A fluorescence polarization assay for the experimental validation of an in silico model of the chemokine CXCL8 binding to receptor-derived peptides.

Peptide based inhibitors of protein-protein interactions are of great interest in proteomics, structural biology and medicinal chemistry. Optimized inhibitors can be designed by experimental approaches or by computational prediction. Ideally, computational models are adjusted to the peptide-protein complex of interest according to experimental data obtained in specific binding experiments. The chemokine CXCL8 (interleukin-8) is an interesting target for drug discovery due to its role in inflammatory diseases. Given the available structural data and information on its receptor interactions it constitutes a basis for the rational design of inhibitor peptides. Starting from the reported structure of CXCL8 in complex with a peptide derived from its receptor CXCR1 we developed a computational docking procedure to estimate the changes in binding energy as a function of individual amino acid exchanges. This indicates whether the respective amino acid residue must be preserved or can be substituted to maintain or improve affinity, respectively. To validate and improve the assumptions made in this docking simulation we established a fluorescence polarization assay for receptor-derived peptides binding to CXCL8. A peptide library was tested comprising selected mutants characterized by docking simulations. A number of predictions regarding electrostatic interactions were confirmed by these experiments and it was revealed that the model needed to be corrected for backbone flexibility. Therefore, the assay presented here is a promising tool to systematically improve the computational model by iterative cycles of modeling, experimental validation and refinement of the algorithm, leading to a more reliable model and peptides with improved affinity.

Controlling doping efficiency in organic semiconductors by tuning short-range overscreening.

Conductivity doping has emerged as an indispensable method to overcome the inherently low conductivity of amorphous organic semiconductors, which presents a great challenge in organic electronics applications. While tuning ionization potential and electron affinity of dopant and matrix is a common approach to control the doping efficiency, many other effects also play an important role. Here, we show that the quadrupole moment of the dopant anion in conjunction with the mutual near-field host-dopant orientation have a crucial impact on the conductivity. In particular, a large positive quadrupole moment of a dopant leads to an overscreening in host-dopant integer charge transfer complexes. Exploitation of this effect may enhance the conductivity by several orders of magnitude. This finding paves the way to a computer-aided systematic and efficient design of highly conducting amorphous small molecule doped organic semiconductors.

Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo.

Gas vesicles are gas-filled protein structures increasing the buoyancy of cells. The gas vesicle envelope is mainly constituted by the 8 kDa protein GvpA forming a wall with a water excluding inner surface. A structure of GvpA is not available; recent solid-state NMR results suggest a coil-α-ß-ß-α-coil fold. We obtained a first structural model of GvpA by high-performance de novo modelling. Attenuated total reflection (ATR)-Fourier transform infrared spectroscopy (FTIR) supported this structure. A dimer of GvpA was derived that could explain the formation of the protein monolayer in the gas vesicle wall. The hydrophobic inner surface is mainly constituted by anti-parallel ß-strands. The proposed structure allows the pinpointing of contact sites that were mutated and tested for the ability to form gas vesicles in haloarchaea. Mutations in α-helix I and α-helix II, but also in the ß-turn affected the gas vesicle formation, whereas other alterations had no effect. All mutants supported the structural features deduced from the model. The proposed GvpA dimers allow the formation of a monolayer protein wall, also consistent with protease treatments of isolated gas vesicles.

Thulium laser (Revolix) vapoenucleation of the prostate is a safe procedure in patients with an increased risk of hemorrhage.

PURPOSE: To evaluate the feasibility and safety of thulium:yttrium-aluminium-garnet laser vapoenucleation of the prostate (ThuVEP) in patients with chronic anticoagulation and bleeding disorders. METHODS: We retrospectively analyzed the clinical data (transfusion rate, hemoglobin changes, residual urine, bleeding complications, complications and residual urine) of patients with chronic anticoagulation and bleeding disorders treated with ThuVEP. Anticoagulation was not paused for surgery. RESULTS: We identified 39 patients who fulfilled the inclusion criteria (32 with chronic anticoagulation, 3 with bleeding disorder, and 4 with both). Mean preoperative hemoglobin was 12.9 g/l; the postoperative hemoglobin was 11.7 g/l. One patient received a blood transfusion. Mean residual urine was 166 ml preoperatively and 47 ml postoperatively, respectively; spontaneous voiding postoperatively was feasible in 36 patients. During follow-up, 5 patients suffered from gross hematuria, which was treated conservatively. CONCLUSIONS: ThuVEP is a safe procedure in patients with therapeutic anticoagulation, bleeding disorders and platelet aggregation inhibitor medication.

Selective dispersion of single-walled carbon nanotubes with specific chiral indices by poly(N-decyl-2,7-carbazole).

