A novel approach to tag and identify geranylgeranylated proteins

A recently developed proteomic strategy, the “GG‐azide”‐labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido‐geranylgeranyl analog and chemoselective derivatization of azido‐geranylgeranyl‐modified proteins by the “click” chemistry, using a tetramethylrhodamine‐alkyne. The resulting conjugated proteins can be separated by 1‐D or 2‐D and pH fractionation, and detected by fluorescence imaging. This method is compatible with downstream LC‐MS/MS analysis. Proteomic analysis of conjugated proteins by this approach identified several known geranylgeranylated proteins as well as Rap2c, a novel member of the Ras family. Furthermore, prenylation of progerin in mouse embryonic fibroblast cells was examined using this approach, demonstrating that this strategy can be used to study prenylation of specific proteins. The “GG‐azide”‐labeling approach provides a new tool for the detection and proteomic analysis of geranylgeranylated proteins, and it can readily be extended to other post‐translational modifications.     

Integrating DEA-oriented performance assessment and target setting using interactive MOLP methods

Data envelopment analysis (DEA) and multiple objective linear programming (MOLP) are tools that can be used in management control and planning. Whilst these two types of model are similar in structure, DEA is directed to assessing past performances as part of management control function and MOLP to planning future performance targets. This paper is devoted to investigating equivalence models and interactive tradeoff analysis procedures in MOLP, such that DEA-oriented performance assessment and target setting can be integrated in a way that the decision makers’ preferences can be taken into account in an interactive fashion. Three equivalence models are investigated between the output-oriented dual DEA model and the minimax reference point formulations, namely the super-ideal point model, the ideal point model and the shortest distance model. These models can be used to support efficiency analysis in the same way as the conventional DEA model does and also support tradeoff analysis for setting target values by individuals or groups. A case study is conducted to illustrate how DEA-oriented efficiency analysis can be conducted using the MOLP methods and how such performance assessment can be integrated into an interactive procedure for setting realistic target values.     

π-Extended and six-coordinate iron(II) complexes: structures, magnetic properties, and the electrochemical synthesis of a conducting iron(II) metallopolymer

Herein, we describe the preparation of three new bidentate π-extended derivatives of the ligand N-phenyl-2-pyridinalimine (ppi) containing a 3-thienyl (4) substituent at position 4 of the aniline ring or 2-thienyl (6) or phenyl (2) substituents at each of the 2,5 positions of the aniline rings. Three iron(2+) complexes (7-9) containing these ligands were prepared by combining two equivalents each of 2, 4, or 6 with Fe(NCS)(2), and the resulting neutral, six-coordinate complexes were fully characterized, including with single crystal X-ray diffraction experiments in the case of complexes 7 and 9. Variable temperature magnetic susceptibility and Mo?ssbauer experiments confirm the presence of spin-crossover in complexes 7 and 8, and the unusual solid state variable temperature magnetic properties of complex 9 likely result from crystal packing forces. Electropolymerization of the 2,5-dithienyl-substituted complex (9) produces a conducting and electrochromic metallopolymer film (poly-9).     

Large endohedral fullerenes containing two metal ions, Sm2@D2(35)-C88, Sm2@C1(21)-C90, and Sm2@D3(85)-C92, and their relationship to endohedral fullerenes containing two gadolinium ions

The carbon soot obtained by electric arc vaporization of carbon rods doped with Sm(2)O(3) contains a series of monometallic endohedral fullerenes, Sm@C(2n), along with smaller quantities of the dimetallic endohedrals Sm(2)@C(2n) with n = 44, 45, 46, and the previously described Sm(2)@D(3d)(822)-C(104). The compounds Sm(2)@C(2n) with n = 44, 45, 46 were purified by high pressure liquid chromatography on several different columns. For endohedral fullerenes that contain two metal atoms, there are two structural possibilities: a normal dimetallofullerene, M(2)@C(2n), or a metal carbide, M(2)(μ-C(2))@C(2n-2). For structural analysis, the individual Sm(2)@C(2n) endohedral fullerenes were cocrystallized with Ni(octaethylporphyrin), and the products were examined by single-crystal X-ray diffraction. These data identified the three new endohedrals as normal dimetallofullerenes and not as carbides: Sm(2)@D(2)(35)-C(88), Sm(2)@C(1)(21)-C(90), and Sm(2)@D(3)(85)-C(92). All four of the known Sm(2)@C(2n) endohedral fullerenes have cages that obey the isolated pentagon rule (IPR). As the cage size expands in this series, so do the distances between the variously disordered samarium atoms. Since the UV/vis/NIR spectra of Sm(2)@D(2)(35)-C(88) and Sm(2)@C(1)(21)-C(90) are very similar to those of Gd(2)C(90) and Gd(2)C(92), we conclude that Gd(2)C(90) and Gd(2)C(92) are the carbides Gd(2)(μ-C(2))@D(2)(35)-C(88) and Gd(2)(μ-C(2))@C(1)(21)-C(90), respectively.     

