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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A new method of detecting the presence of deprotonation and determining its position in gas-phase polypeptide cations is described. The method involves 157-nm ultra-violet photodissociation (UVPD) and is based on monitoring the losses of CO2 (44 Da) from electronically excited deprotonated carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+)...(-)...(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding within polypeptide clusters. Collision-activated dissociation (CAD) of decarboxylated cations localizes the position of deprotonation. Fragment abundances can be used for the semiquantitative assessment of the branching ratio of deprotonation among different acidic sites, however, the mechanism of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm UVPD produces abundant radical cations M*+ from protonated molecules through the loss of a hydrogen atom. This method of producing M*+ ions is general and can be applied to any gas-phase peptide cation. The abundance of the molecular radical cations M*+ produced is sufficient for further tandem mass spectrometry (MS/MS), which, in the cases studied, yielded side-chain loss of a basic amino acid as the most abundant fragmentation channel together with some backbone cleavages.
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PMID:Zwitterionic states in gas-phase polypeptide ions revealed by 157-nm ultra-violet photodissociation. 1687 5

The complex [7,10-mu-H-7-CO-7,7-(PPh3)2-isonido-7,8,9-ReC2B7H9] has been synthesized by treatment of the complex salt [NHMe3][3,3-Cl2-3,3-(CO)2-closo-3,1,2-ReC2B9H11] with PPh3 in refluxing THF (tetrahydrofuran) and isolated as intensely colored orange-red microcrystals. Spectroscopic NMR and IR data have suggested that the product has a highly asymmetric structure with two inequivalent PPh3 ligands and a single CO ligand. Measurement of 11B NMR spectra in particular have indicated seven distinct boron vertexes, although the resulting cage degradation by removal of two BH vertexes was confirmed only following X-ray crystallographic analysis, which revealed the pentadecahedral isonido-7,8,9-ReC2B7 architecture. The 11B NMR resonances span an enormous chemical shift range (Deltadelta = 113), and this appears to be a direct consequence of the deshielding of the boron vertex directly opposite the quadrilateral |ReCCB| aperture. The new complex has been shown by electrochemical measurements to undergo a reversible one-electron oxidation. Digitally simulated cyclic voltammograms support a proposed square scheme (E(1/2) = 0.58, 0.69 V vs ferrocene) involving a reversible isonido-closo transition of the metallacarborane cage. Most unusually for a metallacarborane complex, ambient temperature solutions in CH2Cl2 and DMF have been shown to be intensely turquoise-blue fluorescent (lambda(em) = 442 nm, Phi = 0.012). Fluorescence spectroscopy measurements in MeTHF (2-methyltetrahydrofuran) glass at 77 K have indicated that the likely cause of such a broad emission is dual fluorescence (lambda(em) = 404, 505 nm), with both emissions displaying vibronic structure. Following excited-state lifetime decay analysis, the emissive behavior has been accredited to metal-perturbed 1IL states, with the lower energy emission arising from a slight geometric distortion of the initially excited complex.
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PMID:Dual fluorescence from an isonido ReIII rhenacarborane phosphine complex, [7,10-mu-H-7-CO-7,7-(PPh3)2-isonido-7,8,9-ReC2B7H9]. 1693 36

DNA-binding proteins from starved cells (Dps proteins) protect bacteria primarily from oxidative damage. They are composed of 12 identical subunits assembled with 23-symmetry to form a compact cage-like structure known to be stable at temperatures > 70 degrees C and over a wide pH range. Thermosynechococcus elongatus Dps thermostability is increased dramatically relative to mesophilic Dps proteins. Hydrophobic interactions at the dimeric and trimeric interfaces called Dps-like are replaced by salt bridges and hydrogen bonds, a common strategy in thermophiles. Moreover, the buried surface area at the least-extended Dps-like interface is significantly increased. A peculiarity of T. elongatus Dps is the presence of a chloride ion coordinated with threefold symmetry-related arginine residues lining the opening of the Dps-like pore toward the internal cavity. T. elongatus Dps conserves the unusual intersubunit ferroxidase centre that allows the Dps protein family to oxidize Fe(II) with hydrogen peroxide, thereby inhibiting free radical production via Fenton chemistry. This catalytic property is of special importance in T. elongatus (which lacks the catalase gene) in the protection of DNA and photosystems I and II from hydrogen peroxide-mediated oxidative damage.
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PMID:Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus. 1701 59

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding.
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PMID:Sampling the multiple folding mechanisms of Trp-cage in explicit solvent. 1703 4

