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.     

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     

On m-Ary Overpartitions

Presently there are a lot of activities in the study of overpartitions, objects that were discussed by MacMahon, and which have recently proven useful in several combinatorial studies of basic hypergeometric series. In this paper we study some similar objects, which we name m-ary overpartitions. We consider divisibility properties of the number of m-ary overpartitions of a natural number, and we prove a theorem which is a lifting to general m of the well-known Churchhouse congruences for the binary partition function. Received October 11, 2004     

Infinitely many congruences modulo 5 for 4-colored Frobenius partitions

In his 1984 AMS Memoir, Andrews introduced the family of functions \(c\phi _k(n),\) which denotes the number of generalized Frobenius partitions of \(n\) into \(k\) colors. Recently, Baruah and Sarmah, Lin, Sellers, and Xia established several Ramanujan-like congruences for \(c\phi _4(n)\) relative to different moduli. In this paper, employing classical results in \(q\)-series, the well-known theta functions of Ramanujan, and elementary generating function manipulations, we prove a characterization of \(c\phi _4(10n+1)\) modulo 5 which leads to an infinite set of Ramanujan-like congruences modulo 5 satisfied by \(c\phi _4.\) This work greatly extends the recent work of Xia on \(c\phi _4\) modulo 5.     

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.     

Spectroscopic and quantum chemical studies on low-spin FeIV=O complexes: Fe-O bonding and its contributions to reactivity

High-valent FeIV=O species are key intermediates in the catalytic cycles of many mononuclear non-heme iron enzymes and have been structurally defined in model systems. Variable-temperature magnetic circular dichroism (VT-MCD) spectroscopy has been used to evaluate the electronic structures and in particular the Fe-O bonds of three FeIV=O (S = 1) model complexes, [FeIV(O)(TMC)(NCMe)]2+, [FeIV(O)(TMC)(OC(O)CF3)]+, and [FeIV(O)(N4Py)]2+. These complexes are characterized by their strong and covalent Fe-O pi-bonds. The MCD spectra show a vibronic progression in the nonbonding --> pi* excited state, providing the Fe-O stretching frequency and the Fe-O bond length in this excited state and quantifying the pi-contribution to the total Fe-O bond. Correlation of these experimental data to reactivity shows that the [FeIV(O)(N4Py)]2+ complex, with the highest reactivity toward hydrogen-atom abstraction among the three, has the strongest Fe-O pi-bond. Density functional calculations were correlated to the data and support the experimental analysis. The strength and covalency of the Fe-O pi-bond result in high oxygen character in the important frontier molecular orbitals (FMOs) for this reaction, the unoccupied beta-spin d(xz/yz) orbitals, that activates these for electrophilic attack. An extension to biologically relevant FeIV=O (S = 2) enzyme intermediates shows that these can perform electrophilic attack reactions along the same mechanistic pathway (pi-FMO pathway) with similar reactivity but also have an additional reaction channel involving the unoccupied alpha-spin d(z2) orbital (sigma-FMO pathway). These studies experimentally probe the FMOs involved in the reactivity of FeIV=O (S = 1) model complexes resulting in a detailed understanding of the Fe-O bond and its contributions to reactivity.     

Bayesian and Maximum Likelihood Estimation for Gaussian Processes on an Incomplete Lattice

This article proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose a Markov chain Monte Carlo approach for Bayesian inference, and a Monte Carlo expectation-maximization algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides likelihood-based inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference on lattices of sizes up to 512 × 512, and is competitive with two popular methods: composite likelihood and spectral approximations.