Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes

It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.     

Model Analysis for Oral Absorption of a Drug/Cyclodextrin Complex Involving Competitive Inclusion Complexes

The bioavailability parameters of a drug after oral administration of a preparation containing drug/CyD complexes may be modified by formation of competitive inclusion complexes. In this study, we examined the effects of competitors on drug permeation from its CyD complex through in-vitro artificial membranes and in-situ recirculation conditions, for comparison with the results under in-vivo conditions in the bile duct of cannulated rats. Phenacetin, an antipyretic, was used as a model drug, natural CyDs and maltosyl--CyD as host molecules, and benzoic acid derivatives, sodium taurocholate and acetaminophen as competitors. The in-vitro cellophane membrane permeation rate and the in-situ absorption rate of phenacetin were quantitatively predicted by theoretical calculation using the stability constants of drug/CyD and competitor/CyD complexes when CyD weakly interacts with membrane components in lower CyD concentrations (generally below 10 mM). The in-vivo absorption behavior was only qualitatively reproducible by the theoretical calculation, probably because of various physicochemical and physiological factors affecting the absorption. The present results may be useful not only for prediction of intestinal absorption of drugs from CyD preparations, but also for formulation design of CyD preparations containing multi-components.     

Plasma-derived clotting factor VIII: heterogeneity evaluation in the quest for potential inhibitory-antibody stimulating factors

In this study, we investigated the heterogeneity and the purity grade of three commercially available plasma‐derived clotting factor VIII (FVIII) concentrates, which highly differ with regard to purification strategies, relative concentrations of stabilizers (von Willebrand factor, with or without albumin) and virus inactivation strategies (solvent/detergent and/or heat/pasteurization treatments). Western blot analyses were used to evaluate product‐specific variations from Emoclot^®, Alphanate^® and Haemate^® both in the presence and absence of reducing agents (dithiotreithol). All the plasma‐derived concentrates showed a strong heterogeneity, as they all included a significant amount of truncated forms of the full‐length (FL) clotting FVIII protein. The intact protein accounted for the 38% of the total FVIII proteins in Haemate^® and 29 and 23% in Alphanate^® and Emoclot^®, respectively. Lower intact FVIII amounts in Emoclot might be mainly due to the low von Willebrand factor dosage and the absence of albumin. Upon addition of thrombin, both the FL and truncated forms of the FVIII protein were almost completely digested. Indeed, after thrombin activation, we could still observe a mixture of B‐domain truncated forms of the FL protein along with biologically active digested‐A1 forms. Batch‐to‐batch variation was tested with no evident changes appearing among different batches. Despite the variables in manufacturing processes, inter‐product comparisons yielded similar results for all the plasma‐derived FVIII considered in this study. However, we could individuate in Emoclot a band that was not digested by thrombin, which we could characterize as the 200 kDa FVIII heavy chain. This investigation prompts new concerns about the strong heterogeneity observed upon thrombin digestion of plasma‐derived FVIII, which might contribute to the development of inhibitory antibodies at an early stage of therapy, and to which extent these untoward phenomena could be avoided through direct intervention on routine manufacturing processes.     

Pd(II) and Ni(II) complexes featuring a "phosphasalen" ligand: synthesis and DFT study

A phosphorus analog of salen ligands featuring iminophosphorane functionalities in place of the imine groups was synthesised in 2 steps from o-diphenylphosphinophenol via the preparation of the corresponding bis-aminophosphonium salt. This novel tetradentate ligand (1), which we named phosphasalen, was coordinated to Pd(II) and Ni(II) metal centres affording complexes 6 and 7 respectively, which were characterised by multinuclear NMR, elemental and X-ray diffraction analyses. Both neutral complexes adopt a nearly square-planar geometry around the metal with coordination of all iminophosphorane and phenolate moieties. The electronic properties of these new complexes were investigated by cyclic voltammetry and comparison with known salens was made when possible. Moreover, the particular behaviour of the phosphasalen nickel complex 7 was further investigated through magnetic moment measurements and a DFT study.     

