High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

Scalable Biosynthesis of the Seaweed Neurochemical,Kainic Acid

Kainic acid, the flagship member of the kainoid family of natural neurochemicals, is a widely used neuropharmacological agent that helped unravel the key role of ionotropic glutamate receptors, including the kainate receptor, in the central nervous system. Worldwide shortages of this seaweed natural product in the year 2000 prompted numerous chemical syntheses, including scalable preparations with as few as six‐steps. Herein we report the discovery and characterization of the concise two‐enzyme biosynthetic pathway to kainic acid from l ‐glutamic acid and dimethylallyl pyrophosphate in red macroalgae and show that the biosynthetic genes are co‐clustered in genomes of Digenea simplex and Palmaria palmata. Moreover, we applied a key biosynthetic α‐ketoglutarate‐dependent dioxygenase enzyme in a biotransformation methodology to efficiently construct kainic acid on the gram scale. This study establishes both the feasibility of mining seaweed genomes for their biotechnological prowess.     

High-performance liquid chromatographic assay for the antitumor glycoside phyllanthoside and its stability in plasma of several species

Phyllanthoside is a glycoside isolated from the roots of the Central American tree Phyllanthus acuminatus Vahl with antitumor activity against murine B-16 melanoma and P-388 leukemia. We report a reversed-phase high-performance liquid chromatographic assay for phyllanthoside in plasma using a 25-cm RP-18, 5-micron column with a linear 10-min gradient of 50% to 100% methanol in 0.3 M sodium acetate, pH 4.0, at a flow-rate of 1.5 ml/min. Eluting peaks were detected at 270 nm. The lower limit of sensitivity of the assay for phyllanthoside in 0.5 ml plasma following ethyl acetate extraction at pH 7.0 was 0.25 micrograms/ml and the coefficient of variation at 1 microgram/ml was +/- 7.4%. Phyllanthoside was very rapidly broken down by mouse and rat plasma in vitro to an unidentified less polar metabolite. Formation of this metabolite was completely inhibited by preheating mouse plasma to 100 degrees C for 10 min. When mouse plasma was diluted 1:50 with water the half-life of phyllanthoside disappearance at 37 degrees C was 2.0 min. Breakdown of phyllanthoside in plasma from other species was slower than in mouse and the initial half-life at 37 degrees C in dog plasma was 30 min, in monkey plasma 33 min and in human plasma 38 min. The same less polar metabolite as in mouse plasma was formed slowly by plasma of monkey and dog. Phyllanthoside did not accumulate in human red blood cells. Binding of phyllanthoside to human plasma protein determined by ultrafiltration at 4 degrees C was 70%.     

Lanthanide Clusters with Chalcogen Encapsulated Ln: NIR Emission from Nanoscale NdSe(x)

Ln(SePh)(3) (Ln = Ce, Pr, Nd) reacts with elemental Se in the presence of Na ions to give (py)(16)Ln(17)NaSe(18)(SePh)(16), a spherical cluster with a 1 nm diameter. All three rare-earth metals form isostructural products. The molecular structure contains a central Ln ion surrounded by eight five-coordinate Se(2-) that are then surrounded by a group of 16 Ln that define the cluster surface, with additional μ(3) and μ(5) Se(2-), μ(3) and μ(4) SePh(-), and pyridine donors saturating the vacant coordination sites of the surface Ln, and a Na ion coordinating to selenolates, a selenido, and pyridine ligands. NIR emission studies of the Nd compound reveal that this material has a 35% quantum efficiency, with four transitions from the excited state (4)F(3/2) ion to (4)I(9/2), (4)I(11/2), (4)I(13/2), and (4)I(15/2) states clearly evident. The presence of Na(+) is key to the formation of these larger clusters, where reactions using identical concentrations of Nd(SePh)(3) and Se with either Li or K led only to the isolation of (py)(8)Nd(8)Se(6)(SePh)(12).     