Physico-chemical methods to sort single-walled carbon nanotubes (SWNTs) by chiral index are presently lacking but are required for in-depth experimental analysis and also for potential future applications of specific species. Here we report the unexpected selectivity of poly(N-decyl-2,7-carbazole) to almost exclusively disperse semiconducting SWNTs with differences of their chiral indices (n - m) ≥ 2 in toluene. The observed selectivity complements perfectly the dispersing features of the fluorene analogue poly(9,9-dialkyl-2,7-fluorene), which disperses semiconducting SWNTs with (n - m) ≤ 2 in toluene. The dispersed samples are further purified by density gradient centrifugation and analyzed by photoluminescence excitation spectroscopy. All-atom molecular modeling with decamer model compounds of the polymers and (10,2) and (7,6) SWNTs suggests differences in the π-π stacking interaction as origin of the selectivity. We observe energetically favored complexes between the (10,2) SWNT and the carbazole decamer and between the (7,6) SWNT and the fluorene decamer, respectively. These findings demonstrate that subtle structural changes of polymers lead to selective solvation of different families of carbon nanotubes. Furthermore, chemical screening of closely related polymers may pave the way toward simple, low-cost, and index-specific isolation of SWNTs.

Derivatives of molecular surface area and volume: simple and exact analytical formulas.

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.

Computing Charging and Polarization Energies of Small Organic Molecules Embedded into Amorphous Materials with Quantum Accuracy.

The ionization potential, electron affinity, and cation/anion polarization energies (IP, EA, P(+), P(-)) of organic molecules determine injection barriers, charge carriers balance, doping efficiency, and light outcoupling in organic electronics devices, such as organic light-emitting diodes (OLEDs). Computing IP and EA of isolated molecules is a common task for quantum chemistry methods. However, once molecules are embedded in an amorphous organic matrix, IP and EA values change, and accurate predictions become challenging. Here, we present a revised quantum embedding method [Friederich et al. J. Chem. Theory Comput. 2014, 10 (9), 3720-3725] that accurately predicts the dielectric permittivity and ionization potentials in three test materials, NPB, TCTA, and C60, and allows straightforward interpretation of their nature. The method paves the way toward reliable virtual screening of amorphous organic semiconductors with targeted IP/EA, polarization energies, and relative dielectric permittivity.

Probing hot spots on protein-protein interfaces with all-atom free-energy simulation.

Modulation of protein-protein interactions by competitive small-molecule binding emerges as a promising avenue for drug discovery. Hot spots, i.e., amino acids with important contributions to the overall interaction energy, provide useful targets within these interfaces. To avoid time-consuming mutagenesis experiments, computational alanine screening has been developed for the prediction of hot spots based on existing structural information. Here we use the all-atom free-energy force field PFF02 to identify important amino acid residues in the complexes of the chemokine interleukin-8 (CXCL8) and an N-terminal peptide of its cognate receptor CXCR1, and of ERBIN, a molecular marker of the basolateral membrane in epithelial cells, in complex with the ERBIN-binding domain of tyrosin kinase ERBB2. The results of our analysis agree with available experimental functional assays, indicating that this approach is suitable for computational alanine screening and may help to identify competitive peptides as starting points for the development of inhibitors of protein-protein interactions for pharmaceutically relevant targets.

Machine learning of correlated dihedral potentials for atomistic molecular force fields.

Computer simulation increasingly complements experimental efforts to describe nanoscale structure formation. Molecular mechanics simulations and related computational methods fundamentally rely on the accuracy of classical atomistic force fields for the evaluation of inter- and intramolecular energies. One indispensable component of such force fields, in particular for large organic molecules, is the accuracy of molecule-specific dihedral potentials which are the key determinants of molecular flexibility. We show in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy-an effect which is neglected in most state-of-the-art dihedral force fields. We furthermore present an efficient machine learning approach to compute intramolecular conformational energies. We demonstrate with the example of α-NPD, a molecule frequently used in organic electronics, that this approach outperforms traditional force fields by decreasing the mean absolute deviations by one order of magnitude to values smaller than 0.37 kcal/mol (16.0 meV) per dihedral angle.

Rational In Silico Design of an Organic Semiconductor with Improved Electron Mobility.

Organic semiconductors find a wide range of applications, such as in organic light emitting diodes, organic solar cells, and organic field effect transistors. One of their most striking disadvantages in comparison to crystalline inorganic semiconductors is their low charge-carrier mobility, which manifests itself in major device constraints such as limited photoactive layer thicknesses. Trial-and-error attempts to increase charge-carrier mobility are impeded by the complex interplay of the molecular and electronic structure of the material with its morphology. Here, the viability of a multiscale simulation approach to rationally design materials with improved electron mobility is demonstrated. Starting from one of the most widely used electron conducting materials (Alq3 ), novel organic semiconductors with tailored electronic properties are designed for which an improvement of the electron mobility by three orders of magnitude is predicted and experimentally confirmed.

Determination of caspase-3 activation fails to predict chemosensitivity in primary acute myeloid leukemia blasts.

