Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nature-inspired protein ligation and its applications.

ABSTRACT: The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.

SUBMITTER: Pihl R

PROVIDER: S-EPMC10659114 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nature-inspired protein ligation and its applications.

Pihl Rasmus R Zheng Qingfei Q David Yael Y

Nature reviews. Chemistry 20230221 4

The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently fo ...[more]

PMID: 37117416

Similar Datasets

PROTEIN DESIGN. Inspired by nature.

Project description: Not available

| S-EPMC4888937 | biostudies-literature

Innovation Inspired by Nature: Applications of Biomimicry in Engineering Design.

Project description:Sustainable development is increasingly driving the trend toward the application of biomimicry as a strategy to generate environmentally friendly solutions in the design of industrial products. Nature-inspired design can contribute to the achievement of the Sustainable Development Goals by improving efficiency and minimizing the environmental impact of each design. This research conducted an analysis of available biomimetic knowledge, highlighting the most applied tools and methodologies in each industrial sector. The primary objective was to identify sectors that have experienced greater adoption of biomimicry and those where its application is still in its early stages. Additionally, by applying the available procedures and tools to a selected case study (technologies in marine environments), the advantages and challenges of the methodologies and procedures were determined, along with potential gaps and future research directions necessary for widespread implementation of biomimetics in the industry. These results provide a comprehensive approach to biomimicry applied to more sustainable practices in product design and development.

| S-EPMC11429577 | biostudies-literature

Protein Assemblies: Nature-Inspired and Designed Nanostructures.

Project description:Ordered protein assemblies are attracting interest as next-generation biomaterials with a remarkable range of structural and functional properties, leading to potential applications in biocatalysis, materials templating, drug delivery and vaccine development. This Review covers ordered protein assemblies including protein nanowires/nanofibrils, nanorings, nanotubes, designed two- and three-dimensional ordered protein lattices and protein-like cages including polyhedral virus-like cage structures. The main focus is on designed ordered protein assemblies, in which the spatial organization of the proteins is controlled by tailored noncovalent interactions (including metal ion binding interactions, electrostatic interactions and ligand-receptor interactions among others) or by careful design of modified (mutant) proteins or de novo constructs. The modification of natural protein assemblies including bacterial S-layers and cage-like and rod-like viruses to impart novel function, e.g. enzymatic activity, is also considered. A diversity of structures have been created using distinct approaches, and this Review provides a summary of the state-of-the-art in the development of these systems, which have exceptional potential as advanced bionanomaterials for a diversity of applications.

| S-EPMC7007009 | biostudies-literature

Nature-inspired antimicrobial polymers--assessment of their potential for biomedical applications.

Project description:We explored the potential of poly(oxonorbornene)-based synthetic mimics of antimicrobial peptides (SMAMPs), a promising new class of antimicrobial polymers with cell-selectivity and low resistance development potential, for clinical applications. We evaluated their antimicrobial activity against a panel of seven clinical and regulatory relevant bacteria strains, and tested their toxicity with two different kinds of primary human cells. For the antimicrobial activity, we performed the minimum inhibitory concentration (MIC) assay and determined the minimum bactericidal concentration (MBC) according to the NCCLS guidelines. The results revealed specific problems that may occur when testing the antimicrobial activity of amphiphilic cationic polymers, and confirmed the working hypothesis that the more hydrophilic SMAMP polymers in our portfolio were 'doubly selective', i.e. they are not only selective for bacteria over mammalian cells, but also for Gram-positive over Gram-negative bacteria. The data also showed that we could improve the broad-band activity of one SMAMP, and in combination with the results from the cell toxicity experiments, identified this polymer as a promising candidate for further in-vitro and in-vivo testing. Transmission electron studies revealed that the cellular envelopes of both E. coli and S. aureus were severely damaged due to SMAMP action on the bacterial membrane, which strengthened the argument that SMAMPs closely resemble antimicrobial peptides. To test cell toxicity, we used the traditional hemolysis assay with human red blood cells, and the novel xCelligence assay with primary human fibroblasts. The data reported here is the first example in which a hemolysis assay is benchmarked against the xCelligence assay. It revealed that the same trends were obtained using these complementary methods. This establishes the xCelligence assay with primary human cells as a useful tool for SMAMP characterization.

| S-EPMC3767731 | biostudies-literature

Nature-Inspired Hierarchical Steels.

Project description:Materials can be made strong, but as such they are often brittle and prone to fracture when under stress. Inspired by the exceptionally strong and ductile structure of byssal threads found in certain mussels, we have designed and manufactured a multi-hierarchical steel, based on an inexpensive austenitic stainless steel, which defeats this "conflict" by possessing both superior strength and ductility. These excellent mechanical properties are realized by structurally introducing sandwich structures at both the macro- and nano-scales, the latter via an isometric, alternating, dual-phase crystal phases comprising nano-band austenite and nano-lamellar martensite, without change in chemical composition. Our experiments (transmission and scanning electron microscopy, electron back-scattered diffraction, nano-indentation and tensile tests) and micromechanics simulation results reveal a synergy of mechanisms underlying such exceptional properties. This synergy is key to the development of vastly superior mechanical properties, and may provide a unique strategy for the future development of new super strong and tough (damage-tolerant), lightweight and inexpensive structural materials.

| S-EPMC5865137 | biostudies-literature

Nature-inspired recycling of a protein mixture into a green fluorescent protein-based hydrogel.

