Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

Mineralization mechanism of calcium phosphates under three kinds of Langmuir monolayers

Three kinds of Langmuir monolayers formed by dipalmitoylphosphatidylcholine (DPPC), arachidic acid (AA), and octadecylamine (ODA) were used as templates to study the initial stage of nucleation and crystallization of calcium phosphates. It was demonstrated that the combination of calcium ions (or phosphates) to the monolayer/subphase interface is a prerequisite for subsequent nucleation. It was found that calcium phosphate dihydrate (DPCD) formed at 25.0 degrees C for 12 h has a biphasic structure containing both amorphous and crystalline phases. These results showed that calcium phosphates were formed through a multistage assembly process, during which an initial amorphous phase DPCD was followed by a phase transformation into a crystalline phase and then the most stable hydroxyapatite (HAp). This provided new insights into the template-biomineral interaction and a mechanism for biomineralization.     

4,4′‐Bipyridyl N,N′‐dioxide–3‐hydroxy‐2‐naphthoic acid (1/2)

4,4′‐Bipyridyl N,N′‐dioxide crystallizes with 3‐hydr­oxy‐2‐naphthoic acid to give a centrosymmetric three‐component adduct, C₁₀H₈N₂O₂·2C₁₁H₈O₃, which is engineered into a two‐dimensional layer structure by two kinds of π–π inter­actions. Weak C—H⋯O inter­actions further link the two‐dimensional structure into a three‐dimensional structure.     

Two-Dimensional Supramolecular from the Self-Assembly of Dissymmetrical Oxamidato-Bridged Heterometallic Trinuclear Building Blocks: Synthesis, Crystal Structure, and Magnetic Properties

Two heterometallic trinuclear complexes {[Cu(oxbp)]₂Co(H₂O)₂}1.5DMF0.5H₂O (complex 1) and {[Cu(oxbm)]₂Co(H₂O)₂}2DMF (complex 2) were obtained from the self-organization of two new dissymmetrical oxamidato-bridged copper(II) building blocks [Cu(oxbp)]^– and [Cu(oxbm)]^–[H₃oxbp=N-benzoato-N'-(3-aminopropyl)oxamido, H₃oxbm=N-benzoato-N'-(2-amino-2-methylethyl)oxamido, DMF=dimethylformamide]. The crystal structure of complex 1 has been determined. Complex 1 crystallize in triclinic system, space group P-1, a=8.0609(16) Å, b=10.661(2) Å, c=22.279(5) Å, =85.32(3), =86.64(3), =70.90(3), and Z=1. The crystal structure of complex 1 consists of neutral trinuclear complex units, and hydrogen bond involved DMF and water molecules. Through the hydrogen bonds, weak coordination and CuCu weak interactions, complex 1 features a 2-D supramolecular structure. Magnetic susceptibility measurements (5–100 K) indicate that the central Co(II) and terminal copper metal ions are antiferromagnetically coupled with J=–28.09 and J=–29.70 cm^–1 for complex 1 and 2, respectively.     

A new chiral Rh(II) catalyst for enantioselective [2 + 1]-cycloaddition. mechanistic implications and applications

A novel chiral Rh(II) catalyst (1) is introduced for the [2 + 1]-cycloaddition of ethyl diazoacetate to terminal acetylenes and olefins with high enantioselectivity. The catalyst 1 consists of one acetate bridging group and three mono-N-triflyldiphenylimidazoline-2-one bidentate ligands (DPTI) spanning the Rh(II)-Rh(II) metallic center in a structure that was determined by single-crystal X-ray diffraction analysis. A rational mechanism is advanced that provides a straightforward explanation for the enantioselectivity and absolute stereochemical course of the [2 + 1]-cycloaddition reactions. A key element in this explanation is the cleavage of one of the Rh-O bonds of the bridging acetate group in the intermediate Rh-carbene complex to form a new pentacoordinate Rh carbene complex (formally 1.5 valent Rh) that can undergo [2 + 2]-cycloaddition with the C-C pi-bond of the acetylenic or olefinic substrate. Reductive elimination of the resulting adduct affords the cyclopropene or cyclopropane product. The C2-symmetry of the two DPTI ligands orthogonal to the bridging acetate also contributes to the high observed enantioselectivity and mechanistic clarity. The catalyst 1, which functions effectively at 0.5 mol %, can be recovered efficiently for reuse. Its ready availability, robustness, and effectiveness suggest it as a useful addition to the list of practical chiral Rh(II) catalysts for synthesis.     

Middle-phase microemulsions of green surfactant alkyl polyglucosides

Microemulsions are important organized molecular assembles in surfactant solutions and are used in various fields such as tertiary oil recovery, pharmaceutics, cosmetics, nanoparticle synthe-sis and chemical engineering. The more commonly used nonionic surfactants to produce micro- emulsions are the ethylene oxide-based compounds (CiEj). In recent years alkyl polyglucosides have been received considerable attention in producing microemulsions[17]. Alkyl polyglucosides (APG), which are widely…     

Enantioselective binding of an 11-cis-locked cyclopropyl retinal. The conformation of retinal in bovine rhodopsin

[formula: see text] The conformation of the retinal chromophore in rhodopsin is central for understanding the visual transduction process. The absolute twist around the 12-s bond of the chromophore in rhodopsin has been determined by studies with 11-cis-locked 11,12-cyclopropylretinal analogues (11S,12R)-2 and (11R,12S)-3, enantioselectively synthesized with the aid of an enzyme. The finding that enantiomer 2 binds to opsin while the other 3 does not defines the absolute sense of twist around the 12-s bond.     

Copper oxide nanocrystals

It is well-known that inorganic nanocrystals are a benchmark model for nanotechnology, given that the tunability of optical properties and the stabilization of specific phases are uniquely possible at the nanoscale. Copper (I) oxide (Cu(2)O) is a metal oxide semiconductor with promising applications in solar energy conversion and catalysis. To understand the Cu/Cu(2)O/CuO system at the nanoscale, we have developed a method for preparing highly uniform monodisperse nanocrystals of Cu(2)O. The procedure also serves to demonstrate our development of a generalized method for the synthesis of transition metal oxide nanocrystals. Cu nanocrystals are initially formed and subsequently oxidized to form highly crystalline Cu(2)O. The volume change during phase transformation can induce crystal twinning. Absorption in the visible region of the spectrum gave evidence for the presence of a thin, epitaxial layer of CuO, which is blue-shifted, and appears to increase in energy as a function of decreasing particle size. XPS confirmed the thin layer of CuO, calculated to have a thickness of approximately 5 A. We note that the copper (I) oxide phase is surprisingly well-stabilized at this length scale.     

Mass resolved MPI spectra of methyl iodide in the 430-490 nm region

The mass resolved multiphoton ionization (MPI) spectra of methyl iodide were obtained in the 430-490 nm region using a time-of-flight (TOF) mass spectrometer. They have the same vibrational structure, which testifies that the fragment species, in the wavelength region under study, are from the photodissociation of multiphoton ionized molecular parent ions. Some features in the spectra are identified as three-photon excitations to 6p and 7s Rydberg states of methyl iodide. Two new vibrational structures of some Rydberg states are observed. The mechanism of ionization and dissociation is also discussed.