Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry

Direct analysis of intact proteins on a chromatographic time scale is demonstrated on a modified linear ion trap mass spectrometer using sequential ion/ion reactions, electron transfer and proton transfer, to dissociate the sample and to convert the resulting peptide fragments to a mixture of singly and doubly charged species. Proteins are converted to gas-phase, multiply-charged, positive ions by electrospray ionization and then allowed to react with fluoranthene radical anions. Electron transfer to the multiply charged protein promotes random fragmentation of amide bonds along the protein backbone. Multiply charged fragment ions are then deprotonated in a second ion/ion reaction with even-electron benzoate anions. M/z values for the resulting singly and doubly charged ions are used to read a sequence of 15-40 amino acids at both the N-terminus and the C-terminus of the protein. This information, along with the measured mass of the intact protein, are employed to identify known proteins and to detect the presence of post-translational modifications. In this study, we analyze intact proteins from the Escherchia coli 70S ribosomal protein complex and identify 46 of the 55 known unique components in a single, 90 min, on-line, chromatography experiment. Truncated versions of the above proteins along with several post-translational modifications are also detected.     

From structure to function: methods and applications

The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming universally accepted that the scale of the accumulated data for analysis and for prediction necessitate highly efficient computational tools with appropriate application capabilities. The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations. We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments. We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending movements). We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment.     

Holospiniferoside: A New Antitumor Cerebroside from The Red Sea Cucumber Holothuria spinifera: In Vitro and In Silico Studies

Chemical investigation of the methanolic extract of the Red Sea cucumber Holothuria spinifera led to the isolation of a new cerebroside, holospiniferoside (1), together with thymidine (2), methyl-α-d-glucopyranoside (3), a new triacylglycerol (4), and cholesterol (5). Their chemical structures were established by NMR and mass spectrometric analysis, including gas chromatography–mass spectrometry (GC–MS) and high-resolution mass spectrometry (HRMS). All the isolated compounds are reported in this species for the first time. Moreover, compound 1 exhibited promising in vitro antiproliferative effect on the human breast cancer cell line (MCF-7) with IC₅₀ of 20.6 µM compared to the IC₅₀ of 15.3 µM for the drug cisplatin. To predict the possible mechanism underlying the cytotoxicity of compound 1, a docking study was performed to elucidate its binding interactions with the active site of the protein Mdm2–p53. Compound 1 displayed an apoptotic activity via strong interaction with the active site of the target protein. This study highlights the importance of marine natural products in the design of new anticancer agents.     

Microwave-assisted synthesis of borneol esters and their antimicrobial activity

Seventeen borneol esters (1–17) were synthesised by conventional and microwave-assisted methodology using DIC/DMAP, and seven are described for the first time (8, 9, 10, 12, 13, 16 and 17). The microwave-assisted methodology was carried out without use of solvents, displayed short reaction times, and showed equal or higher yields for all the long-chain esters and three aromatic compounds (11, 12 and 14) when compared to the conventional approach. All the borneol esters were evaluated against the bacteria Streptococcus sanguinis, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and the fungus Candida albicans. Compounds 12, 13 and 14 displayed promising antibacterial activity with a MIC equal to ampicilin (62.5 mg mL^?1) for some microorganisms. In fact, bornyl 3′,4′-dimethoxybenzoate (13) was active against all tested bacteria and fungus.     

Monitoring solute interactions with poly(ethylene oxide)-modified colloidal silica nanoparticles via fluorescence anisotropy decay

The fluorescence-based nanosize metrology approach, proposed recently by Geddes and Birch (Geddes, C. D.; Birch, D. J. S. J. Non-Cryst. Solids 2000, 270, 191), was used to characterize the extent of binding of a fluorescent cationic solute, rhodamine 6G (R6G), to the surface of silica particles after modification of the surface with the hydrophilic polymer poly(ethylene oxide) (PEO) of various molecular weights. The measurement of the rotational dynamics of R6G in PEO solutions showed the absence of strong interactions between R6G and PEO chains in water and the ability of the dye to sense the presence of polymer clusters in 30 wt % solutions. Time-resolved anisotropy decays of polymer-modified Ludox provided direct evidence for distribution of the dye between bound and free states, with the bound dye showing two decay components: a nanosecond decay component that is consistent with local motions of bound probes and a residual anisotropy component due to slow rotation of large silica particles. The data showed that the dye was strongly adsorbed to unmodified silica nanoparticles, to the extent that less than 1% of the dye was present in the surrounding aqueous solution. Addition of PEO blocked the adsorption of the dye to a significant degree, with up to 50% of the probe being present in the aqueous solution for Ludox samples containing 30 wt % of low molecular weight PEO. The addition of such agents also decreased the value and increased the fractional contribution of the nanosecond rotational correlation time, suggesting that polymer adsorption altered the degree of local motion of the bound probe. Atomic force microscopy imaging studies provided no evidence for a change in the particle size upon surface modification but did suggest interparticle aggregation after polymer adsorption. Thus, this redistribution of the probe is interpreted as being due to coverage of particles with the polymer, resulting in lower adsorption of R6G to the silica. The data clearly show the power of time-resolved fluorescence anisotropy decay measurements for probing the modification of silica surfaces and suggest that this method should prove useful in characterization of new chromatographic stationary phases and nanocomposite materials.     