Bound anions differentially stabilize multiprotein complexes in the absence of bulk solvent

The combination of ion mobility separation with mass spectrometry is an emergent and powerful structural biology tool, capable of simultaneously assessing the structure, topology, dynamics, and composition of large protein assemblies within complex mixtures. An integral part of the ion mobility-mass spectrometry measurement is the ionization of intact multiprotein complexes and their removal from bulk solvent. This process, during which a substantial portion of protein structure and organization is likely to be preserved, imposes a foreign environment on proteins that may cause structural rearrangements to occur. Thus, a general means must be identified to stabilize protein structures in the absence of bulk solvent. Our approach to this problem involves the protection of protein complex structure through the addition of salts in solution prior to desorption/ionization. Anionic components of the added salts bind to the complex either in solution or during the electrospray process, and those that remain bound in the gas phase tend to have high gas phase acidities. The resulting 'shell' of counterions is able to carry away excess energy from the protein complex ion upon activation and can result in significant structural stabilization of the gas-phase protein assembly overall. By using ion mobility-mass spectrometry, we observe both the dissociation and unfolding transitions for four tetrameric protein complexes bound to populations of 12 different anions using collisional activation. The data presented here quantifies, for the first time, the influence of a large range of counterions on gas-phase protein structure and allows us to rank and classify counterions as structure stabilizers in the absence of bulk solvent. Our measurements indicate that tartrate, citrate, chloride, and nitrate anions are among the strongest stabilizers of gas-phase protein structure identified in this screen. The rank order determined by our data is substantially different when compared to the known Hofmeister salt series in solution. While this is an expected outcome of our work, due to the diminished influence of anion and protein solvation by water, our data correlates well to expected anion binding in solution and highlights the fact that both hydration layer and anion-protein binding effects are critical for Hofmeister-type stabilization in solution. Finally, we present a detailed mechanism of action for counterion stabilization of proteins and their complexes in the gas-phase, which indicates that anions must bind with high affinity, but must dissociate readily from the protein in order to be an effective stabilizer. Anion-resolved data acquired for smaller protein systems allows us to classify anions into three categories based on their ability to stabilize protein and protein complex structure in the absence of bulk solvent.     

The shape of the Sc2(μ2-S) unit trapped in C82: crystallographic, computational, and electrochemical studies of the isomers, Sc2(μ2-S)@C(s)(6)-C82 and Sc2(μ2-S)@C(3v)(8)-C82

Single-crystal X-ray diffraction studies of Sc(2)(μ(2)-S)@C(s)(6)-C(82)·Ni(II)(OEP)·2C(6)H(6) and Sc(2)(μ(2)-S)@C(3v)(8)-C(82)·Ni(II)(OEP)·2C(6)H(6) reveal that both contain fully ordered fullerene cages. The crystallographic data for Sc(2)(μ(2)-S)@C(s)(6)-C(82)·Ni(II)(OEP)·2C(6)H(6) show two remarkable features: the presence of two slightly different cage sites and a fully ordered molecule Sc(2)(μ(2)-S)@C(s)(6)-C(82) in one of these sites. The Sc-S-Sc angles in Sc(2)(μ(2)-S)@C(s)(6)-C(82) (113.84(3)°) and Sc(2)(μ(2)-S)@C(3v)(8)-C(82) differ (97.34(13)°). This is the first case where the nature and structure of the fullerene cage isomer exerts a demonstrable effect on the geometry of the cluster contained within. Computational studies have shown that, among the nine isomers that follow the isolated pentagon rule for C(82), the cage stability changes markedly between 0 and 250 K, but the C(s)(6)-C(82) cage is preferred at temperatures ≥250 °C when using the energies obtained with the free encapsulated model (FEM). However, the C(3v)(8)-C(82) cage is preferred at temperatures ≥250 °C using the energies obtained by rigid rotor-harmonic oscillator (RRHO) approximation. These results corroborate the fact that both cages are observed and likely to trap the Sc(2)(μ(2)-S) cluster, whereas earlier FEM and RRHO calculations predicted only the C(s)(6)-C(82) cage is likely to trap the Sc(2)(μ(2)-O) cluster. We also compare the recently published electrochemistry of the sulfide-containing Sc(2)(μ(2)-S)@C(s)(6)-C(82) to that of corresponding oxide-containing Sc(2)(μ(2)-O)@C(s)(6)-C(82).     