"Through-space" nuclear spin-spin J(PP) coupling in tetraphosphine ferrocenyl derivatives: a (31)P NMR and X-ray structure correlation study for coordination complexes

Herein, we report on (31)P(31)P solution-phase "through-space" nuclear spin-spin coupling constants (J(PP)) from a novel family of organometallic tetraphosphine nickel and palladium complexes. These J(PP) constants were accurately determined through NMR iterative simulation based on the second-order spectra obtained for the compounds. The corresponding solid-state X-ray structures of the complexes were determined, and the "through-space" P.P distances are reported. Due to the blocked conformation of the species in solution, a qualitative and semiquantitative experimental correlation is obtained, which links the geometric parameters and the intensity of the corresponding P.P coupling constant. The lone-pair overlap theory developed for (19)F(19)F and (15)N(19)F "through-space" couplings in organic compounds [J. Am. Chem. Soc. 1973, 95, 7747-7752; 2000, 122, 4108-4116] appears to be a reliable foundation on which to account for our results. Based on the reported observations, the lone-pair overlap model is extended to "through-space" (31)P(31)P coupling, and the model is broadened to encompass metal orbital contributions for coordination complexes. Some of the predictions and consequences of the proposed theory are discussed.     

Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.     

Proteomic characterization of plasma‐derived clotting factor VIII–von Willebrand factor concentrates

Proteomic methods were used to identify the levels of impurities in three commercial plasma‐derived clotting factor VIII‐von Willebrand factor (FVIII/VWF) concentrates. In all three concentrates, significant amounts of other plasma proteins were found. In Octanate and Haemoctin, two concentrates developed in the 1990s, the major impurities identified were inter‐α inhibitor proteins, fibrinogen and fibronectin. These two concentrates were also found to contain additional components such as clotting factor II (prothrombin) that are known activators of FVIII. In Wilate, a recently developed FVIII/VWF concentrate, the amount of these impurities was significantly reduced. Batch‐to‐batch variations and differences between three investigated products were detected using iTRAQ, an isotope labeling technique for comparative MS, demonstrating the potential value of this technique for quality control analysis. The importance of thorough proteomic investigations of therapeutic FVIII/VWF preparations from human plasma is also discussed.     

Revisiting the polyoxometalate-based late-transition-metal-oxo complexes: the "oxo wall" stands

Terminal oxo complexes of the late transition metals Pt, Pd, and Au have been reported by us in Science and Journal of the American Chemical Society. Despite thoroughness in characterizing these complexes (multiple independent structural methods and up to 17 analytical methods in one case), we have continued to study these structures. Initial work on these systems was motivated by structural data from X-ray crystallography and neutron diffraction and (17)O and (31)P NMR signatures which all indicated differences from all previously published compounds. With significant new data, we now revisit these studies. New X-ray crystal structures of previously reported complexes K(14)[P(2)W(19)O(69)(OH(2))] and "K(10)Na(3)[Pd(IV)(O)(OH)WO(OH(2))(PW(9)O(34))(2)]" and a closer examination of these structures are provided. Also presented are the (17)O NMR spectrum of an (17)O-enriched sample of [PW(11)O(39)](7-) and a careful combined (31)P NMR-titration study of the previously reported "K(7)H(2)[Au(O)(OH(2))P(2)W(20)O(70)(OH(2))(2)]." These and considerable other data collectively indicate that previously assigned terminal Pt-oxo and Au-oxo complexes are in fact cocrystals of the all-tungsten structural analogues with noble metal cations, while the Pd-oxo complex is a disordered Pd(II)-substituted polyoxometalate. The neutron diffraction data have been re-analyzed, and new refinements are fully consistent with the all-tungsten formulations of the Pt-oxo and Au-oxo polyoxometalate species.     

Two-dimensional electrophoresis of membrane proteins

One third of all genes of various organisms encode membrane proteins, emphasizing their crucial cellular role. However, due to their high hydrophobicity, membrane proteins demonstrate low solubility and a high tendency for aggregation. Indeed, conventional two-dimensional gel electrophoresis (2-DE), a powerful electrophoretic method for the separation of complex protein samples that applies isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, has a strong bias against membrane proteins. This review describes two-dimensional electrophoretic techniques that can be used to separate membrane proteins. Alternative methods for performing conventional 2-DE are highlighted; these involve replacing the IEF with electrophoresis using cationic detergents, namely 16-benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and cetyl trimethyl ammonium bromide (CTAB), or the anionic detergent SDS. Finally, the separation of native membrane protein complexes through the application of blue and clear native gel electrophoresis (BN/CN-PAGE) is reviewed, as well as the free-flow electrophoresis (FFE) of membranes.     

