Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

The Total Synthesis of (±)-Isocomene by an Intramolecular Ene Reaction. Preliminary communication

The racemic sesquiterpene isocomene ( 1 ) has been synthesized starting from 1,7-octadien-3-one ( 2 ) in a stereoselective manner (Scheme 2). In the key step 4 → 5 the C(7), C(8)-bond was formed by an intramolecular thermal ene reaction. Further elaboration of 5 involved the ring contraction 6 → 7 , the elimination 8 → 9 and the final olefin isomerization 9 → 1 .     

Perturbations in thenp 1,3 P Rydberg sequences of neutralYb probed by Zeeman-effect and lifetime measurements

Thenp P Rydberg sequence of neutral Ytterbium is strongly perturbed. These perturbations were monitored by measuring theg _J factors and lifetimes of 19 states, including both singlets and triplets as well as states from the perturbing configurations. A pulsed laser setup was used. Theg _J factors were obtained from a Zeeman quantum-beat experiment and the lifetimes by direct observation of the decay of the fluorescence light.     

Theoretical and experimental studies of radiative lifetimes of excited electronic states in CO

The electronic dipole transition moment functions of the A ²Π-X ²Σ⁺, B ²Σ⁺-X ²Σ⁺ and B ²Σ⁺-A ²Π transitions and the dipole moment function of the X ²Σ⁺ state of CO⁺ have been calculated using large contracted CI wavefunctions. The computed transition moment functions together with experimental potential energy curves were used to obtain radiative lifetimes of the excited electronic states B ²Σ⁺ and A ²Π. Radiative lifetimes of vibrational levels of the X ²Σ⁺ state were derived from the calculated dipole moment function. The high-frequency deflection technique was used to obtain radiative lifetimes of the ν′ = 0, 1,2 and 3 vibrational levels of the B ²Σ⁺ state and also radiative lifetimes of individual rotational levels of ν′ =0. The calculated radiative lifetimes are shorter than the measured ones by about 10%. The experimental ν′ dependence is reproduced by theoretical calculation. The calculated radiative lifetimes for the A ²Π state are in excellent agreement with lifetimes measured with an ion trap technique.     

AQUEOUS AGGREGATES OF BACTERIOCHLOROPHYLL c AS A MODEL FOR PIGMENT ORGANIZATION IN CHLOROSOMES

Chlorosomes isolated from Chloroflexus aurantiacus were extracted with chloroform/methanol. The extract contained bacteriochlorophylls c and a and lipids, but was devoid of proteins. This crude extract spontaneously formed aggregates when a methanol solution was dispersed in aqueous buffer. The aggregates could be sedimented by ultracentrifugation and appeared in electron micrographs as stain-excluding bodies with diameters between 70 and 170 nm. The absorption spectrum is remarkably similar to that of intact chlorosomes with an absorption maximum of bacteriochlorophyll c at around 740 nm. The circular dichroism spectrum of the aggregate is also very similar to that of intact chlorosomes. A conservative (±) band centered at 740 nm confirms the highly aggregated state of bacteriochlorophyll c in both systems. Steady-state fluorescence studies showed that in the aggregate energy-transfer from bacteriochlorophyll c to a component emitting at 830 nm took place. When the aggregate was suspended in buffer saturated with 1-hexanol the 740 nm form of bacteriochlorophyll c was reversibly converted to a form with spectral properties resembling the monomer absorbing at 670 nm but still in an aggregated state. This form of bacteriochlorophyll c showed no circular dichroism signal.     

Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and N-methylacetamide

Dimethyl disulfide (DMDS) and N-methylacetamide are two first choice model systems that represent the disulfide bridge bonding and the peptide bonding in proteins. These molecules are therefore suitable for investigation of the mechanisms involved when proteins fragment under electron capture dissociation (ECD). The dissociative recombination cross sections for both protonated DMDS and protonated N-methylacetamide were determined at electron energies ranging from 0.001 to 0.3 eV. Also, the branching ratios at 0 eV center-of-mass collision energy were determined. The present results give support for the indirect mechanism of ECD, where free hydrogen atoms produced in the initial fragmentation step induce further decomposition. We suggest that both indirect and direct dissociations play a role in ECD.     

Determination of radiative lifetimes in neutral nitrogen using short laser pulses from a distributed feedback dye laser

Radiative lifetimes were determined for two short-lived states in neutral nitrogen. Following photo-dissociation and two-photon excitation employing the same UV source, excitation to higher states was performed with a distributed feedback dye laser (DFDL). The lifetimes were found to be τ(2p ²4d ⁴ D _7/2)=17(3) ns and τ(2p ²5s ⁴ P _5/2)=22(3) ns.     

Superporous agarose beads as a hydrophobic interaction chromatography support

Superporous agarose beads were used as a support for hydrophobic interaction chromatography. These beads have large connecting flow pores in addition to their normal diffusion pores. The flow pores, which are approximately one fifth of the overall diameter of the superporous agarose beads, were earlier shown to give the beads improved mass transfer properties relative to homogeneous agarose beads (Gustavsson and Larsson, J. Chromatogr. A, 734 (1996) 231–240). Superporous agarose beads and homogeneous agarose beads of the same particle size range (106–180 μm) were derivatized with phenyl groups. The properties of the superporous beads were then compared with the homogeneous beads in the separation of a mixture of three model proteins (ribonuclease A, lysozyme and bovine serum albumin) at various superficial flow velocities from 30 to 600 cm/h. The superporous beads gave satisfactory separation at flow velocities five times higher than was possible for homogeneous beads. The performance of the two types of beads was also compared in the purification of lactate dehydrogenase from a beef heart extract at a superficial flow velocity of 150 cm/h. The superporous beads performed considerably better, leading to twice the purification factor and twice the concentration of the desired product. The results were interpreted using the theoretical treatment given by Carta and Rodrigues (Carta and Rodrigues, Chem. Eng. Sci., 48 (1993) 3927).     

Shake-up and multiplet structure of ESCA satellites of Cu compounds

The ESCA inner shell spectra of Cu compounds are investigated theoretically. It is shown that the large satellites appearing for Cu(II) compounds correspond to shake-up states which are close to the configuration p⁵d⁹ and have the characteristic multiplet splitting of this configuration.