Production of lantipeptides in Escherichia coli

Lantipeptides are ribosomally synthesized and posttranslationally modified peptides containing thioether cross-links. We describe the preparation of seven different lantipeptides in Escherichia coli and demonstrate that this methodology can be used to incorporate nonproteinogenic amino acids.     

Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces

The modulation of the properties of lipid membranes by polyhydroxylated cosolutes such as sugars is a phenomenon of considerable biological, technological and medicinal relevance. A few years ago, we proposed the sugar-like mechanism--binding driven by the release of water molecules--as an attempt to rationalize the preferential affinity of carbohydrate molecules compared to water molecules for the surface of lipid bilayers, which is presumably related to the bioprotective action of these compounds. The goal herein is to gain a better understanding of the driving force underlying this mechanism, in terms of specific interactions or effects, as well as in terms of the energy-entropy partitioning. This is done in the simplest possible context of an apolar rigid-wall model representing the membrane, and mixtures of closely related and possibly artificial species in solution, namely monomers or dimers of Lennard-Jones particles, water with physical or reduced charges, and hydroxymethyl groups. The results indicate that although the sugar-like mechanism seems phenomenologically reasonable, the main driving force underlying this mechanism is not the entropy gain upon releasing water molecules into the bulk, as originally suggested, but rather the hydrophobic effect. Note that the latter effect is a generic concept and may in principle involve both a solvent release and an interaction component, depending on the solute considered.     

Theory of a proton spin maser with two emission coils

A nuclear maser oscillator with two emission coils, coupled solely by a stream of a prepolarized liquid which is initially at negative spin temperature, is investigated theoretically. The second emission coil is assumed to be tuned by a condenser to the proton spin resonance, while the first emission coil can be detuned. If the spin-spin interaction time is sufficiently long, then the voltage amplitude available from the terminals of the second coil can go through two maxima as the first coil is detuned. For maximum detuning of the first coil, a self-modulation effect can arise in the second resonance circuit.     

Ring inversion process for a series of 3,5‐dialkyl‐1‐oxa‐3,5‐diazacyclohexanes: 1H DNMR study and semiempirical calculations

The ring inversion process for a series of 3,5‐dialkyl‐1‐oxa‐3,5‐diazacyclohexanes was studied using proton dynamic nuclear magnetic resonance (¹H DNMR) spectroscopy in conjunction with semiempirical calculations. At low temperature, the ring methylene protons decoalesced into two AB spin systems in a 2:1 ratio. Lineshape simulations of the DNMR spectra provided first‐order rate constants for magnetic exchange. The energy barrier for each inversion reaction was calculated from the respective rate constants. In general, as the size of the N‐alkyl group increased, the barrier to ring inversion decreased. A similar trend was seen in semiempirical calculations that modeled the ring inversion process. Copyright © 2010 John Wiley & Sons, Ltd.     

Sampling of rare events using hidden restraints

A method to enhance sampling of rare events is presented. It makes use of distance or dihedral-angle restraints to overcome an energy barrier separating two metastable states or to stabilize a transition state between the two metastable states. In order not to perturb these metastable end states themselves, a prefactor is introduced into the restraining energy function, which smoothly increases the weight of this function from zero to one at the transition state or on top of the separating energy barrier and then decreases the weight again to zero at the final state. The method is combined with multi-configurational thermodynamic integration and applied to two biomolecular systems, which were difficult to treat using standard thermodynamic integration. As first example the free energy difference of a cyclic alpha-aminoxy-hexapeptide-ion complex upon changing the ion from Cl- to Na+ was calculated. A large conformational rearrangement of the peptide was necessary to accommodate this change. Stabilizing the transition state by (hidden) restraints facilitates that. As a second example, the free energy difference between the 4C1 and the 1C4 conformation of beta-D-glucopyranoside was calculated. In unrestrained simulations the change from the 4C1 into the 1C4 conformation was never observed because of the high energy barrier separating the two states. Using (hidden) restraints, the transition from the 4C1 into the 1C4 state and back could be enforced without perturbing the end states. As comparison, for the same transitions the potential of mean force as obtained by using dihedral-angle constraints is provided.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.