Conformational Determinants of Phosphotyrosine Peptides Complexed with the Src SH2 Domain

The inhibition of specific SH2 domain mediated protein-protein interactions as an effective chemotherapeutic approach in the treatment of diseases remains a challenge. That different conformations of peptide-ligands are preferred by different SH2 domains is an underappreciated observation from the structural analysis of phosphotyrosine peptide binding to SH2 domains that may aid in future drug design. To explore the nature of ligand binding, we use simulated annealing (SA) to sample the conformational space of phosphotyrosine-containing peptides complexed with the Src SH2 domain. While in good agreement with the crystallographic and NMR studies of high-affinity phosphopeptide-SH2 domain complexes, the results suggest that the structural basis for phopsphopeptide- Src SH2 interactions is more complex than the “two-pronged plug two-hole socket” model. A systematic study of peptides of type pYEEX, where pY is phosphotyrosine and X is a hydrophobic residue, indicates that these peptides can assume two conformations, one extended and one helical, representing the balance between the interaction of residue X with the hydrophobic hole on the surface of the Src SH2 domain, and its contribution to the inherent tendency of the two glutamic acids to form an α-helix. In contrast, a β-turn conformation, almost identical to that observed in the crystal structure of pYVNV bound to the Grb2 SH2 domain, predominates for pYXNX peptides, even in the presence of isoleucine at the third position. While peptide binding affinities, as measured by fluorescence polarization, correlate with the relative proportion of extended peptide conformation, these results suggest a model where all three residues C-terminal to the phosphotyrosine determine the conformation of the bound phosphopeptide. The information obtained in this work can be used in the design of specific SH2 domain inhibitors

200 W average power energetic few-cycle fiber laser

A state-of-the-art 8 channel fiber-chirped-pulse-amplifier system delivers 680 W of average power. Two-stage nonlinear compression in gas-filled capillaries yields 400 W, 30fs, >300µJ pulses and 220W, sub-7fs, 170 µJ pulses, respectively

Spectrally tunable ultrashort monochromatized extreme ultraviolet pulses at 100 kHz

We present the experimental realization of spectrally tunable, ultrashort, quasi-monochromatic extreme ultraviolet (XUV) pulses generated at 100 kHz repetition rate in a user-oriented gas high harmonic generation beamline of the Extreme Light Infrastructure—Attosecond Light Pulse Source facility. Versatile spectral and temporal shaping of the XUV pulses is accomplished with a double-grating, time-delay compensated monochromator accommodating the two composing stages in a novel, asymmetrical geometry. This configuration supports the achievement of high monochromatic XUV flux (2.8 ± 0.9 × 1010 photons/s at 39.7 eV selected with 700 meV full width at half maximum bandwidth) combined with ultrashort pulse duration (4.0 ± 0.2 fs using 12.1 ± 0.6 fs driving pulses) and small spot size (sub-100 µm). Focusability, spectral bandwidth, and overall photon flux of the produced radiation were investigated, covering a wide range of instrumental configurations. Moreover, complete temporal (intensity and phase) characterization of the few-femtosecond monochromatic XUV pulses—a goal that is difficult to achieve by conventional reconstruction techniques—has been realized using a ptychographic algorithm on experimentally recorded XUV-infrared pump-probe traces. The presented results contribute to in situ, time-resolved experiments, accessing direct information on the electronic structure dynamics of novel target materials

High-power CEP-stable few-cycle fiber lasers

Summary form only given. Today, carrier-envelope-phase (CEP) stable laser pulses have become a versatile tool for a plethora of scientific applications. Many years their generation relied on either optical parametric amplification or the use of titanium-sapphire amplifiers. Although impressive results have been achieved using these technologies [1, 2], their main drawback is the restricted average power (and therewith repetition rate for a given energy) due to thermo-optical limitations. Here we report on another approach, the nonlinear compression of ultrafast ytterbium-based high-power fiber lasers [3]. The first commercially available source employing this technology is the HR1 laser constructed for the ELI-ALPS research facility in Szeged, Hungary. The Extreme Light Infrastructure (ELI) is currently being installed in several European countries aiming to provide unique user facilities with beyond state-of-the-art laser systems. The attosecond facility ELI-ALPS in Szeged, for example, will host several laser systems that will be used for attosecond pulse generation at unprecedented pulse parameters (energy and repetition rate). One of these laser systems is the HR1 (high repetition rate) laser that targets pulse parameters of 1mJ, 6fs pulses at 100kHz repetition rate (100W average power) and with CEP stable operation in its first implementation phase.We will show detailed measurements and characterization of the CPA system as well as the compression unit. General scaling properties of hollow-fiber compressors towards multi-mJ operation at kW-level average powers will be discussed. Furthermore, a detailed discussion on the CEP stabilization of the system will be given and supported by the latest measurement results using a stereo ATI device

Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered

Amorphization of Atorvastatin Calcium by Mechanical Process: Characterization and Stabilization Within Polymeric Matrix

International audienc

Molecular basis of binding and stability of curcumin in diamide-linked y-cyclodextrin dimers

Curcumin is a naturally occurring molecule with medicinal properties that is unstable in water, whose efficacy as a drug can potentially be enhanced by encapsulation inside a host molecule. In this work, the thermodynamics and mechanism of binding of curcumin to succinamide- and urea-linked γ-cyclodextrin (γ-CD) dimers in water are investigated by molecular dynamics simulations. The simulated binding constants of curcumin to succinamide- and urea-linked γ-CD dimers at 310 K are 11.3 × 10⁶ M ⁻¹ and 1.6 × 10⁶ M ⁻¹, respectively, matching well with previous experimental results of 8.7 × 10⁶ M ⁻¹ and 2.0 × 10⁶ M ⁻¹. The simulations reveal structural information about the encapsulation of curcumin inside the diamide-linked γ-CD dimers, with distinct qualitative differences observed for the two dimers. In particular, (1) the predominant orientation of curcumin inside the urea-linked γ-CD dimer is perpendicular to that in the succinamide-linked γ-CD dimer; (2) the magnitude of the angle between the planes of the cyclodextrins is larger for the succinamide-linked γ-CD dimer; and (3) curcumin exhibits greater configurational freedom inside the urea-linked γ-CD dimer. A consequence of some of these structural differences is that the dimer interior is more accessible to water in the succinamide-linked γ-CD dimer. These observations explain the higher stability and lower binding constant observed experimentally for curcumin in the urea-linked cyclodextrin γ-CD dimer compared with the succinamide-linked γ-CD dimer. More generally, the results demonstrate how stability and binding strength can be decoupled and thus separately optimized in host–guest systems used for drug delivery.Samuel J. Wallace, Tak W. Kee, and David M. Huan