Phosphorus-carbon(pyridyl) bond cleavage on reacting diphenyl-2-pyridylphosphine with triiron dodecacarbonyl

The reaction of [Fe₃(CO)₁₂] with diphenyl-2-pyridylphosphine (PPh₂Py) in refluxing toluene for 1 h afforded three compounds, [Fe₂(CO)₆(μ-PPh₂)(μ-κ²-C,N-C₅H₄N)] (1), [Fe(CO)₄(κ¹-P-PPh₂Py)] (2), and [Fe(CO)₃(κ¹-P-PPh₂Py)₂] (3) in 23%, 10% and 3.5% yields after work-up, respectively. The PPh₂Py ligand acts as a terminal P-donor ligand in 2 and 3, while in 1 it underwent a selective phosphorus-carbon(pyridyl) bond cleavage to afford phosphido- and pyridyl-bridged ligands. The complexes were characterized by elemental analysis, FAB-mass, FTIR, ¹H and ³¹P-{¹H}NMR spectroscopies. Compounds 1 and 2 were also characterized by X-ray single crystal.     

Synthesis and structure of a silanetriol via hydroxodearylation involving C-Si bond cleavage

The reaction of tris-iso-propylphenyl-tert-butyl-difluorosilane with KOH using ultra sonication leads to the selective formation of tert-butylsilanetriol, 3. The hydroxodearylation reaction involves C-Si bond cleavage and its mechanism is discussed on the basis of the steric situation of the starting material, which also explains the selectivity of the reaction. The crystal structure of a new polymorph of 3 features a sheet-like hydrogen bonded network.     

Copper·Lys-Gly-His-Lys mediated cleavage of tRNA: Studies of reaction mechanism and cleavage specificity

The reactivity of [Cu²⁺·Lys-Gly-His-Lys-NH₂]²⁺ and [Cu²⁺·Lys-Gly-His-Lys]⁺ toward tRNA^Phe has been evaluated. The amidated and carboxylate forms of the copper peptides display complex binding behavior with strong and weak sites evident (, for the amide form; and , for the carboxylate form), while Cu²⁺(aq) yielded and . The time-dependence of the reaction of [Cu²⁺·Lys-Gly-His-Lys]⁺ and [Cu²⁺·Lys-Gly-His-Lys-NH₂]²⁺ with tRNA^Phe yielded k_obs ∼ 0.075 h⁻¹ for both complexes. HPLC analysis of the reaction products demonstrated guanine as the sole base product. Mass spectrometric data shows a limited number of cleavage fragments with product peak masses consistent with chemistry occurring at a discrete site defined by the structurally contiguous D and TΨC loops, and in a domain where high affinity magnesium centers have previously been observed to promote hydrolysis of the tRNA^Phe backbone. This cleavage pattern is more selective than that previously observed by Long and coworkers for nickel complexes of a series of C-terminally amidated peptides (Gly-Gly-His, Lys-Gly-His, and Arg-Gly-His), and may reflect variations in structural recognition and a distinct reaction path by the nickel derivatives. The data emphasizes the optimal positioning of the metal-associated reactive oxygen species, relative to scissile bonds, as a major criterion for development of efficient catalytic nucleases or therapeutics.     

Residue 345 of dibenzothiophene (DBT) sulfone monooxygenase is involved in C-S bond cleavage specificity of alkylated DBT sulfones

Rhodococcus erythropolis IGTS8 that possesses dibenzothiophene sulfone monooxygenase mutated at residue 345 (Q345A), can degrade octyl sulfide on which the wild strain cannot grow. Residue 345 and the neighbouring residues were changed by site-directed mutagenesis. Only DszA changed at residue 345 gave an altered C-S bond cleavage pattern of 3-methyl DBT sulfone. This residue is therefore involved in C-S bond cleavage specifically for alkylated DBT sulfone.     