Alkyl (C<Subscript>10</Subscript>, C<Subscript>12</Subscript>, C<Subscript>14</Subscript> and C<Subscript>16</Subscript>) triphenyl phosphonium bromide influenced cloud points of nonionic surfactants (Triton X 100, Brij 56 and Brij 97) and the polymer (Polyvinyl methyl ether)

The clouding points (CP) of the nonionic surfactants p-tert-octyl phenyl polyoxyethylene ether (Triton X 100), Brij-56 and Brij-97, and the water soluble polymer polyvinylmethylether (PVME) have been measured in the presence of the ionic surfactants alkyl (C₁₀, C₁₂, C₁₄ and C₁₆) triphenyl phosphonium bromides (ATPBs). The threshold additive concentrations required for efficient CP enhancement of the systems that were studied have been determined. Considering CP as the threshold state of phase separation, the energetics of the process at different additive concentrations has been evaluated. The spontaneity of free energy of the clouding process (G _c ⁰ ) at the transition concentrations followed the order PVME > TX 100  Bj 56 > Bj 97. The clouding process has been found to be energetically endothermic with fairly large enthalpy and entropy changes that nicely compensate each other. The compensation temperature has been evaluated and compared with different types of the clouding agents.This revised version was published online in January 2005 with corrections to the names of the authors.     

Mono-, di-, and trinuclear luminescent silver(I) and gold(I) N-heterocyclic carbene complexes derived from the picolyl-substituted methylimidazolium salt: 1-methyl-3-(2-pyridinylmethyl)-1H-imidazolium tetrafluoroborate

The N-heterocyclic carbene (NHC) precursor, 1-methyl-3-(2-pyridinylmethyl)-1H-imidazolium tetrafluoroborate, [HCH3im(CH2py)]BF4, reacted with AgBF4 in the presence of aqueous NaOH to produce the silver complex [Ag(CH3im(CH2py))2]BF4 (1) which was then reacted with Au(tht)Cl to form the corresponding gold(I) complex, [Au(CH3im(CH2py))2]BF4 (2). Complex 2 reacted with 1 equiv of AgBF4 to produce the mixed-metal species [AuAg(CH3im(CH2py))2](BF4)2 (3). The reaction of 2 with 1 equiv of Au(tht)Cl followed by metathesis with NaBF4 produces the dimetallic gold complex [Au2(CH3im(CH2py))2](BF4)2 (4). The reaction of [Ag(CH3im(CH2py))2]BF4 (1) with 1 equiv of AgBF4 produces the trinuclear [Ag3(CH3im(CH2py))3(NCCH3)2](BF4)3 (5) complex, which appears to dissociate into a dimetallic complex in solution. Complexes 1-5 were characterized by 1H NMR, 13C NMR, UV-vis, luminescence spectroscopy, elemental analysis, mass spectrometry, and X-ray crystallography. The CH3im(CH2py) ligands in 3 are arranged in a head-to-head fashion spanning a Au-Ag separation of 3.0318(5) A with the carbene portion of the ligand remaining coordinated to the Au(I) center. In 4, the ligands are arranged in a head-to-tail fashion with an Au-Au separation of 3.1730(5) A. In 5, the ligands bridge the nearly symmetrical Ag3 triangular core with short Ag-Ag separations of 2.7765(8), 2.7832(8), and 2.7598(8) A. All of these complexes, including the ligand precursor, are intensely luminescent in solution and the solid state.     

A rapid method for the determination of Mark–Houwink constants from GPC and viscosity data on a single sample

A straightforward and rapid method for the determination of Mark–Houwink constants from GPC and viscometry is described. A single original polymer is sufficient since other samples were prepared by sonication. The use of a number of samples in this way is shown to improve the accuracy over determinations where only two polymer samples are used.     

Arylene ethynylene macrocycles prepared by precipitation-driven alkyne metathesis

A convenient, multigram-scale synthesis of arylene ethynylene macrocycles near room temperature is described. Driven by the precipitation of a diarylacetylene byproduct, alkyne metathesis produces the desired macrocycles in one step from monomers in high yields.     

Microwave promoted amination of 3-bromoisoxazoles

This Letter describes the amination of 3-bromoisoxazoles by a nucleophilic aromatic substitution reaction. We have found 3-bromoisoxazoles to be inert to substitution under thermal conditions, however, the employment of phosphazene bases under microwave irradiation facilitates the amination process and allows the corresponding 3-aminoisoxazoles to be isolated in moderate yield.