The reaction of [N(PPh(3))(2)][CpCo(CN)(3)] and [Cb*Co(NCMe)(3)]PF(6) (Cb* = C(4)Me(4)) in the presence of K(+) afforded {K subset[CpCo(CN)(3)](4)[Cb*Co](4)}PF(6), [KCo(8)]PF(6). IR, NMR, ESI-MS indicate that [KCo(8)]PF(6) is a high-symmetry molecular box containing a potassium ion at its interior. The analogous heterometallic cage {K subset[Cp*Rh(CN)(3)](4)[Cb*Co](4)}PF(6) ([KRh(4)Co(4)]PF(6)) was prepared similarly via the condensation of K[Cp*Rh(CN)(3)] and [Cb*Co(NCMe)(3)]PF(6). Crystallographic analysis confirmed the structure of [KCo(8)]PF(6). The cyanide ligands are ordered, implying that no Co-CN bonds are broken upon cage formation and ion complexation. Eight Co-CN-Co edges of the box bow inward toward the encapsulated K(+), and the remaining four mu-CN ligands bow outward. MeCN solutions of [KCo(8)](+) and [KRh(4)Co(4)](+) were found to undergo ion exchange with Cs(+) to give [CsCo(8)](+) and [CsRh(4)Co(4)](+), both in quantitative yields. Labeling experiments involving [(MeC5H4)Co(CN)(3)]- demonstrated that Cs(+)-for-K(+) ion exchange is accompanied by significant fragmentation. Ion exchange of NH(4+) with [KCo(8)](+) proceeds to completion in THF solution, but in MeCN solution, the exclusive products were [Cb*Co(NCMe)(3)]PF(6) and the poorly soluble salt NH(4)CpCo(CN)(3). The lability of the NH(4+)-containing cage was also indicated by the rapid exchange of the acidic protons in [NH(4)Co(8)](+). Oxidation of [MCo(8)](+) with 4 equiv of FcPF(6) produced paramagnetic (S = 4/2) [Co(8)](4+), releasing Cs(+) or K(+). The oxidation-induced dissociation of M(+) from the cages is chemically reversed by treatment of [Co(8)](4+) and CsOTf with 4 equiv of Cp(2)Co. Cation recognition by [Co(8)] and [Rh(4)Co(4)] cages was investigated. Electrochemical measurements indicated that E(1/2)(Cs(+))--E(1/2)(K(+)) approximately 0.08 V for [MCo(8)](+).
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PMID:Redox-switched complexation/decomplexation of K(+) and Cs(+) by molecular cyanometalate boxes. 1726 Sep 85

The study was undertaken to investigate the uptake of mercury in salmon throughout the entire farming period at the net cage. Mercury concentrations in muscle, liver, kidney, and gill and responses to the various dietary mercury concentrations were determined. The accumulation of mercury is in the order of kidney>gill=liver>muscle. The highest mercury peak concentrations were observed for both kidney and gill at the parr-smolt period, while liver and muscle mercury peaked one month later after caging at the grow-out site. High dietary sodium and calcium fed to the salmon contributed to the elevation of mercury in kidney and gill during the smolting process. The mercury burden over the grow-out period increased sharply with a linear relationship of mercury uptake. The tissue mercury burden per gram of growth was calculated using the slope of mercury burden and the slope of growth over the period of each stage. The results showed dietary mercury loadings on marketable salmon were within tolerance limits of FDA and US EPA. Rapid growth of salmon and low dietary mercury progressively reduces the uptake of mercury in salmon. The time series of mercury monitoring showed that mercury concentrations in salmon were greater at the parr stage in freshwater than at the grow-out stage in salt water.
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PMID:A time series of mercury accumulation and improvement of dietary feed in net caged Atlantic salmon (Salmo salar). 1738 70

Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.
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PMID:Fluorescence probe of Trp-cage protein conformation in solution and in gas phase. 1748 69

