Identification of Two Palmitoyl Groups in Octopus Rhodopsin

Abstract— We determined the structure and site of fatty acid incorporated in octopus rhodopsin using a combination of fluorescence label and enzymatic cleavage methods in conjunction with fast-atom bombardment (FAB) mass spectrometry. A single peptide containing two adjacent cysteines, Cys337 and Cys338, was successfully isolated using the fluorescence from a dye conjugated to Cys345. The FAB mass spectrometric analysis of the peptide (323phe-³⁴⁰phe) revealed that two palmitoyl groups are linked to Cys337 and Cys338 via thioester bonds in octopus rhodopsin as in bovine rhodopsin.     

Phosphorylation Within DNA Duplexes. Synthesis of Modified Oligodeoxyribonucleotide

Abstract

An effective method was suggested for the activation of phos-phomonoester groups in nicks of a double-strand DNA (1,2). This approach allows to incorporate various sugar phosphate backbone modifications at a particular site when DNA duplexes are being assembled. A modifying group is first introduced at the 5′- or 3′-termini of oligonucleotides, then a duplex is formed and oligomers are coupled on the complementary template using water-soluble l-ethyl-3-(3-dimethyl-aminopropyl)carbodiimide or cyanogen bromide as the condensing agents. Various DNA duplexes containing not only natural phosphodiester but also phosphoramidate and pyrophospha-te internucleotide bonds, as well as phosphodiester bonds between nucleotide residues with modified sugar analogs (ribo-, arabino- and xylo-derivatives) were assembled by this method.     

Identification and Characterization of a Single High‐Affinity Fatty Acid Binding Site in Human Serum Albumin

A single high‐affinity fatty acid binding site in the important human transport protein serum albumin (HSA) is identified and characterized using an NBD (7‐nitrobenz‐2‐oxa‐1,3‐diazol‐4‐yl)‐C₁₂ fatty acid. This ligand exhibits a 1:1 binding stoichiometry in its HSA complex with high site‐specificity. The complex dissociation constant is determined by titration experiments as well as radioactive equilibrium dialysis. Competition experiments with the known HSA‐binding drugs warfarin and ibuprofen confirm the new binding site to be different from Sudlow‐sites I and II. These binding studies are extended to other albumin binders and fatty acid derivatives. Furthermore an X‐ray crystal structure allows locating the binding site in HSA subdomain IIA. The knowledge about this novel HSA site will be important for drug depot development and for understanding drug‐protein interaction, which are important prerequisites for modulation of drug pharmacokinetics.     

Heavier Tetrylenes as Single Site Catalysts

An overview of the development of compounds with heavier low-valent group 14 elements (known as tetrylenes) as single component catalyst for organic transformation has been provided. Compounds with heavier group 14 elements possess stereochemically active lone pairs and energetically accessible π-antibonding orbitals, thereby resembling the electronic configuration of transition-metal compounds. Such compounds with low-valent group 14 elements has been known for small molecule activation since Power's report of dihydrogen activation by a digermyne, but their utilization in catalysis remained as a “Holy Grail” in main group chemistry. In recent years, numerous methodologies have been discovered epitomizing the use of Si(II), Ge(II) and Sn(II) compounds as single site catalysts for hydroboration of aldehydes, ketones, pyridines, cyanosilylation of aldehydes and ketones, N-formylations aromatic amines, dehydrocoupling reactions. This mini-review highlights these significant developments with an emphasis on the mechanistic investigation.     

Rhodopsin in a new model bilayer membrane

In search of a planar and uniform model membrane presenting a wide interaction-surface for the study of photobiological processes, we have succeeded in depositing lipid bilayer on a single face of a porous disc. Using a method that combines the Langmuir-Blodgett dipping and the touching procedures, a symmetrical or asymmetrical bilayer membrane has been obtained. The illumination of rhodopsin-containing membranes appears to increase the permeability to K⁺, Na⁺, and Ca²⁺ with a high selectivity for Ca²⁺. The bilayer adsorption on the porous disc is discussed and an attempt is made to explain the failure of the dipping method in our experimental conditions for preparing an artificial membrane. A comparative look at model membranes is also presented.     