One-bead, one-compound peptide library sequencing via high-pressure ammonia cleavage coupled to nanomanipulation/nanoelectrospray ionization mass spectrometry

Biological screening of one-bead, one-compound (OBOC) combinatorial peptide libraries is routinely carried out with the peptide remaining bound to the resin bead during screening. After a hit is identified, the bead is isolated, the peptide is cleaved from the bead, and its sequence is determined. We have developed a new technique for cleavage of peptides from resin beads whereby exposure of a 4-hydroxymethyl benzoic acid (HMBA)-linked peptide to high-pressure ammonia gas led to efficient cleavage in as little as 5 min. Here we also report a new method of extracting peptide from individual library beads for its introduction into a mass spectrometer that uses nanomanipulation combined with nanoelectrospray ionization mass spectrometry (NSI MS). Single beads analyzed by nanomanipulation/NSI MS were found to give identical MS results to those of bulk samples. Detection of 18 unique cleaved peptides 1 to 8 amino acids in length, and sequencing of 14 different peptide sequences 4 to 8 amino acids in length, was demonstrated on a combination of bulk samples and ones from individual beads of an OBOC library. The method was highly reproducible, with 100% of attempts to extract peptide resulting in high-quality MS data. This new collection of techniques allows rapid, reliable, environmentally responsible sequencing of hit beads from combinatorial peptide libraries.     

Revisiting 23-iodospirostanes. New facts and full characterization

In addition to a previous report, the reaction of tigogenin acetate with ICl in refluxing CHCl₃ produced the hitherto unknown 23R-iodotigogenin acetate, bearing an axial iodine atom at C-23 and its already reported 23S-epimer. The same treatment of sarsasapogenin acetate led to a single diasteromer characterized as 23S-iodosarsasapogenin acetate. A full characterization of the obtained compound including ¹H, ¹³C NMR, MS and X-ray diffraction is provided.     

A comparison of vanadyl acetylacetonate complexes of N2O heteroscorpionate ligands that vary systematically in donor set

We have successfully prepared a series of vanadyl complexes with N₂O heteroscorpionate ligands and have characterized their cis and trans geometrical isomers both in solution and the solid state. The major difference between the isomers, and between the various oxygen atom donors of the N₂O scorpionate ligands, is in their redox potentials which can span almost a volt for this ostensively similar set of compounds. Such data may be useful in screening vanadium complexes for potential biological activity.     

Identification of an intermolecular disulfide bond in barley hemoglobin

The present study was designed to investigate properties of ion channels in undifferentiated rabbit mesenchymal stem cells (MSCs) from bone marrow using whole-cell patch-clamp and RT-PCR techniques. It was found that three types of outward currents were present in rabbit MSCs, including an inward rectifier K(+) current (I(Kir)), a noise-like Ca(2+)-activated K(+) current (I(KCa)) co-present with delayed rectifier K(+) current (IK(DR)). I(Kir) was inhibited by Ba(2+), while I(KCa) was inhibited by paxilline (a blocker of big conductance I(KCa) channels) and clotrimazole (an inhibitor of intermediate conductance I(KCa) channels). IK(DR) exhibited a slow inactivation, "U-shaped" voltage-dependent inactivation, and slow recovery from inactivation, and the current was inhibited by tetraethylammonium or 4-aminopyridine. RT-PCR revealed the molecular identities for the functional ionic currents, including Kir1.1 (possibly responsible for I(Kir)), KCa1.1 and KCa3.1 (possibly responsible for I(KCa)), and Kv1.2, Kv2.1, and Kv2.2 (possibly responsible for IK(DR)). These results demonstrate for the first time that three types of functional ion channel currents (i.e., I(Kir), I(KCa), and IK(DR)) are present in rabbit MSCs from bone marrow.     

DNA cleavage activity of VO(acac)2 and derivatives

The DNA cleavage activity of several β-diketonate vanadyl complexes is examined. Vanadyl acetylacetonate, V^IVO(acac)₂, 1, shows a remarkable activity in degrading plasmid DNA in the absence of any activating agents, air and photoirradiation. The cleaving activity of several related complexes V^IVO(hd)₂ (2, Hhd = 3,5-heptanedione), V^IVO(acac-NH₂)₂ (3, Hacac-NH₂ = acetoacetamide) and V^IVO(acac-NMe₂)₂ (4, Hacac-NMe₂ = N,N-dimethylacetoacetamide) is also evaluated. It is shown that 2 exhibits an activity similar to 1, while 3 and 4 are much less efficient cleaving agents. The different activity of the complexes is related to their stability towards hydrolysis in aqueous solution, which follows the order 1∼2 ? 3∼4. The nature of the pH buffer was also found to be determinant in the nuclease activity of 1 and 2. In a phosphate buffered medium DNA cleavage by these agents is much more efficient than in tris, hepes, mes or mops buffers. The reaction seems to take place through a mixed mechanism, involving the formation of reactive oxygen species (ROS), namely OH radicals, and possibly also direct cleavage at phosphodiester linkages induced by the vanadium complexes.     

