Review
Biochemistry & Molecular Biology
Simona Notova, Anne Imberty
Summary: Lectins are glycan binding proteins that can decode the structure and function of complex glycans. They are used as biomarkers for monitoring glycosylation changes in diseases and have therapeutic applications. Manipulating lectin specificity and topology is crucial for improving their utility, and combining lectins with additional domains can provide novel functionalities. We discuss current strategies, particularly synthetic biology approaches, that enable the generation of lectins with enhanced specificity and novel applications in biotechnology or therapy.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Yitong Ma, Mark W. Budde, Junqin Zhu, Michael B. Elowitz
Summary: Methylation of cytosines in CG dinucleotides (CpGs) within promoters leads to gene silencing in mammals. Recent research has shown that the recruitment of methyltransferases (DNMTs) at specific loci can effectively silence gene expression. The distribution of CpGs within the target promoter plays a crucial role in DNA methylation-based silencing. This study found a strong correlation between silencing rate and CpG content, providing insights into the regulatory link between CpG content and gene silencing rate.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Oskar Staufer, Franziska Dietrich, Rahul Rimal, Martin Schroeter, Sebastian Fabritz, Heike Boehm, Smriti Singh, Martin Moeller, Ilia Platzman, Joachim Pius Spatz
Summary: Extracellular vesicles play a crucial role in intercellular communication and cell physiology, but quantitative knowledge on their signaling mechanisms is lacking, hampering their therapeutic applications. By using a synthetic approach, researchers have shown that synthetic EVs have functionalities similar to natural EVs and can be used for therapeutic purposes in wound healing and neovascularization. Transcriptome profiling has enabled a systematic decoding of synergistic effects between individual EV constituents, leading to a better understanding of EV signaling.
Review
Biochemistry & Molecular Biology
Zhi-Gang Qian, Sheng-Chen Huang, Xiao-Xia Xia
Summary: This article reviews the unique properties of protein condensates and discusses the prospects and challenges of utilizing them for targeted design and manipulation of biological functions. Recent advances in mining protein components and engineering approaches for creating and manipulating designer condensates are highlighted. These advances will have significant impacts on synthetic biology.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Andrew Lezia, Arianna Miano, Jeff Hasty
Summary: The design and construction of synthetic gene circuits have made significant progress, with applications in medicine, biosensing, and industrial chemical production. The focus has shifted from isolated circuits to complex systems, and design methods now include detailed models of host genome interaction with synthetic gene circuits.
PROCEEDINGS OF THE IEEE
(2022)
Article
Chemistry, Physical
J. Brandao, D. A. Dugato, M. V. Puydinger dos Santos, Fanny Beron, J. C. Cezar
Summary: This study demonstrates the observation of spin spirals and individual skyrmions in synthetic Pt/CoGd/Pt ferrimagnetic multilayers at room temperature. The stable skyrmions with antiparallel exchange-coupling have potential applications in energy-efficient data storage and processing.
APPLIED SURFACE SCIENCE
(2022)
Review
Biotechnology & Applied Microbiology
Kangsan Kim, Minjeong Kang, Byung-Kwan Cho
Summary: In recent years, there has been increasing interest in gut commensal engineering for therapeutic applications. Recent advancements in synthetic biology and systems biology have enabled effective utilization of gut commensals for therapy and diagnosis, including the rational design of synthetic microbial consortia and the construction of synthetic cells that can detect specific signals in the intestine and deliver therapeutic drugs in real-time.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Agnese Barbensi, Naya Yerolemou, Oliver Vipond, Barbara Mahler, Pawel Dabrowski-Tumanski, Dimos Goundaroulis
Summary: Understanding how knotted proteins fold is a challenging problem in biology, with researchers proposing different models for their folding pathways. Recent simulations show variations in folding behavior between deeply and shallow knotted proteins. Analyzing open-ended trefoil knot proteins using a topologically inspired metric allows researchers to probe different folding pathways based on the geometry and topology of their native states. Additionally, the folding pathway of shallow knotted proteins involves the creation of a double-looped structure, contrary to other observed trefoil proteins.
