Alcohol reduces muscle fatigue through atomistic interactions with nicotinic receptors.

Alcohol consumption affects many organs and tissues, including skeletal muscle. However, the molecular mechanism of ethanol action on skeletal muscle remains unclear. Here, using molecular dynamics simulations and single channel recordings, we show that ethanol interacts with a negatively charged amino acid within an extracellular region of the neuromuscular nicotinic acetylcholine receptor (nAChR), thereby altering its global conformation and reducing the single channel current amplitude. Charge reversal of the negatively charged amino acid abolishes the nAChR-ethanol interaction. Moreover, using transgenic animals harboring the charge-reversal mutation, ex vivo measurements of muscle force production show that ethanol counters fatigue in wild type but not homozygous αE83K mutant animals. In accord, in vivo studies of motor coordination following ethanol administration reveal an approximately twofold improvement for wild type compared to homozygous mutant animals. Together, the converging results from molecular to animal studies suggest that ethanol counters muscle fatigue through its interaction with neuromuscular nAChRs.

Accelerated Molecular Dynamics Study of the Effects of Surface Hydrophilicity on Protein Adsorption.

The adsorption of streptavidin is studied on two surfaces, graphite and titanium dioxide, using accelerated molecular dynamics. Adsorption on graphite leads to strong conformational changes while the protein spreads out over the surface. Interestingly, also adsorption on the highly hydrophilic rutile surface induces considerable spreading of the protein. We pin down the cause for this unfolding to the interaction of the protein with the ordered water layers above the rutile surface. For special orientations, the protein penetrates the ordered water layers and comes into direct contact with the surface where the positively charged amino acids settle in places adjacent to the negatively charged top surface atom layer of rutile. We conclude that for both surface materials studied, streptavidin changes its conformation so strongly that it loses its potential for binding biotin. Our results are in good qualitative agreement with available experimental studies.

Forced Desorption of Bovine Serum Albumin and Lysozyme from Graphite: Insights from Molecular Dynamics Simulation.

We use molecular dynamics (MD) simulation to study the adsorption and desorption of two widely different proteins, bovine serum albumin (BSA) and lysozyme, on a graphite surface. The adsorption is modeled using accelerated MD to allow the proteins to find optimum conformations on the surface. Our results demonstrate that the "hard protein" lysozyme retains much of its secondary structure during adsorption, whereas BSA loses it almost completely. BSA has a considerably larger adsorption energy compared to that of lysozyme, which does not scale with chain length. Desorption simulations are carried out using classical steered MD. The BSA molecule becomes fully unzipped during pull-off, whereas several helices survive this process in lysozyme. The unzipping process shows up in the force-distance curve of BSA as a series of peaks, whereas only a single or few, depending on protein orientation, force peaks occur for lysozyme. The maximum desorption force is larger for BSA than for lysozyme, but only by a factor of about 2.3.

Accelerating Steered Molecular Dynamics: Toward Smaller Velocities in Forced Unfolding Simulations.

The simulation of forced unfolding experiments, in which proteins are pulled apart, is conventionally done using steered molecular dynamics. We present here a hybrid scheme in which accelerated molecular dynamics is used together with steered molecular dynamics. We show that the new scheme changes the force-distance curves mainly in the region around the force maximum and thus demonstrate that the improved equilibration of the protein-solvent system brought about by using accelerated molecular dynamics makes the simulation more comparable to experimental data.

A structural feature of the non-peptide ligand interactions with mice mu-opioid receptors.

By binding to and activating the G-protein coupled µ-, κ- and δ-opioid receptors in the central nervous system, opiates are known to induce analgesic and sedative effects. In particular, non-peptide opioid ligands are often used in clinical applications to induce these therapeutically beneficial effects, due to their superior pharmacokinetics and bioavailability in comparison to endogenous neuropeptides. However, since opioid alkaloids are highly addictive substances, it is necessary to understand the exact mechanisms of their actions, specifically the ligand-binding properties of the target receptors, in order to safely apply opiates for therapeutic purposes. Using an in silico molecular docking approach (AutoDock Vina) combined with two-step cluster analysis, we have computationally obtained the docking scores and the ligand-binding pockets of twelve representative non-peptide nonendogenous agonists and antagonists at the crystallographically identified µ-opioid receptor. Our study predicts the existence of two main binding sites that are congruently present in all opioid receptor types. Interestingly, in terms of the agonist or antagonist properties of the substances on the receptors, the clustering analysis suggests a relationship with the position of the ligand-binding pockets, particularly its depth within the receptor structure. Furthermore, the binding affinity of the substances is directly correlated to the proximity of the binding pockets to the extracellular space. In conclusion, the results provide further insights into the structural features of the functional pharmacology of opioid receptors, suggesting the importance of the binding position of non-peptide agonists and antagonists- specifically the distance and the level of exposure to the extracellular space- to their dissociation kinetics and subsequent potency.

Enhancing protein adsorption simulations by using accelerated molecular dynamics.

The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s) and experiment (up to hours), and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface.

The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.