Reactions of 1,8-bis(diphenylphosphino)naphthalene with ruthenium cluster carbonyls: C-H and C-P bond cleavage reactions

Reactions between Ru₃(CO)₁₂ and 1,8-bis(diphenylphosphino)naphthalene (dppn) have given the four complexes Ru₃(μ-H){μ₃-PPh₂(nap)PPh(C₆H₄)}(CO)₈ (1), Ru₄(μ-H){μ₃-PPh₂(nap)PPh(C₆H₄)}(μ-CO)₃(CO)₇ (2) and Ru₄(μ-H)(μ₃-C₆H₄){μ-PPh(nap)PPh₂}(CO)₁₁ (3) (in refluxing thf), and Ru₄{μ₄-P(nap)PPh₂}(μ₄-C₆H₄)(μ-CO)(CO)₉ (4) (in refluxing toluene) which have been characterised by single crystal X-ray studies. They have been formed by aryl C-H and aryl C-P bond cleavage reactions, presumably from an initial (unobserved) chelate dppn complex. The unchanged chelating ligand is found in Ru₃(μ-dppm)(CO)₈(dppn) (5), obtained from Ru₃(μ-dppm)(CO)₁₀ and dppn in refluxing thf.     

Oxidative cleavage of the C-C bond of 3,6-dialkylcyclohexane-1,2-diones by cell suspension cultures of Marchantia polymorpha

Biotransformation of 3,6-dialkylcyclohexane-1,2-diones by cell suspension cultures of Marchantia polymorpha involves regioselective oxidative cleavage of the C-C bond to give the corresponding oxocarboxylic acids shortened by one carbon unit. In the case of cyclohexane-1,2-dione, adipic acid was obtained.     

Reactivity of phenyldi(2-thienyl)phosphine towards group 7 metal carbonyls: Carbon-phosphorus bond activation

Addition of phenyldi(2-thienyl)phosphine (PPhTh₂) to [Re₂(CO)_10−n(NCMe)_n] (n = 1, 2) affords the substitution products [Re₂(CO)_10−n(PhPTh₂)_n] (1, 2) together with small amounts of fac-[ClRe(CO)₃(PPhTh₂)₂] (3) (n = 2). Reaction of [Re₂(CO)₁₀] with PPhTh₂ in refluxing xylene affords a mixture which includes 2, [Re₂(CO)₇(PPhTh₂)(μ-PPhTh)(μ-H)] (4), [Re₂(CO)₇(PPhTh₂)(μ-PPhTh)(μ-η¹,κ¹(S)-C₄H₃S)] (5) and mer-[HRe(CO)₃(PPhTh₂)₂] (6). Phosphido-bridged 4 and 5 are formed by the carbon-phosphorus bond cleavage of the coordinated PPhTh₂ ligand, the cleaved thienyl group being retained in the latter. Reaction of [Mn₂(CO)₁₀] with PPhTh₂ in refluxing toluene affords [Mn₂(CO)₉(PPhTh₂)] (7) and the carbon-phosphorus bond cleavage products [Mn₂(CO)₆(μ-PPhTh)(μ-η¹,η⁵-C₄H₃S)] (8) and [Mn₂(CO)₅(PPhTh₂)(μ-PPhTh)(μ-η¹,η⁵-C₄H₃S)] (9). Both 8 and 9 contain a bridging thienyl ligand which is bonded to one manganese atom in a η⁵-fashion.     

Complete disulfide bond assignment of a recombinant immunoglobulin G4 monoclonal antibody

Surface plasmon resonance biosensor analysis was used to evaluate the thermodynamics and binding kinetics of naturally occurring and synthetic cobalamins interacting with vitamin B(12) binding proteins. Cyanocobalamin-b-(5-aminopentylamide) was immobilized on a biosensor chip surface to determine the affinity of different cobalamins for transcobalamin, intrinsic factor, and nonintrinsic factor. A solution competition binding assay, in which a surface immobilized cobalamin analog competes with analyte cobalamin for B(12) protein binding, shows that only recombinant human transcobalamin is sensitive to modification of the corrin ring b-propionamide of cyanocobalamin. A direct binding assay, where recombinant human transcobalamin is conjugated to a biosensor chip, allows kinetic analysis of cobalamin binding. Response data for cyanocobalamin binding to the transcobalamin protein surface were globally fitted to a bimolecular interaction model that includes a term for mass transport. This model yields association and dissociation rate constants of k(a) = 3 x 10(7) M(-1) s(-1) and k(d) = 6 x 10(-4) s(-1), respectively, with an overall dissociation constant of K(D) = 20 pM at 30 degrees C. Transcobalamin binds cyanocobalamin-b-(5-aminopentylamide) with association and dissociation rates that are twofold slower and threefold faster, respectively, than transcobalamin binding to cyanocobalamin. The affinities determined for protein-ligand interaction, using the solution competition and direct binding assays, are comparable, demonstrating that surface plasmon resonance provides a versatile way to study the molecular recognition properties of vitamin B(12) binding proteins.     

