Post-translational modifications (PTMs) are used by organisms to control protein structure and function after protein translation, but their study is complicated and their roles are not often well ...understood as PTMs are difficult to introduce onto proteins selectively. Designing reagents that are both good mimics of PTMs, but also only modify select amino acid residues in proteins is challenging. Frequently, both a chemical warhead and linker are used, creating a product that is a misrepresentation of the natural modification. We have previously shown that biotin-chloromethyl-triazole is an effective reagent for cysteine modification to give S-Lys derivatives where the triazole is a good mimic of natural lysine acylation. Here, we demonstrate both how the reactivity of the alkylating reagents can be increased and how the range of triazole PTM mimics can be expanded. These new iodomethyl-triazole reagents are able to modify a cysteine residue on a histone protein with excellent selectivity in 30 min to give PTM mimics of acylated lysine side-chains. Studies on the more complicated, folded protein SCP-2L showed promising reactivity, but also suggested the halomethyl-triazoles are potent alkylators of methionine residues.
Abstract
Given a graph , the ‐mixing problem asks: Starting with a ‐colouring of , can one obtain all ‐colourings of by changing the colour of only one vertex at a time, while at each step ...maintaining a ‐colouring? More generally, for a graph , the ‐mixing problem asks: Can one obtain all homomorphisms , starting from one homomorphism , by changing the image of only one vertex at a time, while at each step maintaining a homomorphism ? This paper focuses on a generalization of ‐colourings, namely, ‐circular colourings. We show that when , a graph is ‐mixing if and only if for any ‐colouring of , and any cycle of , the wind of the cycle under the colouring equals a particular value (which intuitively corresponds to having no wind). As a consequence we show that ‐mixing is closed under a restricted homomorphism called a fold. Using this, we deduce that ‐mixing is co‐NP‐complete for all , and by similar ideas we show that if the circular chromatic number of a connected graph is , then folds to . We use the characterization to settle a conjecture of Brewster and Noel, specifically that the circular mixing number of bipartite graphs is 2. Lastly, we give a polynomial time algorithm for ‐mixing in planar graphs when .
Let p and q be positive integers with p/q≥2. The “reconfiguration problem” for circular colourings asks, given two (p,q)-colourings f and g of a graph G, is it possible to transform f into g by ...changing the colour of one vertex at a time such that every intermediate mapping is a (p,q)-colouring? We show that this problem can be solved in polynomial time for 2≤p/q<4 and that it is PSPACE-complete for p/q≥4. This generalizes a known dichotomy theorem for reconfiguring classical graph colourings. As an application of the reconfiguration algorithm, we show that graphs with fewer than (k−1)!/2 cycles of length divisible by k are k-colourable.
Palladium catalysed reactions are ubiquitous in synthetic organic chemistry in both organic solvents and aqueous buffers. The broad reactivity of palladium catalysis has drawn interest as a means to ...conduct orthogonal transformations in biological settings. Successful examples have been shown for protein modification, in vivo drug decaging and as palladium-protein biohybrid catalysts for selective catalysis. Biological media represents a challenging environment for palladium chemistry due to the presence of a multitude of chelators, catalyst poisons and a requirement for milder reaction conditions e.g. lower temperatures. This review looks to identify successful examples of palladium-catalysed reactions in the presence of proteins or cells and analyse solutions to help to overcome the challenges of working in biological systems.
A review covering the use of palladium in biological media, exploring how challenges such as toxicity, unspecific metal binding and inhibition have been overcome in four areas: protein modification, Pd reactions for medicinal applications, one-pot Pd/enzyme catalysis and in the design of biohybrid Pd catalysts. Display omitted
•Palladium reactions as new tools for selective protein modification.•Bioorthogonal and biocompatible palladium complexes and their reactions.•Enzymes plus palladium – use in cascade reactions and as biohybrid catalysts.•Toxicity and non-specific metal binding reduce utility of Pd in vivo.•Judicious use of ligands and buffer maximise the use of Pd reactions in biological media.
A linear programming algorithm to compute the broadcast domination number and the multipacking number of a strongly chordal graph is described. It runs in time cubic in the number of vertices of the ...input graph. A new linear-time algorithm to find the broadcast domination number of a tree is given, as is a simplified linear algorithm to find the multipacking number of a tree.
