Kinetic and regiospecific interrogation of covalent intermediates in the nonribosomal peptide synthesis of yersiniabactin

For interrogation of enzyme-bound intermediates in nonribosomal peptide synthetases (NRPSs), mass spectrometry is used to read out the kinetics and substrate specificity of this medicinally important class of enzymes. The protein HMWP2 (230 kDa) catalyzes 11 chemical reactions, four of which could be resolved by fast quench approaches combined with mass spectrometry. The rate of complex intermediate accumulation at the PCP1 active site was observed to occur with a rate of 19 s(-1), with the rate of cysteine acylation faster than that of intermediate translocation. Use of alternative substrates for salicylic acid (at the ArCP carrier domain) and l-cysteine (at the PCP1 carrier domain) revealed a high penalty for omission of the salicyl alcohol. For some substrates, large discrepancies were found between prior adenylation assays and the current MS-based readouts. Indirect evidence for condensation via a thiolate attack (vs an amino group) was also accumulated. This is the first report to correlate the percent occupancy of multiple active sites in parallel with kinetic and structural resolution of intermediates and provides new evidence of interdomain and intermodule communication within thiotemplate assembly lines.     

Cofactor-dependent enzyme catalysis in functionalized ionic solvents

Functionalized, hydrogen-bonding ionic liquids have been successfully evaluated as media for the performance of cofactor-dependent enzyme catalysed oxidations; the effects of incorporating hydroxyl groups into both the cation and anion have been studied and the dependence of activity upon water content has been evaluated.     

Diphosphine-phosphenium coordination complexes representing monocations with pendant donors and ligand tethered dications

Homoatomic P-P coordinate bonding is exploited to prepare the first examples of triphosphorus monocations and tetraphosphorus dications using dimethylphosphenium or diphenylphosphenium Lewis acceptors with diphosphinomethane, diphosphinoethane, diphosphinohexane, or diphosphinobenzene ligands. Solid-state structures and spectroscopic characterization data for complexes involving bis(diphenylphosphino)methane ligands show coordination of only one donor site of the diphosphine ligand in the monocations, and chelate complexation is not observed. Tetraphosphorus dications are observed with longer diphosphines, in which the ligand tethers two phosphenium acceptors. The structural preferences between monocations with pendant phosphines and tethered dications are dependent on intramolecular steric interactions and the flexibility of the tether.     

Synthesis, structure, and complexation of a large 28-mer macrocycle containing two binding sites for either anions or metal ions

The "one-pot" synthesis and characterization of a large 28-mer macrocycle (H(4)L(2)) with oxamido units capable of complexing guest ions through oxygen or nitrogen donor atoms is reported. Single-crystal structure determination of H(8)L(2)(NO(3))(4) and (Cu(2)[H(2)L(2)](H(2)O)(2))(NO(3))(2) demonstrated that the macrocycle contains two sites capable of complexing two nitrate anions or two copper(II) ions, involving a large structural reorganization in the conformation of the macrocyclic framework on coordination of the copper(II) ions when compared to the nitrate. Electrochemical and magnetic susceptibility measurements on the dinuclear Cu(II) complex and the related mononuclear and trinuclear Cu(II) complexes derived from the related 14-mer macrocycle were carried out and illustrate the role of the oxamido groups in mediating metal-metal interaction and delocalization.     

Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design

It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.     

Synthesis and biological evaluation of new inhibitors of UDP-Galf transferase--a key enzyme in M. tuberculosis cell wall biosynthesis

Two iminosugars have been designed and synthesized as potential inhibitors of UDP-Galf transferase, an enzyme involved in Mycobacterium tuberculosis cell wall biosynthesis. The design is based on a proposed model of the transition state for the transferase reaction. One of the two racemic compounds is the first reported inhibitor of the target enzyme from M. smegmatis.     

Lewis acid catalysis in heterolysis reactions of glycol ether radicals mimicking diol dehydratase-catalyzed reactions

Zinc bromide-catalyzed heterolysis reactions of glycol ether radicals were studied by laser flash photolysis methods, which gave the binding constants and catalytic rate constants for fragmentation. The Lewis acid-catalyzed heterolysis reactions mimic a putative reaction pathway in diol dehydratase-catalyzed reactions and are potentially useful polar processes for incorporation into conventional radical chain reaction sequences. [reaction: see text]     

Mineral–water interfacial structures revealed by synchrotron X-ray scattering

Chemical reactions occurring at the mineral–water interface are controlled by an interfacial layer, nanometers thick, whose properties may deviate from those of the respective bulk mineral and water phases. The molecular-scale structure of this interfacial layer, however, is poorly constrained, and correlations between macroscopic phenomena and molecular-scale processes remain speculative. The application of high-resolution X-ray scattering techniques has begun to provide substantial new insights into the molecular-scale structure of the mineral–water interface. In this review, we describe the characteristics of synchrotron-based X-ray scattering techniques that make them uniquely powerful probes of mineral–water interfacial structures and discuss the new insights that have been derived from their application. In particular, we focus on efforts to understand the structure and distribution of interfacial water as well as their dependence on substrate properties for major mineral classes including oxides, carbonates, sulfates, phosphates, silicates, halides and chromates. We compare these X-ray scattering results with those from other structural and spectroscopic techniques and integrate these to provide a conceptual framework upon which to base an understanding of the systematic variation of mineral–water interfacial structures.