Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations

Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing dynamics of the CO ligand are in agreement with dephasing dynamics calculated with molecular dynamics (MD) simulations for MbCO with the residue histidine-64 (His64) having its imidazole epsilon nitrogen protonated (N(epsilon)-H). The two conformational substate structures B(epsilon) and R(epsilon) observed in the MD simulations are assigned to the spectroscopic A(1) and A(3) conformational substates of MbCO, respectively, based on the agreement between the experimentally measured and calculated dephasing dynamics for these substates. In the A(1) substate, the N(epsilon)-H proton and N(delta) of His64 are approximately equidistant from the CO ligand, while in the A(3) substate, the N(epsilon)-H of His64 is oriented toward the CO, and the N(delta) is on the surface of the protein. The MD simulations show that dynamics of His64 represent the major source of vibrational dephasing of the CO ligand in the A(3) state on both femtosecond and picosecond time scales. Dephasing in the A(1) state is controlled by His64 on femtosecond time scales, and by the rest of the protein and the water solvent on longer time scales.     

Deoxy-nitrosugars 12th communication Synthesis of isosteric mono-phosphonate analogues of β-and α-D-fructose 2,6-bisphosphate

A synthesis of the isosteric mono-phosphonate analogues 2a and 19 of the β-and α-D -fructose 2,6-bisphosphate, respectively, is described. Chain elongation of the 1-deoxy-1-nitro-D -arabinose 3 (Scheme 1) by a Henry reaction with paraformaldehyde followed by protection of the resulting alcohol (methoxymethyl ether) and a radical-chain substitution by nitromethane anion gave the key intermediates, the gluco-anhydroalditol 6 and the manno-anhydroalditol 7 . These products equilibrated under basic conditions. Conversion of 7 to the aldehyde 9 , Abramov reaction of 9 with diphenyl phosphite followed by deoxygenation according to Barton gave the phosphonate 11 (Scheme 2). Selective hydrogenolysis of 11 , phosphorylation and deprotection gave 2 which was converted to the tetrasodium salt 2a . Similarly, 6 was transformed into the isosteric phosphonate analogue 19 of the α-D -fructose 2,6-bisphosphate (Scheme 3).     

Uranium-sulfilimine chemistry. The preparation of Cp2*UCl2(HNSPh2) and its hydrolysis with HNSPh2 · H2O

The reaction of Cp₂*UCl₂ with HNSPh₂ produces Cp₂*UCl₂(HNSPh₂), which is the first structurally characterized complex of a sulfilimine. The hydrolysis of Cp₂*UCl₂(HNSPh₂) with HNSPh₂ · H₂O yields a tetrauranium cluster whose heavy atom structure has been determined by x-ray diffraction and which is formulated as a U^IV/U^V complex: [Cp*(Cl)(HNSPh₂)U(μ₃-O)(μ₂-O)₂U(Cl)(HNSPh₂)₂]₂.     

Fragmentation of Homoallylic Alkoxides. Preparation of 1-(3′-cyclopentenyl)-2-alkanones from 2-substituted bicyclo[2.2.1]hept-5-en-2-ols

The potassium 2-substituted bicyclo[2.2.1]hept-5-en-2-alkoxides derived from alcohols 2–9 at 30° in hexamethylphosphoric triamide (HMPA) afford 1-(3′-cyclopentenyl)-2-alkanones 10–19 via heterolytic C(1), C(2)-allylic bond cleavage in the substrate alkoxide followed by intramolecular protonation of the resultant transient allylic anion.     

Synthesis of functionalized rab GTPases by a combination of solution- or solid-phase lipopeptide synthesis with expressed protein ligation

Prenylated proteins with non-native functionalities are generally very difficult to obtain by recombinant or enzymatic means. The semisynthesis of preparative amounts of prenylated Rab guanosine triphosphatases (GTPases) from recombinant proteins and synthetic prenylated peptides depends largely on the availability of functionalised prenylated peptides corresponding to the proteins' native structure or modifications thereof. Here, we describe and compare solution-phase and solid-phase strategies for the generation of peptides corresponding to the prenylated C terminus of Rab7 GTPase. The solid-phase with utilisation of a hydrazide linker emerges as the more favourable approach. It allows a fast and practical synthesis of pure peptides and gives a high degree of flexibility in their modification. To facilitate the analysis of semisynthetic proteins, the synthesised peptides were equipped with a fluorescent group. Using the described approach, we introduced fluorophores at several different positions of the Rab7 C terminus. The position of the incorporated fluorescent groups in the peptides did not influence the protein-ligation reaction, as the generated peptides could be ligated onto thioester-tagged Rab7. However, it was found that the positioning of the fluorescent group had an influence on the functionality of the Rab7 proteins; analysis of the interaction of the semisynthetic Rab7 proteins with REP (Rab escort protein) and GDI (guanosine diphosphate dissociation inhibitor) molecules revealed that modification of the peptide side chains or of the C-terminal isoprenoid did not significantly interfere with complex formation. However, functionalisation of the C terminus was found to have an adverse effect on complex formation and stability, possibly reflecting low structural flexibility of the Rab GDI/REP molecules in the vicinity of the lipid-binding site.     

