Peptide asparaginyl ligases——renegade peptide bond makers

Making peptide bonds is tightly controlled by genetic code and machinery which includes cofactors,ATP,and RNAs.In this regard,the stand-alone and genetic-code-independent peptide ligases constitute a new family of renegade peptide-bond makers.A prime example is butelase-1,an Asn/Asp(Asx)-specific ligase that structurally belongs to the asparaginyl endopeptidase family.Butelase-1 specifically recognizes a C-terminal Asx-containing tripeptide motif,Asn/Asp-Xaa-Yaa(Xaa and Yaa are any amino acids),to form a site-specific Asn-Xaa peptide bond either intramolecularly as cyclic proteins or intermolecularly as modified proteins.Our work in the past five years has validated that butelase-1 is a potent and versatile ligase.Here we review the advances in ligases,with a focus on butelase-1,and their applications in engineering bioactive peptides and precision protein modifications,antibody-drug conjugates,and live-cell labeling.     

Enantioselective Total Synthesis of (R,R)-Blumenol B and d9-(R,R)-Blumenol B

C₁₃-norisoprenoids are of particular importance to grapes and wines, as these molecules influence wine aroma and have been shown to significantly contribute to the distinct character of various wine varieties. Blumenol B is a putative precursor to a number of important wine aroma compounds, including the well-known compounds theaspirone and vitispirane. The enantioselective synthesis of (R,R)-blumenol B from commercially available 4-oxoisophorone was achieved using a short and easily scaleable route, which was then successfully applied to the synthesis of poly-deuterated d9-blumenol B.     

Experimental and theoretical study of the reaction of the ethynyl radical with nitrous oxide, C2H + N2O

We investigated the rate constants and reaction mechanism of the gas phase reaction between the ethynyl radical and nitrous oxide (C(2)H + N(2)O) using both experimental methods and electronic structure calculations. A pulsed-laser photolysis/chemiluminescence technique was used to determine the absolute rate coefficient over the temperature range 570 K to 836 K. In this experimental temperature range, the measured temperature dependence of the overall rate constants can be expressed as: k(T) (C(2)H + N(2)O) = 2.93 × 10(-11) exp((-4000 ± 1100) K/T) cm(3) s(-1) (95% statistical confidence). Portions of the C(2)H + N(2)O potential energy surface (PES), containing low-energy pathways, were constructed using the composite G3B3 method. A multi-step reaction route leading to the products HCCO + N(2) is clearly preferred. The high selectivity between product channels favouring N(2) formation occurs very early. The pathway corresponds to the addition of the terminal C atom of C(2)H to the terminal N atom of N(2)O. Refined calculations using the coupled-cluster theory whose electronic energies were extrapolated to the complete basis set limit CCSD(T)/CBS led to an energy barrier of 6.0 kcal mol(-1) for the entrance channel. The overall rate constant was also determined by application of transition-state theory and Rice-Ramsperger-Kassel-Marcus (RRKM) statistical analyses to the PES. The computed rate constants have similar temperature dependence to the experimental values, though were somewhat lower.     

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.     

Modulation of Stacking Interactions by Transition‐Metal Coordination: Ab Initio Benchmark Studies

A series of ab initio calculations are used to determine the C? H???π and π???π‐stacking interactions of aromatic rings coordinated to transition‐metal centres. Two model complexes have been employed, namely, ferrocene and chromium benzene tricarbonyl. Benchmark data obtained from extrapolation of MP2 energies to the basis set limit, coupled with CCSD(T) correction, indicate that coordinated aromatic rings are slightly weaker hydrogen‐bond acceptors but are significantly stronger hydrogen‐bond donors than uncomplexed rings. It is found that π???π stacking to a second benzene is stronger than in the free benzene dimer, especially in the chromium case. This is assigned, by use of energy partitioning in the local correlation method, to dispersion interactions between metal d and benzene π orbitals. The benchmark data is also used to test the performance of more efficient theoretical methods, indicating that spin‐component scaling of MP2 energies performs well in all cases, whereas various density functionals describe some complexes well, but others with errors of more than 1 kcal mol^?1.     