Microorganisms can be programmed to perform chemical synthesis via metabolic engineering. However, despite an increasing interest in the use of de novo metabolic pathways and designer whole‐cells for ...small molecule synthesis, the inherent synthetic capabilities of native microorganisms remain underexplored. Herein, we report the use of unmodified E. coli BL21(DE3) cells for the reduction of keto‐acrylic compounds and apply this whole‐cell biotransformation to the synthesis of aminolevulinic acid from a lignin‐derived feedstock. The reduction reaction is rapid, chemo‐, and enantioselective, occurs under mild conditions (37 °C, aqueous media), and requires no toxic transition metals or external reductants. This study demonstrates the remarkable promiscuity of central metabolism in bacterial cells and how these processes can be leveraged for synthetic chemistry without the need for genetic manipulation.
Alkene‐reducing bugs: The microorganism Escherichia coli BL21(DE3) was found to reduce a range of keto‐acrylic alkene substrates without the need for genetic modification. The biocompatibility of the reaction was examined in a cellular setting and used to inform the metal‐free synthesis of aminolevulinic acid from a lignin‐derived substrate.
The design and development of artificial metal‐free photoenzymes aims to combine the selectivity of enzymatic reactions with the benefits of modern synthetic photocatalysts. Removing the need for ...rare earth metals and allowing for milder reaction conditions, leading to a more sustainable catalytic system. Here, we present the design of a novel artificial photoenzyme by integrating an organophotocatalytic moiety based on a donor‐acceptor design into a steroid carrier protein (SCP‐2L). SCP‐2L possesses a hydrophobic tunnel facilitating substrate binding in aqueous media. The photocatalyst was site‐selectively bound to three SCP‐2L variants, possessing a non‐native cysteine residue strategically placed around the hydrophobic tunnel of the protein. The three modified photoenzymes were shown to be selective for the oxidation of organic sulfides giving up to 192 turnovers.
A metal‐free artificial photoenzyme was designed based on the human steroid carrier protein (SCP‐2L), which possesses a hydrophobic tunnel and facilitates substrate binding. Three variants of SCP‐2L were bioconjugated with a photocatalytic moiety and used for selective oxidation of organic sulfides giving up to 192 turnovers depending on the binding side of the photocatalyst.
A mixed graph is a set of vertices together with an edge set and an arc set.
An $(m,n)$-mixed graph $G$ is a mixed graph whose edges are each assigned one
of $m$ colours, and whose arcs are each ...assigned one of $n$ colours. A
\emph{switch} at a vertex $v$ of $G$ permutes the edge colours, the arc
colours, and the arc directions of edges and arcs incident with $v$. The group
of all allowed switches is $\Gamma$.
Let $k \geq 1$ be a fixed integer and $\Gamma$ a fixed permutation group. We
consider the problem that takes as input an $(m,n)$-mixed graph $G$ and asks if
there a sequence of switches at vertices of $G$ with respect to $\Gamma$ so
that the resulting $(m,n)$-mixed graph admits a homomorphism to an
$(m,n)$-mixed graph on $k$ vertices. Our main result establishes this problem
can be solved in polynomial time for $k \leq 2$, and is NP-hard for $k \geq 3$.
This provides a step towards a general dichotomy theorem for the
$\Gamma$-switchable homomorphism decision problem.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we ...demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms.
This work brings together ideas of mixing graph colorings, discrete homotopy, and precoloring extension. A particular focus is circular colorings. We prove that all the (k,q)‐colorings of a graph G ...can be obtained by successively recoloring a single vertex provided k/q≥2col(G) along the lines of Cereceda, van den Heuvel, and Johnson's result for k‐colorings. We give various bounds for such mixing results and discuss their sharpness, including cases where the bounds for circular and classical colorings coincide. As a corollary, we obtain an Albertson‐type extension theorem for (k,q)‐precolorings of circular cliques. Such a result was first conjectured by Albertson and West. General results on homomorphism mixing are presented, including a characterization of graphs G for which the endomorphism monoid can be generated through the mixing process. As in similar work of Brightwell and Winkler, the concept of dismantlability plays a key role.
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