Exploring the substrate specificity of OxyB, a phenol coupling P450 enzyme involved in vancomycin biosynthesis

OxyB is a cytochrome P450 enzyme that catalyzes the first oxidative phenol coupling reaction during vancomycin biosynthesis. The preferred substrate is a linear peptide linked as a C-terminal thioester to a peptide carrier protein (PCP) domain of the glycopeptide antibiotic non-ribosomal peptide synthetase. Previous studies have shown that OxyB can efficiently oxidize a model hexapeptide-PCP conjugate (R-Leu(1)-R-Tyr(2)-S-Asn(3)-R-Hpg(4)-R-Hpg(5)-S-Tyr(6)-S-PCP) (Hpg = 4-hydroxyphenylglycine) into a macrocyclic product by phenolic coupling of the aromatic rings in residues-4 and -6. In this work, the substrate specificity of OxyB has been explored using a series of N-terminally truncated peptides related in sequence to this model hexapeptide-PCP conjugate. Deletion of one or three residues from the N-terminus afforded a penta- (Ac-Tyr-Asn-Hpg-Hpg-Tyr-S-PCP) and a tri- (Ac-Hpg-Hpg-Tyr-S-PCP) peptide that were also efficiently transformed into the corresponding macrocyclic cross-linked product by OxyB. The tripeptide, representing the core of the macrocycle in vancomycin created by OxyB, is thus sufficient, as a thioester with the PCP domain, for phenol coupling to occur. The related tetrapeptide-PCP thioester was not cyclized by OxyB, neither was a related model hexapeptide containing tryptophan in place of tyrosine-6, nor were tripeptides (related to the natural product K-13) with the sequence Ac-Tyr-Tyr-Tyr-S-PCP cross-linked by OxyB.     

Theory for spin-lattice relaxation of spin probes on weakly deformable DNA

The weakly bending rod (WBR) model of double-stranded DNA (dsDNA) is adapted to analyze the internal dynamics of dsDNA as observed in electron paramagnetic resonance (EPR) measurements of the spin-lattice relaxation rate, R(1e), for spin probes rigidly attached to nucleic acid-bases. The WBR theory developed in this work models dsDNA base-pairs as diffusing rigid cylindrical discs connected by bending and twisting springs whose elastic force constants are kappa and alpha, respectively. Angular correlation functions for both rotational displacement and velocity are developed in detail so as to compute values for R(1e) due to four relaxation mechanisms: the chemical shift anisotropy (CSA), the electron-nuclear dipolar (END), the spin rotation (SR), and the generalized spin diffusion (GSD) relaxation processes. Measured spin-lattice relaxation rates in dsDNA under 50 bp in length are much faster than those calculated for the same DNAs modeled as rigid rods. The simplest way to account for this difference is by allowing for internal flexibility in models of DNA. Because of this discrepancy, we derive expressions for the spectral densities due to CSA, END, and SR mechanisms directly from a weakly bending rod model for DNA. Special emphasis in this development is given to the SR mechanism because of the lack of such detail in previous treatments. The theory developed in this paper provides a framework for computing relaxation rates from the WBR model to compare with magnetic resonance relaxation data and to ascertain the twisting and bending force constants that characterize DNA.     

Recurrent random walks on homogeneous spaces of p-adic algebraic groups of polynomial growth

Let G be a p-adic algebraic group of polynomial growth and H be a closed subgroup of G. We prove the growth conjecture for the homogeneous space G/H, that is, G/H supports a recurrent random walk if and only if G/H has polynomial growth of degree atmost two. Received: 23 November 2007     

Real closed fields with non-standard and standard analytic structure

We consider the ordered field which is the completion of thePuiseux series field over equipped with a ring of analyticfunctions on [–1, 1]ⁿ which contains the standard subanalyticfunctions as well as functions given by t-adically convergentpower series, thus combining the analytic structures of Denefand van den Dries [Ann. of Math. 128 (1988) 79–138] andLipshitz and Robinson [Bull. London Math. Soc. 38 (2006) 897–906].We prove quantifier elimination and o-minimality in the correspondinglanguage. We extend these constructions and results to rankn ordered fields _n (the maximal completions of iterated Puiseuxseries fields). We generalize the example of Hrushovski andPeterzil [J. Symbolic Logic 72 (2007) 119–122] of a sentencewhich is not true in any o-minimal expansion of (shown in [Bull.London Math. Soc. 38 (2006) 897–906] to be true in ano-minimal expansion of the Puiseux series field) to a towerof examples of sentences _n, true in _n, but not true in any o-minimalexpansion of any of the fields , ₁, ..., _n–1.     

