting the potential of metagenomic datasets and genetic code expansion for new biotechnologies in the circular plastics economy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Applied
Shuangqi Tian, Ke Du, Feng Yan, Yongheng Li
Summary: This study compared the hydrolysis effects of different enzymes on wheat germ albumin (WGA) and found that papain exhibited the best proteolytic activity. Papain hydrolysis led to increased solubility of WGA, while apparent viscosity and foam stability decreased. Additionally, the proportions of certain amino acids in the enzymatic hydrolysis products were altered.
Article
Biochemistry & Molecular Biology
Konrad Pawlak, Pawel Blazej, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Synonymous codon usage is influenced by mutations and selection at both the nucleotide and amino acid levels. The proposed mutation-selection model demonstrates that the selection of amino acids based on physicochemical properties can result in biases in codon usage. Alternative genetic codes tend to exhibit greater codon bias than the standard genetic code, and the mutational pressures on cytosine and guanine content further affect usage bias. The study emphasizes the importance of considering amino acid selection in understanding codon usage patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Muhammad Usman Sadiq, Stephanie Langella, Kelly S. Giovanello, Peter J. Mucha, Eran Dayan
Summary: Functional network redundancy shows a significant association with age over the human lifespan, with a stronger link than other major topological measures. The accumulation of redundancy in midlife followed by a decline in old age mediates the association between age and executive function, suggesting that functional redundancy plays a role in mitigating the effects of age on cognition.
Article
Quantum Science & Technology
Zihan Lei
Summary: This article introduces the definitions of the given topological hypermap H through the complementary hypermaps H-Delta and H-del of the ordinary dual hypermap H-*, as well as their edge hypermap quantum codes C-Delta and C-del. Then it proves that when there is a natural relationship between the sets of special darts, the duality between the two ordinary hypermap quantum codes, i.e., C from H and C-* from H-*, can be simplified to the duality between C-Delta and C-del.
QUANTUM INFORMATION PROCESSING
(2023)
Article
Neurosciences
Christian Quaia, Incheol Kang, Bruce G. Cumming
Summary: Direction selective neurons in macaque primary visual cortex are narrowly tuned for orientation, but are affected by the aperture problem. In the middle temporal (MT) area, some cells are able to solve this problem and respond to pattern motion direction. This study shows that a pattern motion signal is present at the population level, revealing the diversity of single-cell responses.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Chanhee Lee, Young-Bum Kim, Hyesung Ji, Yeonsoo Lee, Yuna Hur, Heuiseok Lim
Summary: The paper examines the redundancy in the ranks of neural network parameters and introduces a regularization method to reduce it, resulting in significant improvements in training dynamics and fewer trainable parameters. Experimental results confirm the efficacy of the proposed approach, showcasing a substantial increase in accuracy and speedup in training steps, as well as a reduction in network size by 30.65%.
APPLIED SCIENCES-BASEL
(2021)
Article
Biotechnology & Applied Microbiology
Osher Gueta, Ortal Sheinenzon, Rotem Azulay, Hadas Shalit, Daniela S. Strugach, Dagan Hadar, Sigal Gelkop, Anat Milo, Miriam Amiram
Summary: The incorporation of non-canonical amino acids using engineered aminoacyl-tRNA synthetases allows for the expansion of the chemical repertoire of proteins. This study identified high-performance aaRS variants that enable efficient multi-site incorporation of different aromatic ncAAs. It also demonstrated the impact of aromatic ncAAs on the properties and functions of protein-based polymers, providing insight for the design of new polymers with improved properties.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Pharmacology & Pharmacy
Dimitra Stavroulaki, Iro Kyroglou, Dimitrios Skourtis, Varvara Athanasiou, Pandora Thimi, Sosanna Sofianopoulou, Diana Kazaryan, Panagiota G. Fragouli, Andromahi Labrianidou, Konstantinos Dimas, Georgios Patias, David M. Haddleton, Hermis Iatrou
Summary: This study presents the synthesis of novel hybrid block copolypeptides based on PEO, PHis, and PCys, which self-assemble into micellar structures in aqueous media. The topology of PCys significantly influences the structure and release profile of the nanoparticles. The nanoparticles show pH and redox responsiveness and have potential for drug delivery applications.