On graphs whose Laplacian matrices have distinct integer eigenvalues

In this paper, we investigate graphs for which the corresponding Laplacian matrix has distinct integer eigenvalues. We define the set S_i,n to be the set of all integers from 0 to n, excluding i. If there exists a graph whose Laplacian matrix has this set as its eigenvalues, we say that this set is Laplacian realizable. We investigate the sets S_i,n that are Laplacian realizable, and the structures of the graphs whose Laplacian matrix has such a set as its eigenvalues. We characterize those i < n such that S_i,n is Laplacian realizable, and show that for certain values of i, the set S_i,n is realized by a unique graph. Finally, we conjecture that S_n,n is not Laplacian realizable for n ≥ 2 and show that the conjecture holds for certain values of n. © 2005 Wiley Periodicals, Inc. J Graph Theory     

Line graphs: Their maximum nullities and zero forcing numbers

The maximum nullity over a collection of matrices associated with a graph has been attracting the attention of numerous researchers for at least three decades. Along these lines various zero forcing parameters have been devised and utilized for bounding the maximum nullity. The maximum nullity and zero forcing number, and their positive counterparts, for general families of line graphs associated with graphs possessing a variety of specific properties are analysed. Building upon earlier work, where connections to the minimum rank of line graphs were established, we verify analogous equations in the positive semidefinite cases and coincidences with the corresponding zero forcing numbers. Working beyond the case of trees, we study the zero forcing number of line graphs associated with certain families of unicyclic graphs.     

Trigonal (-3) symmetry octahedral lanthanide(III) complexes of zwitterionic tripodal ligands: luminescence and magnetism

Sandwich coordination complexes, [Ln^III(H₃L)₂]X₃?solvents, of Tb(III), Eu(III), Dy(III), Ho(III) and Er(III) were prepared with two new zwitterionic ester-substituted tripodal amine ligands, tris((2-hydroxy-5-n-butyl benzoate)aminoethyl)-amine (H₃L¹) and tris((2-hydroxy-5-methyl benzoate)aminoethyl)-amine (H₃L²). These ligands were synthesised by condensation of the appropriately substituted salicylaldehyde with tris(2-aminoethyl)amine (tren) followed by in situ reduction of the tris-imine to tris-amine. Subsequent 2:1 reaction with lanthanide(III) ions yields [Ln^III(H₃L)₂]X₃?solvents (L = L¹, L²; X = Cl^?, NO₃^?; solvents = MeOH or H₂O). All complexes were characterised by microanalysis, infrared spectroscopy, high resolution mass spectrometry and solid-state photoluminescence measurements. The crystal structures of [Tb^III(H₃L¹)₂]Cl₃·6MeOH, [Dy(H₃L¹)₂]Cl₃·6MeOH, [Eu^III(H₃L¹)₂]Cl₃·6MeOH and [Tb^III(H₃L¹)₂](NO₃)₃ reveal high-crystallographic ?3 symmetry at the O₆-coordinated octahedral lanthanide(III) ions and that the tripodal ligands are bound in zwitterionic form: the protons from the phenolic oxygens have migrated to the amino nitrogens. Photoluminescence measurements indicate various degrees of energy transfer of the ligand chromophore to the lanthanide ions, as both ligand and lanthanide emission features are observed. Despite the high-crystallographic symmetry and the likely small transverse magnetic anisotropy of the complexes, no evidence of slow relaxation of the magnetisation, characteristic of a single-molecule magnet, was observed for [Tb^III(H₃L¹)₂]Cl₃·MeOH·3H₂O, [Dy^III(H₃L¹)₂]Cl₃·6H₂O, [Ho^III(H₃L¹)₂](NO₃)₃·2H₂O, [Er^III(H₃L¹)₂]·H₂O and [Tb^III(H₃L¹)₂](NO₃)₃ down to 2.0 K.     

Kibdelones: novel anticancer polyketides from a rare Australian actinomycete

The kibdelones are a novel family of bioactive heterocyclic polyketides produced by a rare soil actinomycete, Kibdelosporangium sp. (MST-108465). Complete relative stereostructures were assigned to kibdelones A-C (1-3), kibdelone B rhamnoside (5), 13-oxokibdelone A (7), and 25-methoxy-24-oxokibdelone C (8) on the basis of detailed spectroscopic analysis and chemical interconversion, as well as mechanistic and biosynthetic considerations. Under mild conditions, kibdelones B (2) and C (3) undergo a facile equilibration to kibdelones A-C (1-3), while kibdelone B rhamnoside (5) equilibrates to a mixture of kibdelone A-C rhamnosides (4-6). A plausible mechanism for this equilibration is proposed and involves air oxidation, quinone/hydroquinone redox transformations, and a choreographed sequence of keto/enol tautomerizations that aromatize ring C via a quinone methide intermediate. Kibdelones exhibit potent and selective cytotoxicity against a panel of human tumor cell lines and display significant antibacterial and nematocidal activity.