The rate of spontaneous cleavage of the glycosidic bond of adenosine

Previous estimates of the rate of spontaneous cleavage of the glycosidic bond of adenosine were determined by extrapolating the rates of the acid- and base-catalyzed reactions to neutral pH. Here we show that cleavage also proceeds through a pH-independent mechanism. Rate constants were determined as a function of temperature at pH 7 and a linear Arrhenius plot was constructed. Uncatalyzed cleavage occurs with a rate constant of 3.7 × 10⁻¹² s⁻¹ at 25 °C, and the rate enhancement generated by the corresponding glycoside hydrolase is ∼5 × 10¹²-fold.     

A fluorescence assay for tetradecyltrimethylammonium mono-oxygenase activity that catalyzes the cleavage of the C-N bond with the production of trimethylamine

This article describes a simple fluorescence method for the determination of tetradecyltrimethylammonium mono-oxygenase (TTAB mono-oxygenase) activity involving N-dealkylation of tetradecyltrimethylammonium bromide with concomitant production of trimethylamine (TMA). Activity was determined by measuring the formation of TMA using the morin reagent and aluminum (Al). Morin reacts with Al to form a fluorescent complex, Al-morin. In the presence of TMA, Al is tightly associated with TMA and cannot be sequestered by morin, thus providing evidence for formation of the Al-TMA complex. The concentration of TMA is estimated by calibration graphs constructed by plotting the fluorescence intensity of the Al-morin complex versus TMA concentration. The fluorescence intensities of the Al-morin complexes quenched by TMA are linearly dependent on both the time of the TTAB mono-oxygenase reaction and the amount of protein used in the reaction. The kinetic behavior is characterized by K_0.5 = 4.26 × 10⁻⁴ M, and the apparent Hill coefficient (n_app) = 2.24. These values are both comparable to those determined by GC-MS (K_0.5 = 4.41 × 10⁻⁴ M and n_app = 2.35). The advantages of this assay include rapid and efficient implementation and potential employment for routine accurate determinations of TTAB mono-oxygenase activity over a wide range of substrate concentrations.     

A study of dihydrogen bond interactions through three-centre bond and group indices

We report here an investigation into the correlation between dihydrogen bond energies, three-centre bond indices and group indices in some dihydrogen-bonded dimers. This kind of bond is generated by interaction between proton-donator and proton-acceptor groups, XH^σ+…H′^σ ? M, where X is a more electronegative atom and M a less electronegative atom than hydrogen. The different electronegativities of the X atoms, as well the M atoms, would affect the correlations between H^σ+…H′^σ ?  distances and bond energies of these systems. In this work it will be shown that three-centre bond indices and group indices exhibit a better correlation with bond energies when compared to H^σ+…H′^σ ?  distances for this kind of system.     

Assessment of proteasomal cleavage probabilities from kinetic analysis of time-dependent product formation

Proteasomes are multicatalytic cellular protease complexes that degrade intracellular proteins into smaller peptides. Proteasomal in vitro digests have revealed that the various peptide bonds of a given substrate are cleaved in a highly selective manner. Regarding the key role of proteasomes as the main supplier of antigenic peptides for MHC class I-mediated antigen presentation, it is important to know to what extent these preferences for specific peptide bonds may vary among proteasomes of different cellular origin and of different subunit composition. Here, we quantify such cleavage rates by means of a kinetic proteasome model that relates the time-dependent changes of the amount of any generated peptide to the rates with which this peptide can be either generated from longer precursor peptides or degraded into smaller successor peptides. Numerical values for these rates are estimated by minimizing the distance between simulated and measured time-courses. The proposed method is applied to kinetic data obtained by combining HPLC fractionation and mass spectrometry (MS) to trace the degradation of two model peptides (pp89-25mer and LLO-27mer) by either the constitutive (T2) or immunoproteasome (T2.27). To convert the intensity of the MS signals into the respective peptide amounts, we use two methods leading to similar results: experimental calibration curves and theoretically determined linear scaling functions based on a novel approach using mass conservation rules. Comparison of the cleavage probabilities and procession rates obtained for the two types of proteasomes reveals that the striking differences between the time-dependent peptide profiles can be accounted for mainly by a generally higher turnover rate of the immunoproteasome. For the pp89-25mer, there is no significant change of the cleavage probabilities for any of the ten observed cleavage sites. For the LLO-27mer, there appears to be a significant change in the cleavage probabilities for four of the nine observed cleavage sites when switching from the constitutive to the immunoproteasome.     

