Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Synthesis and structure of oligomeric dimesitylgermyl-substituted carbodiimides; characterization of higher oligomers

New cyclic oligomers of dimesitylgermylene carbodiimides (Mes2GeNCN)n (n = 3 (1) and 4 (2)) were synthesized by reactions of dimesityldichlorogermane with either cyanamide in the presence of triethylamine or lithium cyanamide. The reactions always gave 1, the trimer of the hypothetical (Mes2GeN−CN), as the major compound. Higher oligomers 3 (n up to 20−30) also can be isolated, depending on the reaction conditions. In THF solution at room temperature, 2 and 3 slowly isomerize to 1, which seems to be the most stable compound. X-ray analysis of trimer 1 and tetramer 2 shows unstrained tetrahedral germanium atoms and linear diimine linkers.

Metal complexes with atropisomeric sulfur ligands in asymmetric hydroformylation X-ray structure of [Rh2(μ-biphes)(cod)2] (H2biphes = 4,4′-biphenanthrene-3,3′-dithiol)

The addition of the atropisomeric racemic sulfur compound 4,4′-biphenanthrene-3,3′-dithiol (H2 biphes) to a dichloromethane solution of [{M(μ-OMe)(cod)}2] (M = Rh, Ir, cod = cycloocta-1,5-diene) afforded the dithiolate-bridged complexes [{Rh2(μ-biphes)(cod)2}n] (n = 2 5 or n = 1 6) and [{Ir2(μ-biphes)(cod)2}n]·nCH2Cl27. When 1,1′-binaphthalene-2,2′-dithiol (H2 binas) reacted with [{Ir(μ-OMe)(cod)}2], complex [Ir2(μ-binas)(cod)2] 8 was obtained. Complexes 5 and 6 reacted with carbon monoxide to give the dinuclear tetracarbonyl complex [Rh2(μ-biphes)(CO)4] 9. The reaction of 9 with PR3 provided the mixed-ligand complexes [{Rh2(μ-biphes)(CO)2(PR3)2}2] · xCH2Cl2 (R = Ph, x = 2 10, C6H11, x = 1 11) and [{Rh2(μ-biphes)(CO)3(PR3)}2] · CH2Cl212 (R = OC6H4But-o). The crystal structure of 6 was determined by X-ray diffraction. Reaction of the dithioether ligand Me2biphes with [Rh(cod)2]ClO4 in CH2Cl2 solution afforded the cationic complex [Rh(cod)(Me2biphes)]ClO4 · CH2Cl213. Asymmetric hydroformylation of styrene was performed using the complexes described. The extent of aldehyde conversion ranges from 53 to 100%, with selectivities towards branched aldehydes in the range 51 to 96%. The enantioselectivities were quite low and did not exceed 20%.

Synthesis, X-ray crystal structure and reactivity of the polymeric copper(II) dicarboxylic acid complex {Cu2(η1η1μ2-oda)2(py)4(H2O)2}n(odaH2 = octanedioic acid, PY = pyridine)

An aqueous solution of the α-ω-dicarboxylic acid octanedioic acid (odaH2) reacts with [Cu2(μ-O2CCH3)4(H2O)2] in the presence of an excess of pyridine (py) to give the crystalline copper(II) complex {Cu2(η1η1μ2-oda)2(py)4(H2O)2}n (1). structure of 1, as determined by X-ray crystallography, consists of polymeric chains in which bridging oda2− anions link two crystallographically identical copper atoms. The copper atoms are also ligated by two transoidal pyridine nitrogens and an oxygen atom from an apical water molecule, giving the metals an overall N2O3 square-pyramidal geometry. If the blue solid 1 is gently heated, or if it is left to stand in its mother liquor for prolonged periods, it loses one molecule of pyridine and half a molecule of water and the green complex {Cu (oda)(py)(H2O)0.5}n (2) is formed. Spectroscopic and magnetic data for both complexes are given, together with the electrochemical and thermogravimetric measurements for 1.