Luminol Oxidation by Hydrogen Peroxide Catalyzed by Tobacco Anionic Peroxidase: Steady-State Luminescent and Transient Kinetic Studies

The properties of a newly isolated anionic tobacco peroxidase from transgenic tobacco plants overexpressing the enzyme have been studied with respect to the chemiluminescent reaction of luminol oxidation. These were compared to the properties of horseradish peroxidase in the cooxidation of luminol and p -iodophenol, the enhanced chemiluminescence reaction. The pH, luminol and hydrogen peroxide concentrations were optimized for maximum sensitivity using the tobacco enzyme. The detection limit for the latter under the optimal conditions (2.5 m M luminol, 2 m M hydrogen peroxide, 100 m M Naborate buffer, pH 9.3) was about 0.1 p M , which is at least five times lower than that for horseradish peroxidase in enhanced chemiluminescence with p -iodophenol. The rate constants for the elementary steps of the enzyme-catalyzed reaction have been determined: k ₁= 4.9 × 10⁶ M ⁻¹ s¹, k ₂= 7.3 × 10⁶ M ⁻¹ s⁻¹, k ³= 2.1 × 10⁶ M ⁻¹ s⁻¹ (pH 9.3). The similarity of these rate constants is unusual for plant peroxidases. The high catalytic activity of tobacco peroxidase in the luminescent reaction is explained by the high reactivity of its Compound II toward luminol and the high stability of the holoenzyme with respect to heme dissociation. This seems to be a unique property of this particular enzyme among other plant peroxidases.     

A novel one-pot method for the preparation of pyrazoles by 1,3-dipolar cycloadditions of diazo compounds generated in situ

A convenient one-pot procedure for the preparation of pyrazoles by 1,3-dipolar cycloaddition of diazo compounds generated in situ has been developed. Diazo compounds derived from aldehydes were reacted with terminal alkynes to furnish regioselectively 3,5-disubstituted pyrazoles. Furthermore, the reaction of N-vinylimidazole and diazo compounds derived from aldehydes gave exclusively 3-substituted pyrazoles in a one-pot process.     

Sizes and interfacial free energies of crystallites formed from fractionated linear polyethylene

Replicas of fracture surfaces of fractions of linear polyethylene, which were crystallized at elevated temperatures for extended time periods, were examined by electron microscopy. Striated. lamella-type crystallites were observed for all molecular weights over the range 3.2 × 10³?5.7 × 10⁵. In agreement with Anderson's previous report, for molecular weights of 12,000 or less, the crystallite thicknesses were comparable to the extended chain length. As the molecular weight increased above this level, however, the crystallite sizes increased only slightly and hence at high molecular weights were very much smaller than the extended chain length. From the measured melting temperatures, crystallite interfacial free energies were calculated from the theory for the melting of finite size crystals comprised of chains of finite length. The crystallite interfacial free energy was found to increase with molecular weight. Based on these results, a crystallization process is outlined which allows for the formation of either extended chain crystallites, or crystallites whose size is much smaller than the extended chain length without any change in nucleation mechanism or arbitrary adjustment in growth mechanism with molecular weight.     

Optimized separation of scopoletin and umbelliferone and cis-trans isomers of ferulic and p-coumaric acids by reverse-phase high-performance liquid chromatography

A systematic optimization strategy for reverse-phase h.p.l.c. is used to produce complete separation of all components of a mixture containing two coumarins, umbelliferone and scopoletin, and the cis-trans isomers of two cinnamic acids, p-coumaric and ferulic. A series of experiments gives retention time data for each of these substances in four citric acid-buffered mobile phases. A mathematical model fitted to this data gives model parameters that provide the basis for a window diagram of relative retentions vs. mobile phase pH. The window diagram gives an estimate of the mobile phase pH required for optimum separation.     

The Raman active internal vibrational modes of potassium nitrate

The Raman active internal vibrational modes of single crystal orthorhombic potassium nitrate have been studied in various polarizations. The full multiplet structure predicted by factor group analysis for the v₂ and v₃ regions has been observed for the first time. The expected site group splitting of the v₄ mode was not observed and can be assumed to be less than 0.5 cm^?1.