Bsoft: Image Processing for Structural Biology.

Bsoft is a software package primarily developed for processing electron micrographs, with the goal of determining the structures of biologically relevant molecules, molecular assemblies, and parts of cells. However, it incorporates many ways to deal with images, from the mundane to very sophisticated algorithms. This article is an introduction into its use, illustrating that it is an extensive toolbox, for manipulating and understanding images.

Dietary influence on urinary excretion of 3-deoxyglucosone and its metabolite 3-deoxyfructose.

3-Deoxyglucosone (3-DG), a reactive 1,2-dicarbonyl compound derived from d-glucose in food and in vivo, is an important precursor for advanced glycation endproducts (AGEs). At present, virtually no information about the metabolic transit of dietary 3-DG is available. One possible metabolic pathway of 3-DG during digestion is enzymatic transformation to less reactive compounds such as 3-deoxyfructose (3-DF).

Molecular dynamics force probe simulations of antibody/antigen unbinding: entropic control and nonadditivity of unbinding forces.

Unbinding of a spin-labeled dinitrophenyl (DNP) hapten from the monoclonal antibody AN02 F(ab) fragment has been studied by force probe molecular dynamics (FPMD) simulations. In our nanosecond simulations, unbinding was enforced by pulling the hapten molecule out of the binding pocket. Detailed inspection of the FPMD trajectories revealed a large heterogeneity of enforced unbinding pathways and a correspondingly large flexibility of the binding pocket region, which exhibited induced fit motions.

Dynamic force spectroscopy of molecular adhesion bonds.

Recent advances in atomic force microscopy, biomembrane force probe experiments, and optical tweezers allow one to measure the response of single molecules to mechanical stress with high precision. Such experiments, due to limited spatial resolution, typically access only one single force value in a continuous force profile that characterizes the molecular response along a reaction coordinate. We develop a theory that allows one to reconstruct force profiles from force spectra obtained from measurements at varying loading rates, without requiring increased resolution.