The establishment of quality systems in veterinary diagnostic testing laboratories in developing countries: experiences with the FAO/IAEA External Quality Assurance Programme

Quality systems, established to internationally accepted standards, are one mechanism that can assist in evaluations of the sustainability of technology transfer, the proficiency of the user, and the reliability and comparability of data generated, resulting in potential enhancement of laboratory credibility. The means of interpreting existing standards and implementing quality systems in developing country veterinary diagnostic laboratories has become a significant adjunct to the technology transfer element within the Food and Agriculture/ International Atomic Energy Agency, FAO/IAEA programme. The FAO/IAEA External Quality Assurance Programme (EQAP) is given as an example for an initial step towards enhancing the “quality” culture in developing country veterinary laboratories. In 1995 the EQAP began as an effort to assure that test results emanating from laboratories using FAO/IAEA ELISA kits for animal disease diagnosis are valid. For this purpose 15 international external quality-assurance rounds have been performed to date for a variety of animal diseases e.g. Rinderpest, brucellosis, trypanosomosis, and foot-and-mouth disease (FMD). Results indicate that the EQAP is a valuable tool in the assessment of both the results provided by, and use of the ELISA kits provided through, the joint FAO/IAEA programme. Furthermore EQAP can assist laboratory diagnosticians to enhance quality control/quality assurance (QC/QA) procedures for conducting FAO/IAEA ELISAs and to advise on the implementation of similar QC/QA procedures in other laboratory activities. Based on the experiences made during the implementation of the EQAP a proposal for establishing a quality system standard was ratified through the World Organization for Animal Health (OIE) general conference in May 2000. The OIE Standard On Management And Technical Requirements For Laboratories Conducting Tests For Infectious Animal Diseases is based on ISO 17025 and provides a clear formula for establishing quality systems in veterinary diagnostic laboratories world-wide.     

Stable ion NMR and GIAO-DFT study of novel cations from 8,16-dicyano[2.2]metacyclophanedienes and from strategically substituted/benzannelated dihydropyrenes: charge-induced tropicity modulation and pi-switching

The dicyanometacyclophanediene 1 is diprotonated at the cyano groups (1H2 2+) in various superacid media. Upon quenching, intact 1 and the ring-closed CPD 2 were obtained in a 3:2 or 3:1 ratio, depending on the superacid system. Compound 2 undergoes ring opening in the superacid to give the ipso-monoprotonated 2H+, which on quenching furnishes 1-cyanopyrene as a major product together with 2 and 1. The dication 3 2+, with strongly deshielded internal methyls, was generated from the epoxyannulene 3. Ketones 4-6 and ester 7 are O/C diprotonated to give paratropic carboxonium-annulenium dications (4H2 2+, 5H2 2+, 6H2 2+, and 7H2 2+, respectively). Ester 8 gives a trication by two-electron oxidation and O-protonation. Conjugated carboxylic acid 9 gives a mixture of two dications by CO and ring protonation. The dibromo derivatives 10 and 11 form carboxonium ions, whereas the monobromo derivative 12 is O/C diprotonated to give an oxonium-annulenium dication. Charge delocalization modes and tropicity in the resulting species are evaluated by NMR and GIAO-DFT. Facile formation of 2 from 1 in quenching experiments indicates that thermal closing can be achieved with the diprotonated dinitrile, without imposing skeletal rearrangement.     

Identifying and alleviating electrochemical side-reactions in light-emitting electrochemical cells

We demonstrate that electrochemical side-reactions involving the electrolyte can be a significant and undesired feature in light-emitting electrochemical cells (LECs). By direct optical probing of planar LECs, comprising Au electrodes and an active material mixture of {poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) + poly(ethylene oxide) (PEO) + KCF3SO3}, we show that two direct consequences of such a side-reaction are the appearance of a "degradation layer" at the negative cathode and the formation of the light-emitting p-n junction in close proximity to the cathode. We further demonstrate that a high initial drive voltage and a high ionic conductivity of the active material strongly alleviate the extent of the side reaction, as evidenced by the formation of a relatively centered p-n junction, and also rationalize our findings in the framework of a general electrochemical model. Finally, we show that the doping concentrations in the doped regions at the time of the p-n junction formation are independent of the applied voltage and relatively balanced at approximately 0.11 dopants/MEH-PPV repeat unit in the p-type region and approximately 0.15 dopants/MEH-PPV repeat unit in the n-type region.     

Carbene-stabilized diphosphorus

The potassium graphite reduction of L:PCl3 leads to the formation of carbene-stabilized diphosphorus molecules, L:P-P:L, 1 (L: = :C{N(2,6-Pri2C6H3)CH}2) and 2 (L: = :C{N(2,4,6-Me3C6H2)CH}2), respectively. The nature of the bonding in 1 and 2 was delineated by DFT computations.     

(Chloromethyl)pentacarbonylmanganese(I): a crystal structure with a non-crystallographic centre of symmetry

There are two molecules in the asymmetric unit of the P2₁/c unit cell of ClCH₂Mn(CO)₅, the first halomethyl complex of manganese to be structurally determined. The molecules are crystallographically independent, despite an apparent local centre of symmetry. The average bond parameters include Mn–C_alkyl 2.128(8) Å, C–Cl 1.811(8) Å and Mn–C–Cl 116.4(4)°.     

An improved solid-phase methodology for the synthesis of putative hexa- and heptapeptide intermediates in vancomycin biosynthesis

The biosynthesis of the vancomycin aglycone involves three oxidative phenol coupling reactions, each catalyzed by a discrete cytochrome P450-like enzyme. Studies on the mechanism and specificity of the enzyme (called OxyB) catalyzing the first coupling, require access to suitable linear peptide precursors, each conjugated as a thioester to a peptide carrier domain of the vancomycin non-ribosomal peptide synthetase. An efficient route to representative free linear peptides is described here. The method makes use of Alloc-chemistry during solid-phase assembly of the peptide backbone, but importantly and in contrast to earlier efforts, largely avoids the use of amino acid side chain protecting groups. In this way, the target linear peptides can be released directly from the solid support under very mild conditions.