Project description:Protein-based materials are biocompatible and have a variety of remarkable properties; consequently, they are finding more and more applications. Nature recycles proteins in multiple ways, ranging from bio-degradation (a slow approach) to fast recycling of protein metabolism. The latter is a wonderful example because a random mixture of proteins gets digested into amino acids (AAs), the fundamental building blocks of proteins. These AAs are then used by cells to produce whichever protein is needed at the time of synthesis. Seen through the lens of recycling, this process transforms a random mixture into something not necessarily present at the start but needed at the moment of recycling. We have recently shown that the process of protein recycling can be performed in vitro and called it NaCRe (Nature Inspired Circular Recycling). In a previous NaCRe proof-of-concept experiment, we started with various protein mixtures but were able to produce only small quantities of recycled protein, in the microgram scale. Here, we show that NaCRe can be used to convert milligrams of a protein mixture containing one of the most common protein materials (silk) into a milligram of an hydrogel made of green fluorescent protein (GFP). We show that in order for NaCRe to be efficient the starting protein mixture must contain a good balance of all AAs and discuss the challenges encountered when scaling up NaCRe.

| S-EPMC11447593 | biostudies-literature

Biosynthesis of Nature-Inspired Unnatural Cannabinoids.

Project description:Natural products make up a large proportion of medicine available today. Cannabinoids from the plant Cannabis sativa is one unique class of meroterpenoids that have shown a wide range of bioactivities and recently seen significant developments in their status as therapeutic agents for various indications. Their complex chemical structures make it difficult to chemically synthesize them in efficient yields. Synthetic biology has presented a solution to this through metabolic engineering in heterologous hosts. Through genetic manipulation, rare phytocannabinoids that are produced in low yields in the plant can now be synthesized in larger quantities for therapeutic and commercial use. Additionally, an exciting avenue of exploring new chemical spaces is made available as novel derivatized compounds can be produced and investigated for their bioactivities. In this review, we summarized the biosynthetic pathways of phytocannabinoids and synthetic biology efforts in producing them in heterologous hosts. Detailed mechanistic insights are discussed in each part of the pathway in order to explore strategies for creating novel cannabinoids. Lastly, we discussed studies conducted on biological targets such as CB1, CB2 and orphan receptors along with their affinities to these cannabinoid ligands with a view to inform upstream diversification efforts.

| S-EPMC8156804 | biostudies-literature

Compact and Thermosensitive Nature-inspired Micropump.

Project description:Liquid transportation without employing a bulky power source, often observed in nature, has been an essential prerequisite for smart applications of microfluidic devices. In this report, a leaf-inspired micropump (LIM) which is composed of thermo-responsive stomata-inspired membrane (SIM) and mesophyll-inspired agarose cryogel (MAC) is proposed. The LIM provides a durable flow rate of 30 μl/h · cm2 for more than 30 h at room temperature without external mechanical power source. By adapting a thermo-responsive polymer, the LIM can smartly adjust the delivery rate of a therapeutic liquid in response to temperature changes. In addition, as the LIM is compact, portable, and easily integrated into any liquid, it might be utilized as an essential component in advanced hand-held drug delivery devices.

| S-EPMC5086846 | biostudies-literature

Site-specific protein double labeling by expressed protein ligation: applications to repeat proteins.

Project description:In the last few years, the use of labeled proteins has significantly expanded in the life sciences. Now, labeled proteins are indispensable tools for a wide spectrum of biophysical and chemical biology applications. In particular, the quest for more sophisticated experimental setups requires the development of new synthetic methodology, especially for multiple site-specific labeling. In this paper, we describe a synthetic strategy based on expressed protein ligation to prepare proteins in high purity and homogeneity, in which two different molecular probes are incorporated specifically at any desired position. Proteins are sequentially labeled in solution, with the advantage that a large excess of probes is not required and the labeled fragments are not restricted to peptide synthesis length limitations. This strategy was applied to selectively label a repeat protein with a fluorophores pair in different positions along the protein sequence. The doubly labeled proteins were prepared at high purity and homogeneity, as required for single molecule FRET studies. Remarkably, this approach can be adapted to the introduction of more than two molecular probes.

| S-EPMC3357005 | biostudies-literature

A comprehensive database of Nature-Inspired Algorithms.

Project description:These data contain a comprehensive collection of all Nature-Inspired Algorithms. This collection is a result of two corresponding surveys, where all Nature-Inspired Algorithms that have been published to-date were gathered and preliminary data acquired. The rapidly increasing number of nature-inspired approaches makes it hard for interested researchers to keep up. Moreover, a proper taxonomy is necessary, based on specific features of the algorithms. Different taxonomies and useful insight into the application areas that the algorithms have coped with is given through these data. This article provides a detailed description of the above mentioned collection.

| S-EPMC7300069 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data