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Lars Packschies

Publications and source records attributed to Lars Packschies.

2 recordsLinked to original sources

Sigma-pi energy separation in homodesmotic reactions.

A well-established quantity for specifying the aromaticity or antiaromaticity of cyclic conjugated molecules is the so-called aromatic stabilization energy (ASE), which can be derived-either experimentally or theoretically-from appropriate homodesmotic reactions. To gain further insight into the origin of aromaticity, several schemes have been devised to partition ASE into nuclear and electronic as well as sigma and pi contributions, some of which have resulted in contradictory statements about the driving force of aromatic stabilization. Currently, these contradictions have not been resolved and have resulted in a confusing distinction between two different types of aromaticity: extrinsic and intrinsic aromaticity. By investigating different homodesmotic reactions we show that, in contrast to ASE itself, the individual contributions that enter the ASE can strongly depend on the type of reaction. Caution is therefore advised if conclusions or physical interpretations are derived from the individual components. The contradictions result from the fact that some reactions suffer from an imbalance in the number of interaction terms at the two sides of the reaction equation. The concept of isointeractional reactions is introduced and results in the elimination of the imbalance. For these reactions, the contradictions disappear and the distinction between intrinsic and extrinsic aromaticity becomes unnecessary. As far as the sigma-pi partitioning is concerned, several schemes proposed in the literature are compared. Contradictory results are obtained depending on the partitioning scheme and reaction used. In this context, it is demonstrated that for the partitioning of the electron-electron interaction, the scheme introduced by Jug and Köster is the one that is most theoretically grounded.

Journal Article↗

Structural dynamics of the DnaK-peptide complex.

The molecular chaperone DnaK recognizes and binds substrate proteins via a stretch of seven amino acid residues that is usually only exposed in unfolded proteins. The binding kinetics are regulated by the nucleotide state of DnaK, which alternates between DnaK.ATP (fast exchange) and DnaK.ADP (slow exchange). These two forms cycle with a rate mainly determined by the ATPase activity of DnaK and nucleotide exchange. The different substrate binding properties of DnaK are mainly attributed to changes of the position and mobility of a helical region in the C-terminal peptide-binding domain, the so-called LID. It closes the peptide-binding pocket and thus makes peptide binding less dynamic in the ADP-bound state, but does not (strongly) interact with peptides directly. Here, we address the question if nucleotide-dependent structural changes may be observed in the peptide-binding region that could also be connected to peptide binding kinetics and more importantly could induce structural changes in peptide stretches using the energy available from ATP hydrolysis. Model peptides containing two cysteine residues at varying positions were derived from the structurally well-documented peptide NRLLLTG and labelled with electron spin sensitive probes. Measurements of distances and mobilities of these spin labels by electron paramagnetic resonance spectroscopy (EPR) of free peptides or peptides bound to the ATP and ADP-state of DnaK, respectively, showed no significant changes of mobility nor distance of the two labels. This indicates that no structural changes that could be sensed by the probes at the position of central leucine residues located in the center of the binding region occur due to different nucleotide states. We conclude from these studies that the ATPase activity of DnaK is not connected to structural changes of the peptide-binding pocket but rather only has an effect on the LID domain or other further remote residues.

Adenosine Triphosphate↗