Interactome modeling

A long-term goal of the field of interactome modeling is to understand how global and local properties of complex macromolecular networks impact on observable biological properties, and how changes in such properties can lead to human diseases. The information available at this stage of development of the field provides strong evidence for the existence of such interesting global and local properties, but also demonstrates that many more datasets will be needed to provide accurate models with increasingly predictive capacity. This review focuses on an early attempt at mapping a multicellular interactome network and on the lessons learned from that attempt.     

Oxidative renal tubular injuries induced by aminocarboxylate-type iron (III) coordination compounds as candidate renal carcinogens

Oxidative renal tubular injuries and carcinogenesis induced by Fe^III-nitrilotriacetate (NTA) and Fe^III–ethylenediamine-N,N′-diacetate (EDDA) have been reported in rodent kidneys, but the identity of iron coordination structure essential for renal carcinogenesis, remains to be clarified. We compared renal tubular injuries caused by various low molecular weight aminocarboxylate type chelators with injuries due to NTA and EDDA. We found that Fe^III-iminodiacetate (IDA), a novel iron-chelator, induced acute tubular injuries and lipid peroxidation to the same extent. We also prepared Fe^III-IDA solutions at different pHs, and studied resultant oxidative injuries and physicochemical properties. The use of Fe^III-IDA at pH 5.2, 6.2, and 7.2 resulted in renal tubular necrosis and apoptotic cell death, but neither tubular necrosis nor apoptosis was observed at pH 8.2. Spectrophotometric data suggested that Fe^III-IDA had the same dimer structure from pH 6.2 to 7.2 as Fe^III-NTA; but at a higher pH, iron polymerized and formed clusters. Fe^III-IDA was crystallized, and this was confirmed by X-ray analysis and magnetic susceptibility measurements. These data indicated that Fe^III-IDA possessed a linear μ-oxo bridged dinuclear iron (III) around neutral pH.     

Isokinetic Relationship in the Oxidation of Cuprous Stellacyanin by Cobalt(III) Complexes

Rate parameters have been obtained for the oxidation of cuprous stellacyanin by cobalt(III) ions of the form cis(N)-[CoN₂O₄]^?, including cis(N)-[Co(NTA)(gly)]^?, cis(N)-[Co(IDA)₂]^?, [Co(en)(ox)₂]^?(μ 0.5 M(phosphate), pH 7.0), and Co(EDTA)^?(μ 0.1 M(NaCl), pH 7.2, 0.001 M phosphate). An excellent isokinetic correlation between the activation parameters ΔH^≠ and ΔS^≠ exists for the reactions of aminopolycarboxylatocobalt(III) ions with reduced stellacyanin (β = 300 ± 12 K; correlation coefficient = 0.995). It is concluded that enthalpy-entropy compensation in these reactions may be understood in terms of differing orientations preferred by the various oxidants in forming precursor complexes with the reduced blue protein. While ΔH^≠ and ΔS^≠ values for electron transfer from stellacyanin to cis(N)-[CoN₂O₄]^? ions vary over ranges of 10.7 kcal/mol and 34 cal/mol-deg, respectively, room temperature rate constants are relatively constant (3.6–34.5 M^?1 sec^?1), as expected from Marcus theory for outer sphere electron transfer.     

Complexation thermodynamics and the structure of the binary and the ternary complexes of Am, Cm and Eu with CDTA and CDTA + IDA

The stability constants and the thermodynamic parameters of the formation of the binary complexes of trivalent Am³⁺, Cm³⁺ and Eu³⁺ with CDTA and of their ternary complexes with CDTA + IDA were determined by solvent extraction measurements in aqueous solutions of I = 6.60 m (NaClO₄) at temperatures of 0-60 °C. The endothermic enthalpy and the positive entropy values reflect the significant effects of cation dehydration and of the rigidity of the ligand structure in the formation of these complexes. TRLFS and NMR (¹H and ¹³C) data provided information on the structure of the ternary complexes in solution. The size and rigidity of CDTA affect the binding mode of IDA in the complexation of M(CDTA)(IDA)(H₂O)³⁻ and M(CDTA)(IDA)³⁻ in which IDA has a bidentate coordination mode in the former and a tridentate coordination mode in the latter.     

The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation

In this study we demonstrate the use of a multiplexed MRM-based assay to distinguish among normal (NL) and iron-metabolism disorder mouse models, particularly, iron-deficiency anemia (IDA), inflammation (INFL), and inflammation and anemia (INFL+IDA). Our initial panel of potential biomarkers was based on the analysis of 14 proteins expressed by candidate genes involved in iron transport and metabolism. Based on this study, we were able to identify a panel of 8 biomarker proteins: apolipoprotein A4 (APO4), transferrin, transferrin receptor 1, ceruloplasmin, haptoglobin, lactoferrin, hemopexin, and matrix metalloproteinase-8 (MMP8) that clearly distinguish among the normal and disease models. Within this set of proteins, transferrin showed the best individual classification accuracy over all samples (72%) and within the NL group (94%). Compared to the best single-protein biomarker, transferrin, the use of the composite 8-protein biomarker panel improved the classification accuracy from 94% to 100% in the NL group, from 50% to 72% in the INFL group, from 66% to 96% in the IDA group, and from 79% to 83% in the INFL+IDA group. Based on these findings, validation of the utility of this potentially important biomarker panel in human samples in an effort to differentiate IDA, inflammation, and combinations thereof, is now warranted. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.     

