Perdita E. Barran

Luminescent, enantiopure, phenylatopyridine iridium-based coordination capsules

The first molecular capsule based on an [Ir(ppy)(2)](+) unit (ppy = 2-phenylatopyridine) has been prepared. Following the development of a method to resolve rac-[(Ir(ppy)(2)Cl)(2)] into its enantiopure forms, homochiral Ir(6)L(4) octahedra where obtained with the tritopic 1,3,5-tricyanobenzene. Solution studies and X-ray diffraction show that these capsules encapsulate four of the six associated counteranions and that these can be exchanged for other anionic guests. Initial photophysical studies have shown that an ensemble of weakly coordinating ligands can lead to luminescence not present in comparable mononuclear systems.

Active-Metal Template Synthesis of a Molecular Trefoil Knot

Tying the knot: The marriage of catalysis and coordination chemistry enables two CuI ions (red; see picture) to work in partnership for the synthesis of a molecular trefoil knot. One ion entangles an acyclic building block to create a loop in the ligand, and the other gathers the ligands reactive end-groups, threads the loop, and catalyzes the covalent capture of the knotted architecture by an alkyne–azide “click” reaction.

Analysis and separation of residues important for the chemoattractant and antimicrobial activities of beta-defensin 3.

β-Defensins are important in mammalian immunity displaying both antimicrobial and chemoattractant activities. Three canonical disulfide intramolecular bonds are believed to be dispensable for antimicrobial activity but essential for chemoattractant ability. However, here we show that HBD3 (human β-defensin 3) alkylated with iodoactemide and devoid of any disulfide bonds is still a potent chemoattractant. Furthermore, when the canonical six cysteine residues are replaced with alanine, the peptide is no longer active as a chemoattractant. These findings are replicated by the murine ortholog Defb14. We restore the chemoattractant activity of Defb14 and HBD3 by introduction of a single cysteine in the fifth position (CysV) of the β-defensin six cysteine motif. In contrast, a peptide with a single cysteine at the first position (CysI) is inactive. Moreover, a range of overlapping linear fragments of Defb14 do not act as chemoattractants, suggesting that the chemotactic activity of this peptide is not dependent solely on an epitope surrounding CysV. Full-length peptides either with alkylated cysteine residues or with cysteine residues replaced with alanine are still strongly antimicrobial. Defb14 peptide fragments were also tested for antimicrobial activity, and peptides derived from the N-terminal region display potent antimicrobial activity. Thus, the chemoattractant and antimicrobial activities of β-defensins can be separated, and both of these functions are independent of intramolecular disulfide bonds. These findings are important for further understanding of the mechanism of action of defensins and for therapeutic design.

Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery

The initial stages of drug discovery are increasingly reliant on development and improvement of analytical methods to investigate protein-protein and protein-ligand interactions. For over 20 years, mass spectrometry (MS) has been recognized as providing a fast, sensitive and high-throughput methodology for analysis of weak non-covalent complexes. Careful control of electrospray ionization conditions has enabled investigation of the structure, stability and interactions of proteins and peptides in a solvent free environment. This critical review covers the use of mass spectrometry for kinetic, dynamic and structural studies of proteins and protein complexes. We discuss how conjunction of mass spectrometry with related techniques and methodologies such as ion mobility, hydrogen-deuterium exchange (HDX), protein footprinting or chemical cross-linking can provide us with structural information useful for drug development. Along with other biophysical techniques, such as NMR or X-ray crystallography, mass spectrometry provides a powerful toolbox for investigation of biological problems of medical relevance (204 references).

New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition

The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor–cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.

Development of an ion mobility quadrupole time of flight mass spectrometer.

We describe here a new ion mobility capable mass spectrometer which comprises a drift cell for mobility separation and a quadrapole time of flight mass spectrometer for mass analysis--the MoQTOF. A commercial QToF instrument (Micromass UK Ltd., Manchester, UK) has been modified by the inclusion of an additional chamber containing a drift cell and ancillary ion optics. The drift cell is 5.1 cm long made from a copper block and is mounted from a top hat flange in a chamber situated post source optics and prior to the quadapole analyzer. Details of this instrument are provided along with information about how it can be used to acquire mobilities of ions along with their mass to charge ratios. The MoQTOF is used to examine conformations of a series of antimicrobial peptides based on a beta-defensin template. In vivo, these cationic cystine-rich amphiphilic peptides are conformationally restrained by three or more disulfide bridges, although recent findings by several groups have cast doubt on the importance of canonical disulfide pairing to antimicrobial activities. By synthesizing a panel of variants to Defb14 (the murine orthologue of HBD3), we exploit ion mobility to distinguish conformational differences which arise due to disulfide formation and to the hydrophobicity of the peptide sequence. Our gas-phase results are interpreted in terms of the antimicrobial and chemotacic properties of beta-defensins, and this mass spectrometry based approach to discern structure may have a role in future design of novel antibiotics.

Ion mobility mass spectrometry for peptide analysis

The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.

Dynamics of Intact Immunoglobulin G Explored by Drift-Tube Ion-Mobility Mass Spectrometry and Molecular Modeling

Collision cross-sections (CCS) of immunoglobulins G1 and G4 have been determined using linear drift-tube ion-mobility mass spectrometry. Intact antibodies and Fc-hinge fragments present with a larger range of CCS than proteins of comparable size. This is rationalized with MD simulations, which indicate significant in vacuo dynamics between linked folded domains. The IgG4 subclass presents over a wider CCS range than the IgG1 subclass.

Shapes of supramolecular cages by ion mobility mass spectrometry

Mass spectrometry and drift tube ion mobility mass spectrometry have been used to analyse several isobaric, multicomponent cages yielding information on three dimensional structure, interactions and dynamics of assembly in the gas phase.

Partial Deletion of Chromosome 8 β-defensin Cluster Confers Sperm Dysfunction and Infertility in Male Mice

β-defensin peptides are a family of antimicrobial peptides present at mucosal surfaces, with the main site of expression under normal conditions in the male reproductive tract. Although they kill microbes in vitro and interact with immune cells, the precise role of these genes in vivo remains uncertain. We show here that homozygous deletion of a cluster of nine β-defensin genes (DefbΔ9) in the mouse results in male sterility. The sperm derived from the mutants have reduced motility and increased fragility. Epididymal sperm isolated from the cauda should require capacitation to induce the acrosome reaction but sperm from the mutants demonstrate precocious capacitation and increased spontaneous acrosome reaction compared to wild-types but have reduced ability to bind the zona pellucida of oocytes. Ultrastructural examination reveals a defect in microtubule structure of the axoneme with increased disintegration in mutant derived sperm present in the epididymis cauda region, but not in caput region or testes. Consistent with premature acrosome reaction, sperm from mutant animals have significantly increased intracellular calcium content. Thus we demonstrate in vivo that β-defensins are essential for successful sperm maturation, and their disruption leads to alteration in intracellular calcium, inappropriate spontaneous acrosome reaction and profound male infertility.