BACKGROUND: Ex-vivo chemosensitivity tests that measure cell death induction may predict treatment outcome and, therefore, represent a powerful instrument for clinical decision making in cancer therapy. Such tests are, however, work intensive and, in the case of the DiSC-assay, require at least four days. Induction of apoptosis is the mode of action of anticancer drugs and should, therefore, result in the induction of caspase activation in cells targeted by anticancer therapy. METHODS: To determine, whether caspase activation can predict the chemosensitivity, we investigated enzyme activation of caspase-3, a key executioner caspase and correlated these data with chemosensitivity profiles of acute myeloid leukemia (AML) blasts. RESULTS: There was, however, no correlation between the ex-vivo chemosensitivity assessed by measuring the overall rates of cell death by use of the DiSC-assay and caspase-3 activation. CONCLUSION: Thus, despite a significant reduction of duration of the assay from four to one day, induction of apoptosis evaluated by caspase-3 activity does not seem to be a valid surrogate marker for chemosensitivity.

Charge carrier mobility and electronic properties of Al(Op)3: impact of excimer formation.

We have studied the electronic properties and the charge carrier mobility of the organic semiconductor tris(1-oxo-1H-phenalen-9-olate)aluminium(III) (Al(Op)3) both experimentally and theoretically. We experimentally estimated the HOMO and LUMO energy levels to be -5.93 and -3.26 eV, respectively, which were close to the corresponding calculated values. Al(Op)3 was successfully evaporated onto quartz substrates and was clearly identified in the absorption spectra of both the solution and the thin film. A structured steady state fluorescence emission was detected in solution, whereas a broad, red-shifted emission was observed in the thin film. This indicates the formation of excimers in the solid state, which is crucial for the transport properties. The incorporation of Al(Op)3 into organic thin film transistors (TFTs) was performed in order to measure the charge carrier mobility. The experimental setup detected no electron mobility, while a hole mobility between 0.6 × 10(-6) and 2.1 × 10(-6) cm(2)·V(-1)·s(-1) was measured. Theoretical simulations, on the other hand, predicted an electron mobility of 9.5 × 10(-6) cm(2)·V(-1)·s(-1) and a hole mobility of 1.4 × 10(-4) cm(2)·V(-1)·s(-1). The theoretical simulation for the hole mobility predicted an approximately one order of magnitude higher hole mobility than was observed in the experiment, which is considered to be in good agreement. The result for the electron mobility was, on the other hand, unexpected, as both the calculated electron mobility and chemical common sense (based on the capability of extended aromatic structures to efficiently accept and delocalize additional electrons) suggest more robust electron charge transport properties. This discrepancy is explained by the excimer formation, whose inclusion in the multiscale simulation workflow is expected to bring the theoretical simulation and experiment into agreement.

Six hydrophobins are involved in hydrophobin rodlet formation in Aspergillus nidulans and contribute to hydrophobicity of the spore surface.

Hydrophobins are amphiphilic proteins able to self-assemble at water-air interphases and are only found in filamentous fungi. In Aspergillus nidulans two hydrophobins, RodA and DewA, have been characterized, which both localize on the conidiospore surface and contribute to its hydrophobicity. RodA is the constituent protein of very regularly arranged rodlets, 10 nm in diameter. Here we analyzed four more hydrophobins, DewB-E, in A. nidulans and found that all six hydrophobins contribute to the hydrophobic surface of the conidiospores but only deletion of rodA caused loss of the rodlet structure. Analysis of the rodlets in the dewB-E deletion strains with atomic force microscopy revealed that the rodlets appeared less robust. Expression of DewA and DewB driven from the rodA promoter and secreted with the RodA secretion signal in a strain lacking RodA, restored partly the hydrophobicity. DewA and B were able to form rodlets to some extent but never reached the rodlet structure of RodA. The rodlet-lacking rodA-deletion strain opens the possibility to systematically study rodlet formation of other natural or synthetic hydrophobins.

Engineering hydrophobin DewA to generate surfaces that enhance adhesion of human but not bacterial cells.

Hydrophobins are fungal proteins with the ability to form immunologically inert membranes of high stability, properties that makes them attractive candidates for orthopaedic implant coatings. Cell adhesion on the surface of such implants is necessary for better integration with the neighbouring tissue; however, hydrophobin surfaces do not mediate cell adhesion. The aim of this project was therefore to investigate whether the class I hydrophobin DewA from Aspergillus nidulans can be functionalized for use on orthopaedic implant surfaces. DewA variants bearing either one RGD sequence or the laminin globular domain LG3 binding motif were engineered. The surfaces of both variants showed significantly increased adhesion of mesenchymal stem cells (MSCs), osteoblasts, fibroblasts and chondrocytes; in contrast, the insertion of binding motifs RGD and LG3 in DewA did not increase Staphylococcus aureus adhesion to the hydrophobin surfaces. Proliferation of MSCs and their osteogenic, chondrogenic and adipogenic differentiation potential were not affected on these surfaces. The engineered surfaces therefore enhanced MSC adhesion without interfering with their functionality or leading to increased risk of bacterial infection.