Structure and spectra of dichloro(hydroxy-methoxy-di(2-pyridyl)methane)copper(II)

The non-electrolyte dichloro(hydroxy-methoxy-di(2-pyridylmethane)copper(II), resulting from the reaction of di(2-pyridyl)ketone and copper(II) chloride in methanol solution, was isolated and characterized and its structure was determined by X-ray diffraction. The pyridyl nitrogens and the chloride anions virtually from a basal plane in which lies the copper atom, while the oxygen of the methoxy group is in an apical position at a distance of 2.497 (3)Å. The nitrogenous base adopts the boat conformation with the pyridyl rings forming a dihedral angle of 108.72 (14)°. The nearest interatomic copper distance of 3.940(3)Å precludes copper-copper interactions, while the proximity of copper to the out-of-plane chlorine atoms [3.109(3)Å] suggests weakly bound chloro-bridged dimers. Spectral changes indicate that protic molecules displace the methoxy group and water affords the corresponding 1,1-diol.

Synthesis and X-ray crystal structure of the copper(I) dicarboxylic acid complex [Cu(η1-bdoaH)(PPh3)3] (bdoaH2 = benzene-1,2- dioxyacetic acid)

The copper(II) complex [Cu(bdoa)(H2O)2] (bdoaH2 = benzene-1,2-dioxyacetic acid) reacts with triphenylphosphine (1:4 mol ratio) to give the colourless copper(I) complex [Cu(η1-bdoaH)(PPh3)3] (1) in good yield. The X-ray crystal structure of the complex shows the copper atom at the centre of a distorted tetrahedron, and is ligated by the phosphorus atoms of the three triphenylphosphines and one carboxylate oxygen atom of the bdoaH− ligand. Significant intermolecular hydrogen-bonding exists between the pendant carboxylate OH function of one molecule and the uncoordinated “ketonic” oxygen of a neighbouring molecule. Complex 1 is non-conducting in chloroform but ionizes readily in acetonitrile. The cyclic voltammogram of an acetonitrile solution of 1 shows a single irreversible anodic peak for the oxidation of the PPh3 ligands and the copper(I) centre, and a single irreversible cathodic peak for the reduction of the bdoaH− ion. IR and mass spectral data for 1 are given.

Synthesis and reactions of [Et3NH]4[Mo8O6]: X-ray crystal structure of [Et3NH]3[NaMo8O26]

[Et3NH]4[Mo8O26] (1) was prepared by reacting triethylamine with either molybdenum trioxide dihydrate or with a solution of ammonium molybdate in aqueous HCl. An aqueous solution of complex 1 reacted with an excess of sodium chloride to give a mixture of [Et3NH]3[NaMo8O26] (2) and [Et3NH]2[Mo6O19] (3). Complex 2 was also formed on reacting sodium molybdate with triethylamine in aqueous HCl. In the reaction of 1 with potassium chloride the nature of the product obtained was critically dependent upon reaction time. After a 5.5 h reflux period a mixture of [Et3NH]3[KMo8O26] (4) and 3 was obtained, whereas upon prolonged reflux (24 h) only K4Mo8O26 · H2O (5) was precipitated. The X-ray crystal structure of 2 shows it to be polymeric, with each Na+ ion sandwiched between two β[Mo8O26]4− ions. Four oxygen atoms on one face of each β[Mo8O26]4− ion are coordinated to a Na+ ion, and four oxygens from the opposite face are bonded to the next Na+ ion in the polymer chain. This produces a zig-zag arrangement of Na+ ions throughout the molecular structure. Spectral, conductivity and voltammetry data are given.