杯[4]芳烃对单糖及嘧啶衍生物的分子识别和分子开关

用AM1和INDO/SCI方法对八羟基杯[4]芳烃与单糖及嘧啶衍生物形成的超分子体系进行理论研究,结果表明,主体通过CH-π相互作用对单糖类进行分子识别,尤其对赤藓糖识别效果更好;主体与嘧啶没有明显的π-π堆砌作用,但能识别含吸电子基团的嘧啶衍生物,据此可设计酸碱调控的分子开关.讨论了配合物的UV谱带与主体相比发生红移的原因.     

Surface architecture of the plant cell: biogenesis of the cell wall, with special emphasis on the role of the plasma membrane in cellulose biosynthesis.

Cell wall structure and biogenesis in the unicellular green alga, Oocystis apiculata, is described. The wall consists of an outer amorphous primary layer and an inner secondary layer of highly organized cellulosic microfibrils. The primary wall is deposited immediately after cytokinesis. Golgi-derived products contribute to this layer. Cortical microtubules underlie the plasma membrane immediately before and during primary wall formation. They function in maintaining the elliptical cell shape. Following primary wall synthesis, Golgi-derived materials accumulate on the cell surface to form the periplasmic layer. This layer functions in the deposition of coating and cross-linking substances which associate with cellulosic microfibrils of the incipient secondary wall. Secondary wall microfibrils are assembled in association with the plasma membrane. Freeze-etch preparations of untreated, living cells reveal linear terminal complexes in association with growing cellulosic microfibrils. These complexes are embedded in the EF fracture face of the plasma membrane. The newly synthesized microfibril lies in a groove of the outer leaflet of the plasma membrane. The groove is decorated on the EF fracture face by perpendicular structures termed "ridges". The ridges interlink with definitive rows of particles associated withe PF fracture face of the innter leaflet of the plasma membrane. These particles are termed "granule bands", and they function in the orientation of the newly synthesized microfibrils. Microfibril development in relation to a coordinated multienzyme complex is discussed. The process of cell wall biogenesis in Oocystis is compared to that in higher plants.     

Context-based identification of protein-protein interfaces and "hot-spot" residues

Reliable determination of protein-protein interaction sites is of critical importance for structure-based design of small molecules modulating protein function through macromolecular interfaces. We present an alignment-free computational method for prediction of protein-protein interface residues. The method ("iPred") is based on a knowledge-based scoring function adapted from the field of protein folding and small molecule docking. Based on a training set of 394 hetero-dimeric proteins iPred achieves sustained accuracy on an external unbound test set. Prediction robustness was assessed from more than 1500 diverse complexes containing homo- and hetero-dimers. The technique does not rely on sequence conservation, so that rapid interface identification is possible even for proteins for which homologs are unknown or lack conserved residue patterns in interface region. Functional "hot-spot" residues are enriched among the predicted interface residues, rendering the method predestined for macromolecular binding site identification and drug design studies aiming at modulating protein-protein interaction that might influence protein function. For a comparative structural model of peptidase HtrA from Helicobacter pylori, we performed mutation studies for predicted hot-spot residues, which were confirmed as functionally relevant for HtrA activity or oligomerization.     

Solvation of uranyl(II), europium(III) and europium(II) cations in "basic" room-temperature ionic liquids: a theoretical study

We report a molecular dynamics study of the solvation of UO2(2+), Eu3+ and Eu2+ ions in two "basic" (Lewis acidity) room-temperature ionic liquids (IL) composed of the 1-ethyl-3-methylimidazolium cation (EMI+) and a mixture of AlCl4- and Cl- anions, in which the Cl-/AlCl4- ratio is about 1 and 3, respectively. The study reveals the importance of the [UO2Cl4]2- species, which spontaneously form during most simulations, and that the first solvation shell of europium is filled with Cl- and AlCl4- ions embedded in a cationic EMI+ shell. The stability of the [UO2Cl4]2- and [Eu(III)Cl6]3- complexes is supported by quantum mechanical calculations, according to which the uranyl and europium cations intrinsically prefer Cl- to the AlCl4- ion. In the gas phase, however, [Eu(III)Cl6]3- and [Eu(II)Cl6]4- complexes are predicted to be metastable and to lose two to three Cl- ions. This contrasts with the results of simulations of complexes in ILs, in which the "solvation" of the europium complexes increases with the number of coordinated chlorides, leading to an equilibrium between different chloro species. The behavior of the hydrated [Eu(OH2)8]3+ complex is considered in the basic liquids; the complex exchanges H2O molecules with Cl- ions to form mixed [EuCl3(OH2)4] and [EuCl4(OH2)3]- complexes. The results of the simulations allow us to better understand the microscopic nature and solvation of lanthanide and actinide complexes in "basic" ionic liquids.     

