The crystallographic structure of thermoNicotianamine synthase with a synthetic reaction intermediate highlights the sequential processing mechanism

We determined the three-dimensional structure of a complex between an archaeal nicotianamine synthase homologue and a chemically synthesised reaction intermediate. This structure suggests that the enzymes cavity allows both an ordered substrate binding and provides energetic coupling of the reaction intermediate formation and translocation.     

The crystal structure of the L1 intermediate of halorhodopsin at 1.9 angstroms resolution

The mutant T203V of the light driven chloride pump halorhodopsin from Halobacterium salinarum was crystallized and the X-ray structure was solved at 1.6 angstroms resolution. The T203V structure turned out to be nearly identical to the wild type protein with a root mean square deviation of 0.43 angstroms for the carbon alpha atoms of the protein backbone. Two chloride binding (CB) sites were demonstrated by a substitution of chloride with bromide and an analysis of anomalous difference Fourier maps. The CB1 site was found at the same position as in the wild type structure. In addition, a second chloride binding site CB2 was identified around Q105 due to higher resolution in the mutant crystal. As T203V showed a 10 times slower decay of its photocycle intermediate L, this intermediate could be trapped with an occupancy of 60% upon illumination at room temperature and subsequent cooling to 120 degrees K. Fourier transform infrared spectroscopy clearly identified the crystal to be trapped in the L1 intermediate state and the X-ray structure was solved to 1.9 angstroms resolution. In this intermediate, the chloride moved by 0.3 angstroms within binding site CB1 as indicated by peaks in difference Fourier density maps. The chloride in the second binding site CB2 remained unchanged. Thus, intraproteinous chloride translocation from the extracellular to the cytoplasmic part of the protein must occur in reaction steps following the L1 intermediate in the catalytic cycle of halorhodopsin.     

3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy

Enzyme catalysis relies on conformational plasticity, but structural information on transient intermediates is difficult to obtain. We show that the three‐dimensional (3D) structure of an unstable, low‐abundance enzymatic intermediate can be determined by nuclear magnetic resonance (NMR) spectroscopy. The approach is demonstrated for Staphylococcus aureus sortase A (SrtA), which is an established drug target and biotechnological reagent. SrtA is a transpeptidase that converts an amide bond of a substrate peptide into a thioester. By measuring pseudocontact shifts (PCSs) generated by a site‐specific cysteine‐reactive paramagnetic tag that does not react with the active‐site residue Cys184, a sufficient number of restraints were collected to determine the 3D structure of the unstable thioester intermediate of SrtA that is present only as a minor species under non‐equilibrium conditions. The 3D structure reveals structural changes that protect the thioester intermediate against hydrolysis.     

A new series of N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives as inhibitors of lumazine synthase and riboflavin synthase: design, synthesis, biochemical evaluation, crystallography, and mechanistic implications

The penultimate step in the biosynthesis of riboflavin is catalyzed by lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the lumazine synthase-catalyzed reaction were synthesized and evaluated as lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis lumazine synthase, Bacillus subtilis lumazine synthase, and Schizosaccharomyces pombe lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.     

Model-independent structure and resonant X-ray spectra of intermediate smectic phases

It is shown that the orientational structure of intermediate smectic phases can be determined using the symmetry properties of the general free energy with arbitrary orientational coupling between smectic layers, without addressing a particular model. The structure of three- and four-layer intermediate phases, obtained in this way, corresponds to experimental data. The same method enables one to predict the structure of intermediate phases with periodicity of five and six layers, which have not been observed experimentally so far. The resonant X-ray spectra of the five- and six-layer intermediate phases with predicted structure have also been calculated. These spectra are characterized by a number of features which enable one to distinguish five-layer and six-layer intermediate phases from phases with smaller periods.     