Synthesis of water-soluble and ether-soluble tetra-μ-acetatodiruthenium(II,III) complexes and X-ray crystal structure of [Ru2(μ-O2CC6H5)4(C2H5OH)2][Ru2(μ-O2CC6H5)4(HSO4)2]

[Ru2(μ-O2CCH3)4Cl] reacts readily with aqueous Ag2SO4 (2: 1 molar ratio) to give the sulphate salt [Ru2(μ-O2CCH3)4(H2O)2]2(SO4) (1). Addition of NaBPh4 to an aqueous solution of 1 produces the ether-soluble tetraphenylborate salt [Ru2(μ-O2CCH3)4(H2O)2][BPh4] (2). A methanolic solution of 1 reacts with Ba(C6H5CCCO2)2 · H2O to give the tetraacetatemonophenylpropynoate complex [Ru2(μ-O2CCH3)4(O2CCCC6H5)] · H2O (3). The reaction of an ethanolic suspension of [Ru2(μ-O2CC6H5)4Cl] with Ag2SO4 and H2SO4 (2 : 1 : 1 molar ratio) leads to the tetra-μ-benzoatodiruthenium(II,III) double complex salt [Ru2(μ-O2CC6H5)4(C2H5OH)2][Ru2(μ-O2CC6H5)4(HSO4)2] (4). Complex 4 is also obtained by reacting an ethanolic solution of 1 with an excess of benzoic acid in the presence of H2SO4. The X-ray crystal structure of 4 shows it to consist of [Ru2(μ-O2CC6H5)4(C2H5OH)2]+ and [Ru2(μ-O2CC6H5)4(HSO4)2]− ions, which are linked together by hydrogen bonds into an infinite polymeric chain. The RuRu distances in the cation and anion are very similar [2.265(2) and 2.272(2) Å, respectively]. Spectroscopic, magnetic, conductivity and cyclic voltammetry data are given for the complexes.

Formation of isopolyoxometallate(VI) anions in the reaction between M(CO)6 (M = W, Mo) and acetic acid: X-ray crystal structure of [W3(μ3-O)2(μ2η2-O2CCH3)6(H2O)3]2[W10O32·solvent

W(CO)6 reacts with a mixture of acetic acid/acetic anhydride to give [W3 (μ3-O)2(μ2η2-O2CCH3)6(H2O)3](CH3CO2)2 (1), which was converted by HClO4 to [W3 (μ3-O)2(μ2η2-O2CCH3)6(H2O)3](ClO4)2 (2). Addition of CH3CO2Na to the above reaction mixture, and prolonged exposure of the solution to air, results in the formation of the WIV/WVI complex salt [W3(μ3-O)2(μ2η2-O2CCH3)6(H2O)3]2[W10O32]·solvent (3). Complex 3 was also prepared by reacting 1 with Na2WO4·2H2O in acetic acid, and it has been characterized by X-ray crystallography. Addition of [CH3(CH2)3]4N(ClO4) to the reaction filtrate remaining after the preparation of [Mo2(μ-O2CCH3)4][from Mo(CO)6, CH3CO2H and (CH3CO)2O], followed by exposure to air, gives ([CH3(CH2)3]4N)2[Mo6O19] (4).

Alkenyl derivatives of the metals. Oxidative addition to intermediate tin(II) alkenyls; isolation, and crystal and molecular structure of n-butyltris(triphenylethenyl)tin(IV)

Reaction of tin(II) chloride with Li(CPhCPh2) at –78 °C in diethyl ether–hexane–tetrahydrofuran affords a deep red solution whose colour fades on warming, and which we believe contains the (unstable) first dialkenyltin(II) species. The latter survives long enough at low temperatures to undergo intermolecular oxidative addition, and one such adduct leads ultimately to the formation of Sn(CPhCPh2)3Bun, which has been fully characterised including a crystal and molecular structure study. The mechanism of formation of the final product has been examined and results are reported.