Review
Polymer Science
Auston L. L. Clemens, Buddhinie S. S. Jayathilake, John J. J. Karnes, Johanna J. J. Schwartz, Sarah E. E. Baker, Eric B. B. Duoss, James S. S. Oakdale
Summary: Alkaline anion exchange membranes (AAEMs) have the potential to reduce cost-per-device in electrochemical devices by enabling the use of non-platinum group electrodes. However, challenges remain in durability, water management, high temperature performance, and selectivity. This review surveys crosslinking as a tool to improve AAEM properties and discusses various synthetic methodologies for incorporating crosslinks during AAEM fabrication.
Article
Multidisciplinary Sciences
Xinqiang Ding, Xingcheng Lin, Bin Zhang
Summary: The study utilized a near-atomistic model to investigate the structure and dynamics of chromatin, revealing multiple pathways connecting chromatin configurations and influencing the in situ relevance of the 30 nm fiber.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Il-Soo Park, Seongchan Kim, Yeajee Yim, Ginam Park, Jinahn Choi, Cheolhee Won, Dal-Hee Min
Summary: This study reports the creation of a synthetic chaperone to control the folding of therapeutic peptides and demonstrates its enhanced therapeutic potential in a tumor model. The synthetic chaperone, based on porous nanoparticles, provides an internal hydrophobic environment which stabilizes the secondary structure of the encapsulated peptides. Additionally, the modified nanoparticles serve as a nanoreactor and effectively deliver the stabilized peptides into cancer cells, resulting in inhibition of cancer growth.
NATURE COMMUNICATIONS
(2022)
Review
Biotechnology & Applied Microbiology
Bhagyashree Bachhav, Jacopo de Rossi, Carlos D. Llanos, Laura Segatori
Summary: The production of high-quality recombinant proteins is crucial for the continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories faces limitations due to proteotoxic stress caused by abnormal accumulation of protein folding intermediates, leading to apoptosis. This review discusses advances in cell engineering, focusing on controlling the expression of recombinant proteins at various levels and highlights the opportunities to use synthetic biology tools for designing programmable cell factories for improved biomanufacturing of therapeutic proteins.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Chemistry, Physical
Antonio Domenech-Carbo, Ana Maria Costero, Salvador Gil, Noemi Montoya, Alejandro Lopez-Carrasco, Jose A. Saez, Pau Arroyo, Maria Teresa Domenech-Carbo
Summary: A new approach was presented for describing the composition of Maya blue, indicating that it results from the tautomerization of indigo to indigo hemienol and subsequent oxidation to dehydroindigo associated with the palygorskite clay framework at temperatures above 100 degrees C. Thermochemical parameters were obtained from various spectroscopic and electrochemical data to characterize the isomerization and redox tuning processes experienced by palygorskite-associated indigo.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Review
Biochemistry & Molecular Biology
Amit Kumar, Jochen Balbach
Summary: Ankyrin repeat proteins, found across all three domains of life, play a crucial role in protein-protein interactions to regulate biological processes. With a basic architecture of repeating modules forming elongated structures and lacking long-range interactions, these proteins exhibit graded stability, impacting both folding and biological functions. The conformational changes of these repeats act as molecular switches for biological regulation, making them versatile for modern drug discovery.
Article
Chemistry, Multidisciplinary
Karol Al Ayed, Ross D. Ballantine, Michael Hoekstra, Samantha J. Bann, Charlotte M. J. Wesseling, Alexander T. Bakker, Zheng Zhong, Yong-Xin Li, Nora C. Bruchle, Mario van der Stelt, Stephen A. Cochrane, Nathaniel I. Martin
Summary: Brevicidine and laterocidine are newly discovered lipopeptide antibiotics with promising antibacterial activity, and can be synthesized to access more samples and potentially provide new structural analogues. These antibiotics exhibit potent antibacterial activity against Gram-negative pathogens.