Dye-tethered ruthenium nitrosyls containing planar dicarboxamide tetradentate N4 ligands: effects of in-plane ligand twist on NO photolability

To examine the steric effects of the in-plane ligands in dye-sensitized {RuNO}(6) nitrosyls on their NO photolability, two new ligands, namely, 1,2-Bis(pyridine-2-carboxamido)-4,5-dimethoxybenzene (H(2)(OMe)(2)bpb) and 1,2-Bis(Isoquinoline-1-carboxamido)-4,5-dimethoxybenzene (H(2)(OMe)(2)IQ1, H's are dissociable carboxamide protons) have been designed and synthesized. The syntheses and spectroscopic properties of {RuNO}(6) nitrosyls derived from these two ligands, namely, [((OMe)(2)bpb)Ru(NO)(Cl)] (4-Cl), [((OMe)(2)IQ1)Ru(NO)(Cl)] (5-Cl), [((OMe)(2)bpb)Ru(NO)(Resf)] (4-Resf), and [((OMe)(2)IQ1)Ru(NO)(Resf)] (5-Resf), are reported. The structures of 5-Cl, 4-Resf, and 5-Resf have been determined by X-ray crystallography. Removal of the in-plane ligand twist in the quinoline-based R(2)bQb(2-) ligand frame (because of steric interactions between the extended quinoline ring systems) in both R(2)bpb(2-) and R(2)IQ1(2-) (pyridine and 1-isoquinoline rings, respectively, instead of quinoline rings in the equatorial plane) results in enhanced solution stability, as well as higher quantum yield values for NO photorelease upon exposure to 500 nm light. Both dye-tethered {RuNO}(6) nitrosyls 4-Resf and 5-Resf exhibit greater sensitivity to visible light compared to the chloro-bound species 4-Cl and 5-Cl. In addition, the dye-tethered nitrosyls are fluorescent and hence can be used as trackable NO donors in cellular studies.     

A simulation test of the optical Kerr mechanism for laser-induced nucleation

Recent experiments have demonstrated that intense, nanosecond laser pulses can induce crystal nucleation from supersaturated solutions that are transparent at the incident wavelengths, a phenomenon termed nonphotochemical laser-induced nucleation (NPLIN). Previous work has proposed that this effect is due to the alignment of solute molecules in solution due to the electric field of the applied laser light, promoting crystalline order. We have used simulations of NPLIN to examine how an orientational bias in solution affects nucleation with Monte Carlo simulations of a Potts lattice gas model. We examine this effect within both a classical, one-step nucleation framework as well as in the context of two-step nucleation. Our results indicate that an orientational bias can reduce the free energy barrier to nucleation within the one-step picture as well as promote the crystallization of amorphous precritical nuclei (the rate-determining step in the two-step picture). However, these effects are only present with field strengths that are much greater than those used in experiments.     

Communication: Bubbles, crystals, and laser-induced nucleation

Short intense laser pulses of visible and infrared light can dramatically accelerate crystal nucleation from transparent solutions; previous studies invoke mechanisms that are only applicable for nucleation of ordered phases or high dielectric phases. However, we show that similar laser pulses induce CO(2) bubble nucleation in carbonated water. Additionally, in water that is cosupersaturated with argon and glycine, argon bubbles escaping from the water can induce crystal nucleation without a laser. Our findings suggest a possible link between laser-induced nucleation of bubbles and crystals.     

Ionic liquid applications in peptide chemistry: synthesis, purification and analytical characterization processes

This review aims to provide a comprehensive overview of the recent advances made in the field of ionic liquids in peptide chemistry and peptide analytics.