Modulating self-assembly of a nanotape-forming peptide amphiphile with an oppositely charged surfactant

A peptide amphiphile (PA) C16-KTTKS, containing a pentapeptide headgroup based on a sequence from procollagen I attached to a hexadecyl lipid chain, self-assembles into extended nanotapes in aqueous solution. The tapes are based on bilayer structures, with a 5.2 nm spacing. Here, we investigate the effect of addition of the oppositely charged anionic surfactant sodium dodecyl sulfate (SDS) via AFM, electron microscopic methods, small-angle X-ray scattering and X-ray diffraction among other methods. We show that addition of SDS leads to a transition from tapes to fibrils, via intermediate states that include twisted ribbons. Addition of SDS is also shown to enhance the development of remarkable lateral ‘‘stripes’’ on the nanostructures, which have a 4 nm periodicity. This is ascribed to counterion condensation. The transition in the nanostructure leads to changes in macroscopic properties, in particular a transition from sol to gel is noted on increasing SDS (with a further reentrant transition to sol on further increase of SDS concentration). Formation of a gel may be useful in applications of this PA in skincare applications and we show that this can be controlled via development of a network of fine stranded fibrils.

Self-assembly of a peptide amphiphile containing l-carnosine and its mixtures with a multilamellar vesicle forming lipid

The self-assembly of the peptide amphiphile (PA) hexadecyl-(β-alaninehistidine) is examined in aqueous solution, along with its mixtures with multilamellar vesicles formed by DPPC (dipalmitoyl phosphatidylcholine). This PA, denoted C16-βAH, contains a dipeptide headgroup corresponding to the bioactive molecule L-carnosine. It is found to selfassemble into nanotapes based on stacked layers of molecules. Bilayers are found to coexist with monolayers in which the PA molecules pack with alternating up−down arrangement so that the headgroups decorate both surfaces. The bilayers become dehydrated as PA concentration increases and the number of layers in the stack decreases to produce ultrathin nanotapes comprised of 2−3 bilayers. Addition of the PA to DPPC multilamellar vesicles leads to a transition to well-defined unilamellar vesicles. The unique ability to modulate the stacking of this PA as a function of concentration, combined with its ability to induce a multilamellar to unilamellar thinning of DPPC vesicles, may be useful in biomaterials applications where the presentation of the peptide function at the surface of self-assembled nanostructures is crucial.

Conductance of amyloid β based peptide filaments: structure–function relations.

Controlling the morphology of self-assembled peptide nanostructures, particularly those based on amyloid peptides, has been the focus of intense research. In order to exploit these structures in electronic applications, further understanding of their electronic behavior is required. In this work, the role of peptide morphology in determining electronic conduction along self-assembled peptide nanofilament networks is demonstrated. The peptides used in this work were based on the sequence AAKLVFF, which is an extension of a core sequence from the amyloid b peptide. We show that the incorporation of a non-natural amino acid, 2-thienylalanine, instead of phenylalanine improves the obtained conductance with respect to that obtained for a similar structure based on the native sequence, which was not the case for the incorporation of 3-thienylalanine. Furthermore, we demonstrate that the morphology of the self-assembled structures, which can be controlled by the solvent used in the assembly process, strongly affects the conductance, with larger conduction obtained for a morphology of long, straight filaments. Our results demonstrate that, similar to natural systems, the assembly and folding of peptides could be of great importance for optimizing their function as components of electronic devices. Hence, sequence design and assembly conditions can be used to control the performance of peptide based structures in such electronic applications.

Slow-release RGD-peptide hydrogel monoliths

We report on the formation of hydrogel monoliths formed by functionalized peptide Fmoc-RGD (Fmoc: fluorenylmethoxycarbonyl) containing the RGD cell adhesion tripeptide motif. The monolith is stable in water for nearly 40 days. The gel monoliths present a rigid porous structure consisting of a network of peptide fibers. The RGD-decorated peptide fibers have a β-sheet secondary structure. We prove that Fmoc-RGD monoliths can be used to release and encapsulate material, including model hydrophilic dyes and drug compounds. We provide the first insight into the correlation between the absorption and release kinetics of this new material and show that both processes take place over similar time scales.

Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C-18O labelling, polarised infrared spectroscopy and molecular combing

A novel combination of site-specific isotope labelling, polarised infrared spectroscopy and molecular combing reveal local orientational ordering in the fibril-forming peptide YTIAALLSPYSGGRADS. Use of 13C-18O labelled alanine residues demonstrates that the Nterminal end of the peptide is incorporated into the cross-beta structure, while the C-terminal end shows orientational disorder