Effects of Multiple-Bond Ruptures in Force Spectroscopy Measurements of Interactions between Fullerene C_(60) Molecules in Water

Interactions between fullerene C_(60) molecules in water were measured by force spectroscopy. Fullerene molecules were covalently connected to bifunctional water-soluble poly(ethylene glycol) (PEG) linkers and subsequently tethered to the substrate and to the tip of the atomic force microscope to facilitate single molecule detection and avoid spurious surface effects. The distributions of rupture forces for substrates prepared with different incubation times of C_(60)-PEG-NH_2 exhibit high rupture forces that cannot be explained by the theoretical distribution of single molecule binding. Moreover, the relative amplitude of the high force peak in the histogram increases with incubation time. These observations are explained by attributing the measured high forces to the rupture of multiple bonds between fullerene molecules. Force spectroscopy data analysis based on the most probable forces gives significantly different dissociation rates for samples that exhibit different amplitudes of the high force peak. An approximate analytical model that considers ruptures of two bonds that are simultaneously loaded by tethers with different lengths is proposed. This model successfully fits the distributions of the rupture forces using the same set of kinetic parameters for samples prepared with different grafting densities. It is proposed that this model can be used as a common tool to analyze the probability distributions of rupture forces that contain peaks or shoulders on the high force side of the distribution

Effects of multiple-bond ruptures on kinetic parameters extracted from force spectroscopy measurements: Revisiting biotin-streptavidin interactions

Force spectroscopy measurements of the rupture of the molecular bond between biotin and streptavidin often results in a wide distribution of rupture forces. We attribute the long tail of high rupture forces to the nearly simultaneous rupture of more than one molecular bond. To decrease the number of possible bonds, we employed hydrophilic polymeric tethers to attach biotin molecules to the atomic force microscope probe. It is shown that the measured distributions of rupture forces still contain high forces that cannot be described by the forced dissociation from a deep potential well. We employed a recently developed analytical model of simultaneous rupture of two bonds connected by polymer tethers with uneven length to fit the measured distributions. The resulting kinetic parameters agree with the energy landscape predicted by molecular dynamics simulations. It is demonstrated that when more than one molecular bond might rupture during the pulling measurements there is a noise-limited range of probe velocities where the kinetic parameters measured by force spectroscopy correspond to the true energy landscape. Outside this range of velocities, the kinetic parameters extracted by using the standard most probable force approach might be interpreted as artificial energy barriers that are not present in the actual energy landscape. Factors that affect the range of useful velocities are discussed

A 3D structure database of components from Chinese traditional medicinal herbs

This article described a 3D structure database of components extracted from Chinese Traditional Medicinal (CTM) herbs. It offers not only basic molecular properties and optimized 3D structure of the compounds but also detailed information on their herbal origin, including basic herbal category (e.g. English name, Latin name, and family), effective parts, and clinical effects. An easy to use, interactive GUI browser allows users to perform various searches via complex logical query builder. Combined with the latest network database engine (MySQL), it can achieve excellent performance under both a local network and an Internet environment. We have tested it on the design of inhibitors of NS3-NS4A protease. Results show that the structure database of components extracted from Chinese medicinal herbs can be a rich source in searching the lead compound