Engineering Oriented Protein-Labelled Surfaces

Current protein immobilization techniques lack defined control over protein orientation. Protein orientation is important for making biosensors and biomaterials that are sensitive and efficient and can be crucial for designing some devices such as immunosensors or direct electron transferring biocells. A new method of protein immobilization is proposed that takes advantage of amber stop codon suppression to incorporate a tetrazine containing non-canonical amino acid that can undergo an inverse-electron demand Diels-Alder cycloaddition with strained trans-cyclooctene-labelled surfaces. This allows for site specific protein immobilization that is fast, biorthogonal, and effective in mild aqueous conditions. This new method is compared to standard glutaraldehyde immobilization to lysine residues and shown to be faster and retain more activity when immobilized.Keywords: Protein immobilization, Protein Engineering, Biosensors and biomaterialsKeywords: Protein immobilization, Protein Engineering, Biosensors and biomaterial

Monitoring Replication Protein A (RPA) Dynamics in Homologous Recombination Through Site-specific Incorporation of Non-canonical Amino Acids

An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance

Engineering bioorthogonal reactions on proteins in live cells

This project deals with a method to optimize in vivo labeling using small fluorescent molecules via bioorthogonal reactions. The reaction used involves our unnatural amino acid 4-(6-methyl-s-tetrazin-3-yl)aminophenylalanine (AMT-Phe). The amino acid is site-specifically incorporated into GFP and then reacted with a labeled, strained trans-cyclooctene, resulting in a labeled protein. However we have noticed that the label becomes detached from the protein. The conditions and influential factors that cause this are unknown, so tests to determine the stability of AMT-Phe were run using mass spectrometry. Results have shown that AMT-Phe might be decomposing once incorporated in the protein over time, suggesting that it’s not very stable. AMT-Phe contains tetrazine functionality, with a methyl group attached to the tetrazine. A potentially more stable version of AMT-Phe is to replace the methyl group with a phenyl group. This potentially more stable and reactive amino acid, 4-(6-methyl-s-tetrazin-3-yl)aminophenyl- alanine (APT-Phe), was synthesized, and a series of tests on incorporation and reactive rates were run to compare with AMT-Phe. Although APT-Phe didn’t incorporate into GFP very well, preliminary data shows that it has a 6-fold faster reaction rate than AMT-Phe

Engineering bioorthogonal reactions on proteins in live cells

This project deals with a method to optimize in vivo labeling using small fluorescent molecules via bioorthogonal reactions. The reaction used involves our unnatural amino acid 4-(6-methyl-s-tetrazin-3-yl)aminophenylalanine (AMT-Phe). The amino acid is site-specifically incorporated into GFP and then reacted with a labeled, strained trans-cyclooctene, resulting in a labeled protein. However we have noticed that the label becomes detached from the protein. The conditions and influential factors that cause this are unknown, so tests to determine the stability of AMT-Phe were run using mass spectrometry. Results have shown that AMT-Phe might be decomposing once incorporated in the protein over time, suggesting that it’s not very stable. AMT-Phe contains tetrazine functionality, with a methyl group attached to the tetrazine. A potentially more stable version of AMT-Phe is to replace the methyl group with a phenyl group. This potentially more stable and reactive amino acid, 4-(6-methyl-s-tetrazin-3-yl)aminophenyl- alanine (APT-Phe), was synthesized, and a series of tests on incorporation and reactive rates were run to compare with AMT-Phe. Although APT-Phe didn’t incorporate into GFP very well, preliminary data shows that it has a 6-fold faster reaction rate than AMT-Phe

Superconducting and charge-density wave instabilities in ultrasmall-radius carbon nanotubes

We perform a detailed analysis of the band structure, phonon dispersion, and electron-phonon coupling of three types of small-radius carbon nanotubes (CNTs): (5,0), (6,0), and (5,5) with diameters 3.9, 4.7, and 6.8 \AA respectively. The large curvature of the (5,0) CNTs makes them metallic with a large density of states at the Fermi energy. The density of states is also strongly enhanced for the (6,0) CNTs compared to the results obtained from the zone-folding method. For the (5,5) CNTs the electron-phonon interaction is dominated by the in-plane optical phonons, while for the ultrasmall (5,0) and (6,0) CNTs the main coupling is to the out-of-plane optical phonon modes. We calculate electron-phonon interaction strengths for all three types of CNTs and analyze possible instabilities toward superconducting and charge-density wave phases. For the smallest (5,0) nanotube, in the mean-field approximation and neglecting Coulomb interactions, we find that the charge-density wave transition temperature greatly exceeds the superconducting one. When we include a realistic model of the Coulomb interaction we find that the charge-density wave is suppressed to very low temperatures, making superconductivity dominant with the mean-field transition temperature around one K. For the (6,0) nanotube the charge-density wave dominates even with the inclusion of Coulomb interactions and we find the mean-field transition temperature to be around five Kelvin. We find that the larger radius (5,5) nanotube is stable against superconducting and charge-density wave orders at all realistic temperatures.Comment: 5 pages. 2 figure