Synthesis and complexation of "back-to-back" capped bis-dioxocyclams

Pyridine-capped 5,12-dioxocyclams were coupled "back-to-back" directly, with one or two intervening phenyl groups, an ethynyl group, or a diazo group via Suzuki, Sonogashira, or reductive coupling of the 4-nitropyridine monocyclam. These bis-dioxocyclams linked through extended pi-conjugated systems were complexed to copper(II) and cobalt(III), producing bis-metal complexes which were characterized spectroscopically and electrochemically. These studies gave little evidence for electronic communication between metal centers across the pi-conjugated linkers.     

"Asymmetric" catalysis by lanthanide complexes

Catalysis with lanthanide (Ln) complexes has been underestimated for long time, although Ln(III) complexes have great advantages as Lewis acid catalysts for "asymmetric" carbon-carbon bond-forming reactions. Lanthanide complexes are highly active in ligand-substitution reactions, especially with hard ligands. The association with substrates and dissociation of products are achieved fast enough for high catalyst efficiency. The asymmetric catalysis of organic reactions can be greatly advanced by the use of Ln complexes with chiral ligands such as binaphthol (binol). Ln(II) complexes are good reducing agents, which can be used in a wide variety of synthetically important reactions; when chiral ligands are used, many of these reactions are highly stereoselective. In the context of "green chemistry", the development of asymmetric Ln catalysts, and their recyclable use, is of increasing importance. This review gives an overview of the most recent developments in catalysis with lanthanide(II) and lanthanide(III) complexes.     

Production and use of glucosyltransferases fromLeuconostoc mesenteroides NRRL B-1299 for the synthesis of oligosaccharides containing α-(1→2) linkages

Glucosyltransferase activities, produced by batch culture ofLeuconostoc mesenteroides NRRL B-1299, were recovered both in the culture supernatant (SGT) and associated with the insoluble part of the culture (IGT). A total glucosyltransferase activity of 3.5 U/mL was measured in batch culture. The enzymes from the supernatant were purified 313 times using aqueous two-phase partition between dextran and PEG phases, yielding a preparation with 18.8 U/mg protein. It was shown that both SGT and IGT preparations catalyze acceptor reactions and transfer the glucose unit from sucrose onto maltose to produce glucooligosaccharides. Some of the glucooligosaccharides synthesized (L_n series) contain α-(l→6) osidic linkages and a maltose residue at the reducing end. They were completely hydrolyzed by glucoamy-lase and dextranase. The other glucooligosaccharides synthesized (Bn series) resisted the action of these enzymes. The tetrasaccharide of this series has been characterized by¹³C NMR. Its structure was determined as 2–O–α–D–glucosylpanose. The oligosaccharides synthesized by the maltose acceptor reaction with the SGT and IGT preparations only differed in the relative amounts in which they were produced. The difference may arise from diffusional limitations appearing when the insoluble catalyst is used. Under the assay conditions, the glucanase resistant oligosaccharide yield was 35% with both glucosyltrans-ferase preparations.     

Unraveling the molecular recognition of "three methylene spacer" bis(benzimidazolium) moiety by dibenzo-24-crown-8: pseudorotaxanes under study

"Three methylene spacer" bis(benzimidazolium) derivatives act as a new template for threading dibenzo-24-crown-8 into [2]pseudorotaxanes. In this Article we sought to unveil the difference in the extent of threading of various "three methylene spacer" bis-benzimidazolium moieties based on differences in aromatic methyl substituent positions and anions through the macrocycle dibenzo-24-crown-8. The temperature of the systems were also varied (low temperatures of 240 K and 253 K), when such interwinding of the thread and crown were not detected at room temperature of 308 K. The presence of such threaded complexes was determined based on (1)H-NMR initially and finally corroborated by high resolution mass spectrometry and DFT calculations. 2D-NMR experiments ((1)H-(1)H-NOESY) proved to be a very important tool in elucidating the interaction present between the components of the pseudorotaxanes. The dethreading/rethreading process was studied. DFT optimized structures suggest lower energy H-bonding orientations and compare the effect of methyl substituents on the axle.     