Differential binding of ICln in platelets to integrin-derived activating and inhibitory peptides

The capacity of platelets to form a thrombus is mediated by integrin α_IIbβ₃. The cytoplasmic tail of α_IIb contains a highly conserved motif, ⁹⁸⁹KVGFFKR⁹⁹⁵, which plays a critical role in regulating integrin activation and acts as a recognition site for various intracellular proteins, e.g. CIB1, PP1, ICln and RN181. Previously, we demonstrated that a cell-permeable integrin-derived activating (IDA) peptide, KVGFFKR, induces platelet activation, whereas an integrin-derived inhibitory (IDI) peptide, KVGAAKR, is antithrombotic. To elucidate the molecular mechanism underlying these opposite effects we investigate the affinity of known integrin α_IIb binding proteins for the two immobilized peptides in dependence on the activation state of platelets by means of peptide-affinity chromatography, blotting techniques and protein:peptide docking studies.Our results provide a model for the inhibition of ICln interaction with the integrin in activated platelets by the IDI-peptide. Thus, ICln:IDI-peptide interaction profiles can have a pivotal purpose in the search for consensus pharmacophores specifically inhibiting ICln function in platelets potentially leading to the development of integrin-derived antithrombotic drugs.     

Recent advances in bioprocessing application of membrane chromatography

Compared to traditional chromatography using resins in packed-bed columns, membrane chromatography is a relatively new and immature bioseparation technology based on the integration of membrane filtration and liquid chromatography into a single-stage operation. Over the past decades, advances in membrane chemistry have yielded novel membrane devices with high binding capacities and improved mass transfer properties, significantly increasing the bioprocessing efficiency for purification of biomolecules. Due to the disposable nature, low buffer consumption, and reduced equipment costs, membrane chromatography can significantly reduce downstream bioprocessing costs. In this review, we discuss technological merits and disadvantages associated with membrane chromatography as well as recent bioseparation applications with a particular attention on purification of large biomolecules.     

Monoliths for microfluidic devices in proteomics

We report here on the preparation of monolithic capillary columns in view to their integration in a microsystem for on-chip sample preparation before their on-line analysis by electrospray and mass spectrometry (ESI-MS). These monolithic columns are based on polymer materials and consist of reverse phases for peptide separation and/or desalting. They were prepared using lauryl methacrylate (LMA), ethylene dimethacrylate (EDMA) as well as a suitable porogenic mixture composed of cyclohexanol and ethylene glycol. The resulting stationary phases present thus a C12-functionality. The LMA-based columns were first prepared in a capillary format using capillary tubing of 75 microm i.d. and tested in nanoLC-MS experiments for the separation of a commercial Cytochrome C digest composed of 12 peptidic fragments whose isoelectric point values and hydrophobic character cover a wide range. The LMA-based columns were capable of separating the peptidic fragments and their performances were seen to be similar as those of standard commercial columns dedicated to proteomic purposes with calculated separation efficiencies up to 145 x 10(3) plates/m. Monolithic LMA-based phases were then successfully polymerized in microchannels fabricated using the negative photoresist SU-8. After the polymerization, the systems were seen to withstand the pressures applied during the nanoLC-MS separation tests that were carried out in the same conditions as for the monolithic capillary columns. The pressure drop during these tests of the in-microchannel monoliths was as high as 50 bar; however, the separation was not as good as for a capillary format which could be accounted for by the monolith dimensions.     

硫酸亚铁对缺铁性贫血小鼠肠道健康的影响

【目的】旨在探究硫酸亚铁(FeSO4)对缺铁性贫血(iron deficiency anemia, IDA)小鼠肠道健康的影响。【方法】选取45只24日龄体重(16.0±1.2) g的雄性昆明小鼠,随机分成3组,每组15只,即对照组(正常饲料,饮蒸馏水)、IDA组(低铁饲料造模2周,饮去离子水)、IDA-Fe²⁺组(造模结束后灌胃FeSO₄ 3周,饮去离子水),实验结束时采样。【结果】试验结束时,与IDA组相比,IDA-Fe²⁺组小鼠的红细胞、血红蛋白、红细胞压积、平均红细胞体积、平均红细胞血红蛋白量、平均红细胞血红蛋白浓度等贫血指标均恢复至正常水平(P>0.05),表明FeSO4具有改善IDA的功能;与对照组相比,IDA和IDA-Fe²⁺组小鼠的氧化应激指标和肿瘤坏死因子α均显著升高(P<0.01)、紧密连接蛋白Occludin显著降低(P<0.001),IDA-Fe²⁺组与IDA组除结肠总抗氧化能力(TAC)外均无差异显著性(P>0.05)。结肠组织...