Comparing the language style of heads of state in the US, UK, Germany and Switzerland during COVID-19

The COVID-19 pandemic posed a global threat to nearly every society around the world. Individuals turned to their political leaders to safely guide them through this crisis. The most direct way political leaders communicated with their citizens was through official speeches and press conferences. In this report, we compare psychological language markers of four different heads of state during the early stage of the pandemic. Specifically, we collected all pandemic-related speeches and press conferences delivered by political leaders in the USA (Trump), UK (Johnson), Germany (Merkel), and Switzerland (Swiss Federal Council) between February 27th and August 31st, 2020. We used natural language analysis to examine language markers of expressed positive and negative emotions, references to the community (we-talk), analytical thinking, and authenticity and compare these language markers across the four nations. Level differences in the language markers between the leaders can be detected: Trump’s language was characterized by a high expression of positive emotion, Merkel’s by a strong communal focus, and Johnson’s and the Swiss Federal Council by a high level of analytical thinking. Overall, these findings mirror different strategies used by political leaders to deal with the COVID-19 pandemic

Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TyIM1

The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH•••O) hydrogen bonds between the substrate’s sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A)mutations to selectively ablate the CH•••O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in the catalytic efficiency relative to wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions which abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH•••O hydrogen bonding in modulating the catalytic efficiency of TylM1

Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids

Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)—in combination with double electron–electron resonance (DEER) spectroscopy—has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides—including a gem-diethyl-substituted nitroxide with enhanced stability in cells—with rate constants that can exceed 106 M−1 s−1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO–nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification

Many happy returns: combining insights from the environmental and behavioural sciences to understand what is required to make reusable packaging mainstream

The introduction of reusable packaging systems (both refill and return) has the potential to significantly reduce waste from single-use plastic packaging. However, for these schemes to be successful, both the environmental impact and the willingness of consumers to engage with such systems need to be carefully considered. This paper combines and discusses two complementary studies: (i) a life cycle assessment comparing the environmental impacts of single-use, refillable, and returnable containers for a takeaway meal, and (ii) a large online survey of UK adults exploring what types of product and packaging consumers are willing to reuse, how, and why. The findings of the life cycle assessment indicate that reusable containers outperform single-use plastic containers on most measures of environmental impact. The survey found that given the choice of disposal, reuse or recycling, that recycling is the preferred method of dealing with packaging once empty in the UK, and that people's decisions with regards to what types of packaging they are willing to reuse are largely driven by the aspects of the packaging itself (e.g., material and type) rather than the nature of the product inside of the packaging (e.g., state of matter of the contents). The survey also showed that people were more willing to engage in reuse systems with which they were already familiar. Additionally the language used to describe these schemes and the term ‘reuse’ needs to be considered. Combined, these factors can be used to determine the best packaging reuse system for a given product and situation

Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP

Stable surface adhesion of cells is one of the early pivotal steps in bacterial biofilm formation, a prevalent adaptation strategy in response to changing environments. In Pseudomonas fluorescens, this process is regulated by the Lap system and the second messenger cyclic-di-GMP. High cytoplasmic levels of cyclic-di-GMP activate the transmembrane receptor LapD that in turn recruits the periplasmic protease LapG, preventing it from cleaving a cell surface-bound adhesin, thereby promoting cell adhesion. In this study, we elucidate the molecular basis of LapG regulation by LapD and reveal a remarkably sensitive switching mechanism that is controlled by LapD's HAMP domain. LapD appears to act as a coincidence detector, whereby a weak interaction of LapG with LapD transmits a transient outside-in signal that is reinforced only when cyclic-di-GMP levels increase. Given the conservation of key elements of this receptor system in many bacterial species, the results are broadly relevant for cyclic-di-GMP- and HAMP domain-regulated transmembrane signaling.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by eLife Sciences Publications Ltd. The published article can be found at: http://elifesciences.org/