Detoxification of mercury in the environment

In this study, a green chemistry approach was developed as an option for remediation of toxic mercury in the environment. Twenty mercury compounds were treated with an environmentally friendly agent cyclodextrin to produce stable non-toxic mercury in soil and water. The binding efficiency was determined using high performance liquid chromatography with diode-array detection. The stability of the cyclodextrin mercury complexes toward environmental microorganisms in water was estimated under OECD guidelines using gas chromatography–mass spectrometry. The toxicity of the cyclodextrin mercury compounds to terrestrial organisms was investigated by use of internationally recognized toxicity methods using mercuric acetate as a model contaminant. Key process conditions, for example pH, temperature, and amount of detoxifying agent were investigated and found to have significant effects on the toxicity of mercury. It was found that organic and inorganic mercury pollutants could be mineralized in the environment with cyclodextrins. The bound mercury compounds resisted biodegradation and were found to be non-toxic to environmental microorganisms under laboratory conditions.     

Chiral "metallo-spiralenes": helical molecules conformationally stabilised by an organometallic scaffold

The synthesis of a series of chiral cyclomanganated 2-[(eta 6-phenyl)-Cr(CO)3]pyridine complexes derived from (-)-beta-pinene enables, by a "spirogenic transformation", the preparation of four different chiral helical heterobimetallic syn-facial complexes or Cr0/Mn1-spiralenes, among which two possess a right-handed P molecular helicity and two other a left-handed M one. These organometallic helical molecules are synthesised by applying two different methods to the chiral cyclomanganated (eta 6-arene)tricarbonylchromium substrates. The first method is the so-called "Fischer route" which involves a sequential addition of PhLi and MeOTf. The second method based on reaction of the cyclomanganated complex with diphenyldiazomethane which has been tested on achiral bimetallic substrates is a reasonable neutral alternative to the "Fischer methodology" for the synthesis of Cr0/Mn1-spiralenes. The crystal structure of one of these heterobimetallic chiral helical compounds serves as a starting point in the configurational and structural assessment of the synthesised chiral (eta 6-arene)tricarbonylchromium complexes. Application of the "Fischer route" to a cyclomanganated chiral 2-phenylpyridine generates a single chiral eta 3-benzylic complex--or Mn1-spiralene--bearing a left-handed M helicity which has been characterized by X-ray diffraction analysis. Circular dichroic spectroscopic measurements underline the predominant contribution of the chiral and chirally induced aromatic chromophores to the sign of the Cotton effects and confirm the helical configurations of the considered heterobimetallic species.     

Slow complexation dynamics between linear short polyphosphates and polyallylamines: analogies with "layer-by-layer" deposits

Polyelectrolyte "complexes" have been studied for almost a century and find more and more applications in cosmetics and DNA transfection. Most of the available studies focused on the thermodynamic aspects of the "complex" formation, mainly to determine phase diagrams and the influence of diverse physicochemical aspects on the formation of "complexes", but conversely less effort has been given to the kinetics of such processes. We describe herein the "complexation" kinetics of a short linear sodium polyphosphate (PSP) with poly(allylamine hydrochloride) (PAH) in the presence of 10 mM, 0.15 M and 1 M NaCl. We find, by using a combination of physicochemical techniques, that mixtures containing a 1 to 1 molar ratio of phosphate and amino groups allow the formation of "complexes" having a few 100 nm in diameter which progressively grow to particles up to 1.5 microns in hydrodynamic diameter, the growth process being accompanied by some progressive sedimentation. During this slow aggregation kinetics, the polyelectrolytes undergo a release of counterions and the zeta potential changes from a positive value to a negative one of -20 mV which is close to the zeta potential of (PSP-PAH)(n) films deposited under identical physicochemical conditions. Even though the complexes have a negative electrophoretic mobility, they contain an equimolar amount of amino and phosphate groups. This allows us to make some assumption about the structure of such "complexes" and to compare them with other published structures. We will also compare them with the aggregates found during the "layer-by-layer" deposition of the same species under the same conditions.