Article
Chemistry, Multidisciplinary
Huan Sun, Haiyang Jia, Diego A. Ramirez-Diaz, Nediljko Budisa, Petra Schwille
Summary: Mapping and elucidating molecular mechanisms of self-organization in prokaryotic cells using light-mediated assembly of functional protein modules is a promising strategy for creating minimal cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Federica Agostini, Ludwig Sinn, Daniel Petras, Christian J. Schipp, Vladimir Kubyshkin, Allison Ann Berger, Pieter C. Dorrestein, Juri Rappsilber, Nediljko Budisa, Beate Koksch
Summary: Organofluorine compounds are toxic to a variety of organisms, but some organisms (such as bacteria) can adapt to fluorinated molecules and utilize them for the synthesis of cellular macromolecules. Experiments with E. coli exposed to fluorinated amino acids revealed the cellular mechanisms behind adaptation to unnatural amino acids.
ACS CENTRAL SCIENCE
(2021)
Review
Chemistry, Organic
Vladimir Kubyshkin, Rebecca Davis, Nediljko Budisa
Summary: Fluorinated proline replacements, such as (4R)- and (4S)-fluoroproline, have shown advantages in elevating protein expression speed and yields, as well as improving folding profiles. They are considered useful tools in biotechnological applications and may potentially be used for proteome-wide proline-to-fluoroproline substitutions in the future. Furthermore, laboratory evolutionary methods with fluoroprolines could enable the introduction of fluorine into living cells, potentially creating synthetic cells with artificial biodiversity containing fluorine as a bioelement.
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Felix Tobola, Martin Lepsik, Syeda Rehana Zia, Hakon Leffler, Ulf J. Nilsson, Ola Blixt, Anne Imberty, Birgit Wiltschi
Summary: This study introduced non-canonical tryptophan analogues into the ligand binding site of Galectin-1 and found two variants with reduced affinity for certain sugars. Through fluorescence polarization competition assay and molecular modeling, the researchers provided structural clues for the changes in affinity.
Article
Biotechnology & Applied Microbiology
Karolina Haernvall, Patrik Fladischer, Heidemarie Schoeffmann, Sabine Zitzenbacher, Tea Pavkov-Keller, Karl Gruber, Michael Schick, Motonori Yamamoto, Andreas Kuenkel, Doris Ribitsch, Georg M. Guebitz, Birgit Wiltschi
Summary: Environmentally friendly functionalization and recycling processes for synthetic polymers have gained momentum recently, with enzymes playing a crucial role. This study demonstrates that by engineering the amino acid composition of enzymes, their activity towards synthetic polyesters can be enhanced. The findings highlight the potential of non-canonical amino acids for enzyme engineering and provide new insights for the recycling of synthetic polymers using enzymes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Benoit Snella, Benjamin Grain, Jerome Vicogne, Frederic Capet, Birgit Wiltschi, Oleg Melnyk, Vangelis Agouridas
Summary: Latent oxalyl thioester surrogates are a powerful tool for modifying peptides and proteins in diluted conditions. They are designed to be stable and can be activated on demand for ligation reactions with peptide concentrations as low as a few hundred nM at high rates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Hsueh-Wei Tseng, Marcus Moldenhauer, Thomas Friedrich, Eugene G. Maksimov, Nediljko Budisa
Summary: Orange Carotenoid Protein (OCP) is a water-soluble photoreceptor involved in photoprotection of cyanobacteria. By replacing essential residues of the photoactive OCP with non-canonical aromatic analogues, the key contacts with non-canonical amino acids can be controlled and manipulated, altering the state preference of OCP.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Katharina N. Schwaiger, Alena Voit, Birgit Wiltschi, Bernd Nidetzky
Summary: This study successfully integrated cellodextrin phosphorylase into a cellobiose-producing whole-cell catalyst. The coordinated co-expression of the three enzymes balanced their activities, resulting in maximized production of soluble cello-oligosaccharides.