聚环氧乙烷球晶的带状结构与球晶内部的环形裂纹

聚环氧乙烷球晶的带状结构与球晶内部的环形裂纹丁建东，朱军祥，杨玉良（复旦大学高分子科学系、国家教委聚合物分子工程开放实验室，上海，２００４３３）关键词聚合物，带状球晶，裂纹聚环氧乙烷（ＰＥＯ）具有高度的柔顺性，易于结晶，因而被人们选作研究聚合物结晶的...     

Electrochemical Monitoring of ROS/RNS Homeostasis Within Individual Phagolysosomes Inside Single Macrophages

The existence of a homeostatic mechanism regulating reactive oxygen/nitrogen species (ROS/RNS) amounts inside phagolysosomes has been invoked to account for the efficiency of this process but could not be unambiguously documented. Now, intracellular electrochemical analysis with platinized nanowire electrodes (Pt‐NWEs) allowed monitoring ROS/RNS effluxes with sub‐millisecond resolution from individual phagolysosomes impacting onto the electrode inserted inside a living macrophage. This shows for the first time that the consumption of ROS/RNS by their oxidation at the nanoelectrode surface stimulates the production of significant ROS/RNS amounts inside phagolysosomes. These results establish the existence of the long‐postulated ROS/RNS homeostasis and allows its kinetics and efficiency to be quantified. ROS/RNS concentrations may then be maintained at sufficiently high levels for sustaining proper pathogen digestion rates without endangering the macrophage internal structures.     

Kinetic Study of the Copolymerisation of Ethylene with a Single Site Catalyst in Propane Slurry Polymerisation

Summary: The kinetic behaviour of a supported metallocene catalyst in slurry polymerisation of ethylene with 1-hexene under industrially relevant reaction conditions has been studied. Polymerisation experiments were carried out in a 5-litre stirred tank reactor in a temperature range from 60 to 80 °C and ethylene partial pressures from 5 to 15 bar. Comonomer and hydrogen amounts were varied as well. The catalyst showed pronounced activation and slow deactivation during runtimes of about 1 hour. Strong influences of 1-hexene (“hexene effect”) and hydrogen (“hydrogen effect”) on the activity profiles were observed. Based on the experimental results, a kinetic model has been derived in order to describe and predict important polymerisation data such as activity profile, comonomer content and molecular weight distributions with respect to the reaction conditions. The presented kinetic model is able to describe the observed effects of 1-hexene and hydrogen on the activity profiles, as well as the comonomer incorporation across a broad range of polymerisation conditions. The molecular weight distributions can be simulated with good qualitative agreement to the experimental data.     

新一代单活性中心聚烯烃催化剂--水杨醛亚胺基过渡金属化合物

对新型的单活性中心聚烯烃催化剂——以水杨醛亚胺基配体稳定的后过渡金属络合物和前过渡金属络合物催化的结构性能特点、设计合成方法等做了较说尽的评述。     

Simultaneous Identification of Tyrosine Phosphorylation and Sulfation Sites Utilizing Tyrosine-Specific Bromination

Tyrosine phosphorylation and sulfation play many key roles in the cell. Isobaric phosphotyrosine and sulfotyrosine residues in peptides were determined by mass spectrometry using phosphatase or sulfatase to remove the phosphate or the sulfate group. Unique Br signature was introduced to the resulting tyrosine residues by incubation with 32% HBr at −20 °C for 20 min. MS/MS analysis of the brominated peptide enabled unambiguous determination of the phosphotyrosine and the sulfotyrosine sites. When phosphotyrosine and sulfotyrosine as well as free tyrosine were present in the same peptide, they could be determined simultaneously using either phosphatase or sulfatase following acetylation of the free tyrosine.     

Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid

An all-atom molecular dynamics simulation of rhodopsin in a membrane environment has been carried out with lipid composition similar to that of the retinal membrane. The initial conformation of the protein was taken from the X-ray crystallographic structure (1F88), while those of the lipids came from a previous molecular dynamics simulation. During the course of the 12.5 ns simulation, the initially randomly placed lipids adopt an anisotropic solvation structure around the protein. The lipids, having one saturated stearic acid chain and one polyunsaturated docosohexaenoic acid chain with a zwitterionic phosphatidylcholine headgroup, arrange themselves to maximize contact between the polyunsaturated chain and the protein surface. This organization is driven by energetically favorable interactions between the transmembrance helices and the docosohexaenoyl chains that are largely of the van der Waals type. These observations are consistent with various experimental studies on rhodopsin and other G-protein coupled receptors and with the picture of extreme flexibility in polyunsaturated fatty acid chains that has arisen from recent NMR and computational work.     

