A Binding Ensemble PROfiling with (F)photoaffinity Labeling (BEProFL) approach that utilizes photolabeling of HDAC8 with a probe containing a UV-activated aromatic azide, mapping the covalent modifications by liquid chromatography-tandem mass-spectrometry, and a computational method to characterize the multiple binding poses of the probe is described. Using the BEProFL approach two distinct binding poses of the HDAC8 probe were identified. The data also suggest that an “upside-down” pose with the surface binding group of the probe bound in an alternative pocket near the catalytic site may contribute to the binding.
The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.
The accuracy of molecular dynamics (MD) simulations is limited by the availability of parameters for the molecular system of interest. In most force fields parameters of common chemical groups are already present. With the development of novel small organic molecules as probes to study biological system more chemical groups require parameterization. An azide group is often used in studies of biological systems yet computational studies are impeded by the lack of parameters. In this paper we present a set of molecular mechanics (MM) parameters for aromatic and aliphatic azido groups and their application in MD simulations of a photoaffinity probe currently used in our laboratory for mapping the binding modes available in the active site of histone deacetylases. The parameters were developed for the Generalized Amber Force Field (GAFF) using density functional theory calculations (DFT) at B3LYP 6-311G(d) level. The parameters were validated by geometry optimization and MD simulations.
Identifying and naming inorganic
compounds is sometimes a challenge
for many first-year chemistry and engineering students; however, these
difficulties can be overcome after extensive practice using homework
sets based on naming inorganic compounds or applying inorganic nomenclature
rules. Werner is a card game in honor of Professor Alfred Werner for
his great contributions to inorganic chemistry and is intended as
a didactic tool for reinforcing the learning of inorganic chemistry
nomenclature. By playing the game, students practice and apply inorganic
nomenclature rules. During the game, they get to identify compounds
such as acids, bases, and salts as well as practice the systematic
rules of the new chemical elements’ symbols and names. In the
classroom, the game was used immediately after explaining the basic
nomenclature rules. Overall, the students found the game engaging
and enjoyable, and they responded favorably to its use as an educational
didactic tool.
Membrane mechanical elastic properties regulate a variety of cellular processes involving local membrane deformation, such as ion channel function and vesicle fusion. In this work, we used molecular dynamics simulations to estimate the local elastic properties of a membrane. For this, we calculated the energy needed to extract a DOPE lipid molecule, modified with a linker chain, from a POPC bilayer membrane using the umbrella sampling technique. Although the extraction energy entails several contributions related not only to elastic deformation but also to solvation, careful analysis of the potential of mean force (PMF) allowed us to dissect the elastic contribution. With this information, we calculated an effective linear spring constant of 44 ± 4 kJ·nm(-2)·mol(-1) for the DOPC membrane, in agreement with experimental estimates. The membrane deformation profile was determined independently during the stretching process in molecular detail, allowing us to fit this profile to a previously proposed continuum elastic model. Through this approach, we calculated an effective membrane spring constant of 42 kJ·nm(-2)·mol(-1), which is in good agreement with the PMF calculation. Furthermore, the solvation energy we derived from the data is shown to match the solvation energy estimated from critical micelle formation constants. This methodology can be used to determine how changes in lipid composition or the presence of membrane modifiers can affect the elastic properties of a membrane at a local level.
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