Spectroscopic and electronic structure studies of intermediate X in ribonucleotide reductase R2 and two variants: a description of the FeIV-oxo bond in the FeIII-O-FeIV dimer

Spectroscopic and electronic structure studies of the class I Escherichia coli ribonucleotide reductase (RNR) intermediate X and three computationally derived model complexes are presented, compared, and evaluated to determine the electronic and geometric structure of the FeIII-FeIV active site of intermediate X. Rapid freeze-quench (RFQ) EPR, absorption, and MCD were used to trap intermediate X in R2 wild-type (WT) and two variants, W48A and Y122F/Y356F. RFQ-EPR spin quantitation was used to determine the relative contributions of intermediate X and radicals present, while RFQ-MCD was used to specifically probe the FeIII/FeIV active site, which displayed three FeIV d-d transitions between 16,700 and 22,600 cm(-1), two FeIV d-d spin-flip transitions between 23,500 and 24,300 cm(-1), and five oxo to FeIV and FeIII charge transfer (CT) transitions between 25,000 and 32,000 cm(-1). The FeIV d-d transitions were perturbed in the two variants, confirming that all three d-d transitions derive from the d-pi manifold. Furthermore, the FeIV d-pi splittings in the WT are too large to correlate with a bis-mu-oxo structure. The assignment of the FeIV d-d transitions in WT intermediate X best correlates with a bridged mu-oxo/mu-hydroxo [FeIII(mu-O)(mu-OH)FeIV] structure. The mu-oxo/mu-hydroxo core structure provides an important sigma/pi superexchange pathway, which is not present in the bis-mu-oxo structure, to promote facile electron transfer from Y122 to the remote FeIV through the bent oxo bridge, thereby generating the tyrosyl radical for catalysis.     

Synthesis of a key intermediate of novel galbonolide analogues via efficient construction of a conjugated diene system

The development of an efficient synthetic method enabled multi-gram synthesis of a key intermediate, which is useful for the modification at the C6-functional group of galbonolide analogues. The structure of a key intermediate including a conjugated diene was afforded by Horner-Emmons reaction, alkylation of Weinreb amide with alkyl lithium and a subsequent Wittig reaction.     

Interaction of an intermediate structure of Bacillus subtilis α-amylase with alkyl-substituted sepharose 4B

An intermediate form of alpha-amylase from Bacillus subtilis was prepared following a previously reported procedure. Stabilization of this protein structure by various additives and its interaction with alkyl-substituted Sepharose 4B (Sepharose-lipid), used to mimic the role of the alkyl chains of the phospholipid bilayer, were investigated. Exposure of hydrophobic clusters in the protein structure on denaturation was indicated by a greater affinity of the intermediate form for interaction with the alkyl chains on the matrix, as compared with the original native structure. Near- and far-ultraviolet circular dichroism studies supported loss of tertiary structure with retention of secondary structure, as expected from molten globular intermediate forms. Based on the results presented, we suggest that interaction of a protein in its native and nonnative forms with an alkyl-substituted matrix may provide useful information regarding its capacity for insertion into and translocation across the biologic membrane.     

New iron complexes from nucleophile addition/carbonylation of η4-(1,3-diene)tricarbonyliron(0) complexes

A series of novel organoiron complexes has been isolated and studied by ¹H NMR, ¹³C NMR, and IR spectroscopy. Addition of LiC(CH₃)₂CN to (1,3-cyclohexadiene)tricarbonyliron produces an intermediate which is only stable at low temperature and which is assigned the homoallyl—Fe(CO)₃ anion structure. The intermediate rearranges on warming into a stable complex, for which full spectral data support the structure as an allyl—Fe(CO)₃ anionic species. Interception of the first formed intermediate with CO gives an acylferrate complex with an olefin unit still bound to iron, and methylation then occurs at oxygen to produce an unusual internally-bound (alkene)(methoxyalkylidene)tricarbonyliron species.     

Unexpected Intermediate State for the Cylinder‐to‐Gyroid Transition in a Block Copolymer Solution

The cylinder‐to‐gyroid transition in a concentrated solution of polystyrene‐block‐polyisoprene in dibutyl phthalate has been studied using rheology and small angle X‐ray scattering. Following an appropriate temperature quench, the oriented cylinder phase transforms to the gyroid structure epitaxially. Remarkably, an intermediate state appears for a deep quench, whereas for a shallow quench the transition proceeds directly; the intermediate state exhibits scattering signatures consistent with a hexagonally perforated layer structure.     

Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.

BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates. RESULTS: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A resolution, respectively. The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this clan of glycoside hydrolases.     

A m-benzyne to o-benzyne conversion through a 1,2-shift of a phenyl group

Pyrolysis of two differently labeled versions of 3-phenylphthalic anhydride shows that a m-benzyne can form the related o-benzyne through shift of a phenyl group. The highest energy point in the process is the transition structure for a reverse carbon-hydrogen insertion in an intermediate benzopentalene. With the minor addition of an intermediate alkyne formed through a Roger Brown rearrangement, the original mechanism for formation of acenaphthalene accommodates the labeling results.     

Self consistent direct dynamics studies of interfaces

To reach the goal of prediction of electrochemical behavior from first principles, it appears increasingly evident that an intermediate stage, between ab initio calculation and Monte Carlo or classical molecular dynamics, will be required. Here we report progress on the development of such an intermediate computational method, using a self consistent tight binding approach, and report some preliminary results on the structure and dynamics of water on the 110 face of rutile titanium dioxide.     

Features of the phase behavior of gamma-irradiated polytetrafluoroethylene powder

By using the technique of thermomechanical spectroscopy, an amorphous and three crystalline (high melting, intermediate, and low melting) blocks of the topological structures of polytetrafluoroethylene (PTFE) powder were characterized and their behavior under γ-radiation up to 2420 kGy was explored. The powder has an anisotropic topological structure. Starting from a dose of 4 kGy, the structure is radically changed with the long-range orientation of chains in the intermediate and high melting crystalline blocks of PTFE being replaced by a short range orientation of cluster association structures. The temperatures of glass transition and melting point continuously decreased with an increased dose of irradiation. The influence of γ-radiation on the powder and sheet of PTFE are essentially the same, the formation of amorphous character.     

Synthetic studies on altemicidin: stereocontrolled construction of the core framework

The stereoselective synthesis of the key intermediate for altemicidin has been accomplished. The synthesis commenced with a bicyclo[3.3.0] framework, which was readily obtained via an intramolecular C-H insertion reaction. A Curtius rearrangement was employed as a key step to stereoselectively construct the beta-hydroxyl alpha-disubstituted-alpha-amino acid structure. Synthesis of vinylogous urea was achieved using hydrolysis of nitrile intermediate.     

Model‐independent structure and resonant X‐ray spectra of intermediate smectic phases

It is shown that the orientational structure of intermediate smectic phases can be determined using the symmetry properties of the general free energy with arbitrary orientational coupling between smectic layers, without addressing a particular model. The structure of three‐ and four‐layer intermediate phases, obtained in this way, corresponds to experimental data. The same method enables one to predict the structure of intermediate phases with periodicity of five and six layers, which have not been observed experimentally so far. The resonant X‐ray spectra of the five‐ and six‐layer intermediate phases with predicted structure have also been calculated. These spectra are characterized by a number of features which enable one to distinguish five‐layer and six‐layer intermediate phases from phases with smaller periods.     

Synthesis o an 8-deaza analog of the intermediate in the thymidylate synthetase reaction

Synthesis of an 8-deaza analog of the proposed intermediate in the thymidylate synthetase reaction was accomplished from diethyl 8-deazafolic acid an unambiguous proof of the structure is provided.     

Total Syntheses of (−)‐Huperzine Q and (+)‐Lycopladines B and C

Utilizing a late‐stage enamine bromofunctionalization strategy, the twelve‐step total synthesis of (?)‐huperzine Q was accomplished. Furthermore, the first total syntheses of (+)‐lycopladines B and C are described. An unprecedented X‐ray crystal structure of an unusual epoxyamine intermediate is also reported, and the synthetic application of this intermediate in natural product synthesis is demonstrated.