Rhodopsin Activation Switches in a Native Membrane Environment†

The elucidation of structure–function relationships of membrane proteins still poses a considerable challenge due to the sometimes profound influence of the lipid bilayer on the functional properties of the protein. The visual pigment rhodopsin is a prototype of the family of G protein‐coupled transmembrane receptors and a considerable part of our knowledge on its activation mechanisms has been derived from studies on detergent‐solubilized proteins. This includes in particular the events associated with the conformational transitions of the receptor from the still inactive Meta I to the Meta II photoproduct states, which are involved in signaling. These events involve disruption of an internal salt bridge of the retinal protonated Schiff base, movement of helices and proton uptake from the solvent by the conserved cytoplasmic E(D)RY network around Glu134. As the equilibria associated with these events are considerably altered by the detergent environment, we set out to investigate these equilibria in the native membrane environment and to develop a coherent thermodynamic model of these activating steps using UV–visible and Fourier‐transform infrared spectroscopy as complementary techniques. Particular emphasis is put on the role of protonation of Glu134 from the solvent, which is a thermodynamic prerequisite for full receptor activation in membranes, but not in detergent. In view of the conservation of this carboxylate group in family A G protein‐coupled receptors, it may also play a similar role in the activation of other family members.     

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two‐component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the “U”‐”V” transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55‐58]. A model of cooperativity at the transmembrane level is discussed.     

Sulfonium Ion Derivatization,Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation,Identification and Phosphorylation Site Characterization

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS³, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH₃)₂) and ‘heavy’ (S(CD₃)₂) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS³ or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency.     

单中心催化剂用于长链α-烯烃配位聚合研究进展

聚烯烃催化剂技术是聚烯烃工业蓬勃发展的关键,开发对长链α-烯烃聚合具有高活性和高选择性的配位聚合催化剂是聚烯烃催化剂的发展方向,这类催化剂决定了聚烯烃材料可开发的广度和深度.本文综述了近年来长链α-烯烃(1-己烯、1-辛烯、1-癸烯等)配位聚合单中心催化剂的研究进展,重点介绍了以第四族过渡金属为中心的非茂金属催化剂,对...     

On the Retention of Diuretics in Micellar Liquid Chromatography and Their Site of Action Within the Nephron

Abstract

The therapeutical action of diuretics has been attributed to their hydrophobic character, among other properties. Therapeutical and physiological classifications of diuretics are correlated. The site of action of high efficacay diuretics is the loop of Henle, that of intermediate efficacy diuretics is the distal tubule and that of low efficacy diuretics is the proximal and distal tubules, and the collecting duct. Partition coefficients between water and micelles offer a scale for hydrophobicity, which leads to a further correlation between retention in Micellar Liquid Chromatography (MLC), with a sodium dodecyl sulphate mobile phase and an ODS-C₁₈ column, and the sites of action within the nephron. The site of action of those diuretics showing the lower retention in MLC is the proximal tubule (acetazolamide) and the loop of Henle (loop diuretics), for those diuretics with an intermediate retention is the distal tubule (thiazides), and for those with a long retention is the collecting duct (potassium sparing diuretics).     

Identification of the Binding Site of Brucella VirB8 Interaction Inhibitors

Secretion systems translocate virulence factors of many bacterial pathogens, enabling their survival inside the host organism. Consequently, inhibition strongly attenuates pathogenicity and can be considered a target for novel antimicrobial drugs. The type IV secretion system (T4SS) of the intracellular pathogen Brucella is a prerequisite for its virulence, and in this work we targeted the interactions of the?essential assembly factor protein, VirB8, using small-molecule inhibitors. High-throughput screening identified several potent and specific inhibitors, and the target-binding site of these inhibitors was identified by X-ray crystallography, in?silico docking, and analysis of the derivates of the inhibitor B8I-2. VirB8 interaction inhibitors bind to a surface groove opposite to the dimerization interface, and by varying the binding-site residues, we were able to determine which residues are required for inhibitor activity. E115 and K182 were found to be especially important, and changes at R114, Y229, and L151 also reduced inhibitor efficiency.