A survey of hydrogen bond geometries in the crystal structures of amino acids

An analysis of the geometries of the hydrogen bonds observed by neutron diffraction in thirt-two crystal structures of amino acids shows the following results. Of the 168 hydrogen bonds in the data set, 64 involve the zwitterion groups 

and $\text{C}$O₂. Another 18 are from

to sulphate or carbonyl oxygens. The majority, 46, of these

H … O bonds are three-centered (bifurcated). Nine are four-centered (trifurcated). The geometry in which the three-centered hydrogen bond involves both oxygens of the same carboxylate group is not especially favoured. When it does occur, one hydrogen bond is generally shorter and the other longer, than when the bonding involves oxygens on different carboxylate groups. The shortest hydrogen bonds are the OH … O $\text{C}$, from a carboxylic acid hydroxyl to a carboxylate oxygen, and NH … O$\text{C}$ when the nitrogen is the ring atom in histidine or proline. Carboxylate groups, on average, accept six hydrogen bonds, with no examples of less than four bonds. The reason for the large number of three-centered

H … O$\text{C}$ bonds is therefore a proton deficiency arising from the disparity between the tripled donor property of the

groups and the sextuple, on average, acceptor property of the carboxylate groups. There is good geometrical evidence for the existence of H … O and H … Cl^? hydrogen bonds, especially involving the hydrogen atoms on α-atoms.     

A single molecule assay for measuring site-specific DNA cleavage

Sequence-specific DNA cleavage is a key step in a number of genomic transactions. Here, we report a single-molecule technique that allows the simultaneous measurement of hundreds of DNAs, thereby collecting significant statistics in a single experiment. Microbeads are tethered with single DNA molecules in a microfluidic channel. After the DNA cleavage reaction is initiated, the time of cleavage of each DNA is recorded using video microscopy. We demonstrate the utility of our method by measuring the cleavage kinetics of NdeI, a type II restriction endonuclease.     

Thermodynamics of single peptide bond cleavage in bovine pancreatic trypsin inhibitor (BPTI)

A major goal of this paper was to estimate a dynamic range of equilibrium constant for the opening of a single peptide bond in a model protein, bovine pancreatic trypsin inhibitor (BPTI). Ten mutants of BPTI containing a single Xaa-->Met substitution introduced in different parts of the molecule were expressed in Escherichia coli. The mutants were folded, purified to homogeneity, and cleaved with cyanogen bromide to respective cleaved forms. Conformation of the intact mutants was similar to the wildtype, as judged from their circular dichroism spectra. Substantial conformational changes were observed on the chemical cleavage of three single peptide bonds--Met46-Ser, Met49-Cys, and Met53-Thr--located within the C-terminal helix. Cleavage of those peptide bonds caused a significant destabilization of the molecule, with a drop of the denaturation temperature by 56.4 degrees C to 68 degrees C at pH 4.3. Opening of the remaining seven peptide bonds was related to a 10.8 degrees C to 39.4 degrees C decrease in T(den). Free energies of the opening of 10 single peptide bonds in native mutants (Delta G(op,N)) were estimated from the thermodynamic cycle that links denaturation and cleavage free energies. To calculate those values, we assumed that the free energy of opening of a single peptide bond in the denatured state (Delta G(op,D)) was equal to -2.7 kcal/mole, as reported previously. Calculated Delta G(op,N) values in BPTI were in the range from 0.2 to 10 kcal/mole, which was equivalent to a >1 million-fold difference in equilibrium constants. The values of Delta G(op,N) were the largest for peptide bonds located in the C-terminal helix and significantly lower for peptide bonds in the beta-structure or loop regions. It appears that opening constants for single peptide bonds in various proteins span across 33 orders of magnitude. Typical equilibrium values for a single peptide bond opening in a protein containing secondary structure elements fall into negligibly low values, from 10(-3) to 10(-8), and are efficient to ensure stability against proteolysis.