MICROBIAL CELL FACTORIES
(2022)
Article
Multidisciplinary Sciences
Huan Sun, Haiyang Jia, Olivia Kendall, Jovan Dragelj, Vladimir Kubyshkin, Tobias Baumann, Maria-Andrea Mroginski, Petra Schwille, Nediljko Budisa
Summary: In this study, the authors investigated the halogenation of the prokaryotic cell division protein FtsZ and demonstrated its effects on protein structure and dynamics. They provided valuable insights into the mechanism of halogen influence through experiments and theories.
NATURE COMMUNICATIONS
(2022)
Review
Biotechnology & Applied Microbiology
Felix Tobola, Birgit Wiltschi
Summary: Carbohydrates play a crucial role in encoding biological information and functions, while lectins act as key binding molecules to translate this encoded information. Researchers have altered the binding sites of lectins, changing their affinity, avidity, specificity, and biological efficacy, leading to improvements in biotechnological exploitation and potential medical applications.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Biochemistry & Molecular Biology
Toshiki Takei, Hideaki Tanaka, Nobuaki Okumura, Toshifumi Takao, Luis Moroder, Hironobu Hojo
Summary: In this study, a polypeptide containing three diselenide bonds was synthesized and compared to its cysteine analog in terms of oxidative folding. The results showed that the substitution of disulfide bonds with diselenide bonds is highly isomorphous.
JOURNAL OF PEPTIDE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Nisha Mohanan, Michael C. -H. Wong, Nediljko Budisa, David B. Levin
Summary: In this study, genes encoding an intracellular lipase (LIP3), an extracellular lipase (LIP4), and an intracellular PHA depolymerase (PhaZ) were identified in Pseudomonas chlororaphis PA23. These genes were cloned and expressed in Escherichia coli, and the biochemical and substrate preferences of the enzymes were characterized. The results showed that these enzymes exhibited different properties, but they demonstrated broad substrate specificity and could hydrolyze various polymers, including PHAs, pNP alkanoates, and PLA. Furthermore, the enzymes were able to degrade both biodegradable and synthetic polymers, such as PCL and PES, as evidenced by GPC analyses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Georg Johannes von Freiherr Sass, Matthew Blain-Hartung, Tobias Baumann, Katrina T. Forest, Peter Hildebrandt, Nediljko Budisa
Summary: Orthogonal translation is an efficient tool for parameterization of structural and dynamic phenomena in proteins. Nitrile-containing tryptophan analogs are useful probes for studying local electrostatics and hydrogen bonding. This study reports the engineering of a tyrosyl-tRNA synthetase variant capable of incorporating 5-cyanotryptophan via orthogonal translation, and demonstrates its utility by inserting it into a photosensor protein.
Review
Biochemistry & Molecular Biology
Peter Goettig, Nikolaj G. Koch, Nediljko Budisa
Summary: Amino acids play crucial roles in organisms, being encoded by genetic code and modified post-translationally to generate various functional amino acids. These non-canonical amino acids are important for protein stability and function, and have wide applications in drug development and biological research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Rajeev Pasupuleti, Sabrina Riedl, Laia Saltor Nunez, Marianna Karava, Vajinder Kumar, Robert Kourist, W. Bruce Turnbull, Dagmar Zweytick, Birgit Wiltschi
Summary: In this study, a human lactoferricin-derived synthetic retro di-peptide R-DIM-P-LF11-215 was fused to the lectin Stx1B, which selectively targeted and killed Gb3+ cancer cells. Additionally, the peptide was labeled with a reactive amino acid and a fluorophore for further applications. The lectin-peptide fusion showed high effectiveness in killing Gb3+ cancer cells while leaving Gb3-negative cells unaffected.