Polymerisations of -caprolactone and β-butyrolactone with Zn-, Al- and Mg-based organometallic complexes

The reaction of EtAlCl₂ with 1,2-{LiN(PMes₂)}₂C₆H₄ (Mes = 2,4,6-Me₃C₆H₂) and of butyloctylmagnesium with 1,2-{NH(PPh₂)}₂C₆H₄ gave [AlEt(1,2-{N(PMes₂)}₂C₆H₄-κ²N,N′)(THF)] (1) and [Mg(1,2-{N(PPh₂)}₂C₆H₄-κ²N,N′)(THF)₂] (2), respectively. Complexes 1 and 2 were fully characterised by NMR (¹H, ¹³C, ³¹P) and IR spectroscopy and mass spectrometry. Complexes 1 and 2 were employed as catalysts in the polymerisation of -caprolactone, which produced polymers with a narrow molecular weight distribution. For comparison the polymerisations of -caprolactone and β-butyrolactone were carried out with the Zn complex [ZnPr{1-N(PMes₂)-2-N(PHMes₂)C₆H₄-κ²N,N′}] (3) as catalyst, which produced polymers with narrow molecular weight distributions and high molecular weights.     

The synthesis of potential Neramexane metabolites: cis- and trans-3-amino-1,3,5,5-tetramethylcyclohexanecarboxylic acids

A seven step synthetic route toward potential Neramexane metabolites cis- and trans-3-amino-1,3,5,5-tetramethylcyclohexanecarboxylic acids, cis-1 and trans-1, has been developed from isophorone. The synthetic procedure represents a useful method for the preparation of γ-amino acids with both amino and carboxyl groups situated at tertiary carbon atoms.     

Comparative study of HPLC-DAD and HPTLC for the simultaneous determination of a new multitarget antidiabetic ternary mixture in combined tablets

Qternmet XR® (FDA approval, May 2019) is a multitarget anti-diabetic drug combination composed of metformin (MET), saxagliptin (SAX) and dapagliflozin (DAP). To our present knowledge, no analytical reports were found in the scientific databases for the simultaneous quantification of MET, SAX and DAP in their ternary combined tablets, moreover, no articles have attempted the simultaneous estimation of the cited drugs in any matrix using high-performance liquid chromatography with diode-array detection (HPLC–DAD) or high-performance thin-layer chromatography (HPTLC) technique. The current work represents a comparative study on two developed and validated chromatographic methods for the simultaneous determination of the ternary mixture (MET, SAX and DAP) in pure form and in combined tablet dosage form. The first method is reversed-phase HPLC using Agilent C18 column (4.6 × 250 mm, 5 μm p.s.) with a mobile phase consisting of acetonitrile and acidic aqueous phase pH 3 with a photodiode array detection at 230 nm. The second method is HPTLC in which drug solutions were applied to Merck HPTLC silica gel plates developed with a mixture of chloroform:methanol:water:acetic acid (7.4:2.6:0.5:0.01, v/v) and scanned at 224 nm. Both methods were fully validated following the ICH guidelines in terms of linearity, accuracy, precision, selectivity and robustness.

Representative HPLC (a) and HPTLC (b) chromatograms for a ternary mixture of metformin (MET), saxagliptin (SAX) and dapagliflozin (DAP)

     

Coexistence of domains with distinct order and polarity in fluid bacterial membranes

In this study we sought the detection and characterization of bacterial membrane domains. Fluorescence generalized polarization (GP) spectra of laurdan-labeled Escherichia coli and temperature dependencies of both laurdan's GP and fluorescence anisotropy of 1,3-diphenyl-1,3,5-hexatriene (DPH) (rDPH) affirmed that at physiological temperatures, the E. coli membrane is in a liquid-crystalline phase. However, the strong excitation wavelength dependence of rlaurdan at 37 degrees C reflects membrane heterogeneity. Time-resolved fluorescence emission spectra, which display distinct biphasic redshift kinetics, verified the coexistence of two subpopulations of laurdan. In the initial phase, <50 ps, the redshift in the spectral mass center is much faster for laurdan excited at the blue edge (350 nm), whereas at longer time intervals, similar kinetics is observed upon excitation at either blue or red edge (400 nm). Excitation in the blue region selects laurdan molecules presumably located in a lipid domain in which fast intramolecular relaxation and low anisotropy characterize laurdan's emission. In the proteo-lipid domain, laurdan motion and conformation are restricted as exhibited by a slower relaxation rate, higher anisotropy and a lower GP value. Triple-Gaussian decomposition of laurdan emission spectra showed a sharp phase transition in the temperature dependence of individual components when excited in the blue but not in the red region. At least two kinds of domains of distinct polarity and order are suggested to coexist in the liquid-crystalline bacterial membrane: a lipid-enriched and a proteolipid domain. In bacteria with chloramphenicol (Cam)-inhibited protein synthesis, laurdan showed reduced polarity and restoration of an isoemissive point in the temperature-dependent spectra. These results suggest a decrease in membrane heterogeneity caused by Cam-induced domain dissipation.     

Tubes of even order and flat π.C 2 geometries

Atube of even orderq=2 ^d is a setT={L, } ofq+3 pairwise skew lines in PG(3,q) such that every plane onL meets the lines of in a hyperoval. Thequadric tube is obtained as follows. Take a hyperbolic quadricQ=Q ₃ ⁺ (q) in PG(3,q); letL be an exterior line, and let consist of the polar line ofL together with a regulus onQ.In this paper we show the existence of tubes of even order other than the quadric one, and we prove that the subgroup of PL(4,q) fixing a tube {L, } cannot act transitively on . As pointed out by a construction due to Pasini, this implies new results for the existence of flat .C ₂ geometries whoseC ₂-residues are nonclassical generalized quadrangles different from nets. We also give the results of some computations on the existence and uniqueness of tubes in PG(3,q) for smallq. Further, we define tubes for oddq (replacing hyperoval by conic in the definition), and consider briefly a related extremal problem.Dedicated to luigi antonio rosati on the occasion of his 70th birthday