The synthesis, structure and characterization of the [{Fe3(CO)9(micro3-O)}2H]3- trianion in its [Cs(THF)0.33]+ and [NEt4]+ salt are reported. The title dimeric cluster has been obtained by protonation in water or in organic solvent of the [Fe3(CO)9(micro3-O)]2- dianion to the hydroxo [Fe3(CO)9(micro3-OH)]- derivative and crystallization. The solid state structure of [Cs(THF)0.33]3[{Fe3(CO)9(micro3-O)}2H] is based on ionic packing of [Cs(THF)0.33]+ cations and [{Fe3(CO)9(micro3-O)}2H]3- trianions. The fractional formula is due to the particular packing of Cs+ cations, which are at the vertices of fused cuboctahedral and trigonal antiprismatic polyhedrons. Each cuboctahedron encapsulates a [{Fe3(CO)9(micro3-O)}2H]3- trianion, whereas each trigonal antiprism encapsulates a THF molecule. The possibility that the structure of the [{Fe3(CO)9(micro3-O)}2H]3- trianion could be affected by its confinement in the cuboctahedral cage of Cs+ ions and the heavy disorder of the THF molecule urged a further structural determination of the trianion with a completely different cation. The corresponding [NEt4]3[{Fe3(CO)9(micro3-O)}2H] salt has been, therefore, prepared and structurally characterized. The [{Fe3(CO)9(micro3-O)}2H]3- trianion displays an identical structure and almost coincident molecular parameters in both salts. Its most notable feature is represented by the unique hydrogen atom symmetrically bridging the micro3-O atoms of two different [Fe3(CO)9(micro3-O)]2- molecules and displaying one of shortest O...H...O interaction so far reported in organic, inorganic and organometallic literature. The structure of [Cs(THF)]2[Fe4(CO)13], which has been obtained as a by-product of the synthesis of [Cs(THF)0.33]3[{Fe3(CO)9(micro3-O)}2H], is also briefly reported.
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PMID:Synthesis and X-ray structure of the [{Fe3(CO)9(micro3-O)}2H]3- trianion: dimerization of a metal carbonyl cluster via formation of an exceptionally short hydrogen bond. 1757 89

The occurrence of p(1),n(1) salt when accompanied by substrate self-association can have profound effects on enantiomer separation processes of non-racemic mixtures, impeding the complete recovery of the major enantiomer through formation of an inescapable racemate cage.
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PMID:The racemate cage. Influence of p(1),n(1) salt occurrence on enantiomer separation processes. The case of trans-chrysanthemic acid. 1759 31

In an earlier publication (J. Am. Chem. Soc. 2002, 124, 7111) we showed that polymeric cationic [Ag(P(4)S(3))(n)](+) complexes (n=1, 2) are accessible if partnered with a suitable weakly coordinating counterion of the type [Al(OR(F))(4)](-) (OR(F): poly- or perfluorinated alkoxide). The present work addresses the following questions that could not be answered in the initial report: How many P(4)S(3) cages can be bound to a Ag(+) ion? Why are these complexes completely dynamic in solution in the (31)P NMR experiments? Can these dynamics be frozen out in a low-temperature (31)P MAS NMR experiment? What are the principal binding sites of the P(4)S(3) cage towards the Ag(+) ion? What are likely other isomers on the [Ag(P(4)S(3))(n)](+) potential energy surface? Counterion influence: Reactions of P(4)S(3) with Ag[Al{OC(CH(3))(CF(3))(2)}(4)] (Ag[hftb]) and Ag[{(CF(3))(3)CO}(3)Al-F-Al{OC(CF(3))(3))}(3)] (Ag[al-f-al]) gave [(P(4)S(3))Ag[hftb]](infinity) (7) as a molecular species, whereas [Ag(2)(P(4)S(3))(6)](2+)[al-f-al](-) (2) (8) is an isolated 2:1 salt. We suggest that a maximum of three P(4)S(3) cages may be bound on average to an Ag(+) ion. Only isolated dimeric dications are formed with the largest cation, but polymeric species are obtained with all other smaller aluminates. Thermodynamic Born-Haber cycles, DFT calculations, as well as solution NMR and ESI mass spectrometry indicate that 8 exhibits an equilibrium between the dication [Ag(2)(P(4)S(3))(6)](2+) (in the solid state) and two [Ag(P(4)S(3))(3)](+) monocations (in the gas phase and in solution). Dynamics: (31)P MAS NMR spectroscopy showed these solid adducts to be highly dynamic, to an extent that the (2)J(P,P) coupling within the cages could be resolved (J-res experiment). This is supported by DFT calculations, which show that the extended PES of [Ag(P(4)S(3))(n)](+) (n=1-3) and [Ag(2)(P(4)S(3))(2)](+) is very flat. The structures of alpha- and gamma-P(4)S(3) were redetermined. Their variable-temperature (31)P MAS NMR spectra are discussed jointly with those of all four currently known [Ag(P(4)S(3))(n)](+) adducts with n=1, 2, and 3.
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PMID:Dynamics and counterion-dependence of the structures of weakly bound Ag+-P4S3 complexes. 1761 55


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