Sparse optimization on measures with over-parameterized gradient descent

Mathematical Programming - Minimizing a convex function of a measure with a sparsity-inducing penalty is a typical problem arising, e.g., in sparse spikes deconvolution or two-layer neural networks...     

Acid/Base‐Triggered Switching of Circularly Polarized Luminescence and Electronic Circular Dichroism in Organic and Organometallic Helicenes

Electronic circular dichroism and circularly polarized luminescence acid/base switching activity has been demonstrated in helicene‐bipyridine proligand 1 a and in its “rollover” cycloplatinated derivative 2 a . Whereas proligand 1 a displays a strong bathochromic shift (>160 nm) of the nonpolarized and circularly polarized luminescence upon protonation, complex 2 a displays slightly stronger emission. This strikingly different behavior between singlet emission in the organic helicene and triplet emission in the organometallic derivative has been rationalized by using quantum‐chemical calculations. The very large bathochromic shift of the emission observed upon protonation of azahelicene‐bipyridine 1 a has been attributed to the decrease in aromaticity (promoting a charge‐transfer‐type transition rather than a π–π* transition) as well as an increase in the HOMO–LUMO character of the transition and stabilization of the LUMO level upon protonation.     

Structural impact of GTP binding on downstream KRAS signaling

Oncogenic RAS proteins, involved in ∼30% of human tumors, are molecular switches of various signal transduction pathways. Here we apply a new protocol for the NMR study of KRAS in its (inactive) GDP- and (activated) GTP-bound form, allowing a comprehensive analysis of the backbone dynamics of its WT-, G12C- and G12D variants. We found that Tyr32 shows opposite mobility with respect to the backbone of its surroundings: it is more flexible in the GDP-bound form while more rigid in GTP-complexes (especially in WT- and G12D-GTP). Using the G12C/Y32F double mutant, we showed that the presence of the hydroxyl group of Tyr32 has a marked effect on the G12C-KRAS-GTP system as well. Molecular dynamics simulations indicate that Tyr32 is linked to the γ-phosphate of GTP in the activated states – an arrangement shown, using QM/MM calculations, to support catalysis. Anchoring Tyr32 to the γ-phosphate contributes to the capture of the catalytic waters participating in the intrinsic hydrolysis of GTP and supports a simultaneous triple proton transfer step (catalytic water → assisting water → Tyr32 → O1G of the γ-phosphate) leading to straightforward product formation. The coupled flip of negatively charged residues of switch I toward the inside of the effector binding pocket potentiates ligand recognition, while positioning of Thr35 to enter the coordination sphere of the Mg²⁺ widens the pocket. Position 12 mutations do not disturb the capture of Tyr32 by the γ-phosphate, but (partially) displace Gln61, which opens up the catalytic pocket and destabilizes catalytic water molecules thus impairing intrinsic hydrolysis.

Nucleotide exchange to the physiological, activated, GTP-bound form of KRAS results in the anchoring of Tyr32 within the active site.     

pH-Dependent Hydration Change in a Gd-Based MRI Contrast Agent with a Phosphonated Ligand

The heptadentate ligand L was shown to form an extremely stable Gd complex at neutral pH with a pGd value of 18.4 at pH 7.4. The X-ray crystal structures of the complexes formed with Gd and Tb displayed two very different coordination behaviors being, respectively, octa- and nonacoordinated. The relaxometric properties of the Gd complex were studied by field-dependent relaxivity measurements at various temperatures and by ¹⁷O NMR spectroscopy. The pH-dependence of the longitudinal relaxivity profile indicated large changes around neutral pH leading to a very large value of 10.1 mm ⁻¹⋅s⁻¹ (60 MHz, 298 K) at pH 4.7. The changes were attributed to an increase of the hydration number from one water molecule in basic conditions to two at acidic pH. A similar trend was observed for the luminescence of the Eu complex, confirming the change in hydration state. DOSY experiments were performed on the Lu analogue, pointing to the absence of dimers in solution in the considered pH range. A breathing mode of the complex was postulated, which was further supported by ¹H and ³¹P NMR spectroscopy of the Yb complex at varying pH and was finally modeled by DFT calculations.     

Comparison of different methodologies for the computation of damped nonlinear normal modes and resonance prediction of systems with non-conservative nonlinearities

Nonlinear Dynamics - The nonlinear modes of a non-conservative nonlinear system are sometimes referred to as damped nonlinear normal modes (dNNMs). Because of the non-conservative...     

Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy

In NMR spectroscopy, residual dipolar couplings (RDCs) have emerged as one of the most exquisite probes of biological structure and dynamics. The measurement of RDCs relies on the partial alignment of the molecule of interest, for example by using a liquid crystal as a solvent. Here, we establish bacterial type 1 pili as an alternative liquid-crystalline alignment medium for the measurement of RDCs. To achieve alignment at pilus concentrations that allow for efficient NMR sample preparation, we elongated wild-type pili by recombinant overproduction of the main structural pilus subunit. Building on the extraordinary stability of type 1 pili against spontaneous dissociation and unfolding, we show that the medium is compatible with challenging experimental conditions such as high temperature, the presence of detergents, organic solvents or very acidic pH, setting it apart from most established alignment media. Using human ubiquitin, HIV-1 TAR RNA and camphor as spectroscopic probes, we demonstrate the applicability of the medium for the determination of RDCs of proteins, nucleic acids and small molecules. Our results show that type 1 pili represent a very useful alternative to existing alignment media and may readily assist the characterization of molecular structure and dynamics by NMR.     

含氟CaO-P2O5-SiO2-Na2O-B2O3玻璃陶瓷的制备及性能表征

采用溶胶-凝胶法制备CaO-P₂O₅-SiO₂-Na₂O-B₂O₃体系前驱体粉末,用CaF₂替代部分CaO再次制备前驱体粉末。 通过TG-DSC分析确定结晶温度为865 ℃,经过热处理获得主晶相为Na₆Ca₃Si₆O₁₈的玻璃陶瓷。 通过X射线衍射(XRD)、傅里叶红外光谱(FTIR)、扫描电子显微镜(SEM)等技术手段及体外生物活性实验分析玻璃陶瓷的显微结构及性能。 结果表明,CaF₂的加入能提高玻璃陶瓷的体积密度、抗折强度和弹性模量,并且不会破坏玻璃陶瓷的生物活性。     

Pickering Interfacial Catalysis for Biphasic Systems: From Emulsion Design to Green Reactions

Pickering emulsions are surfactant‐free dispersions of two immiscible fluids that are kinetically stabilized by colloidal particles. For ecological reasons, these systems have undergone a resurgence of interest to mitigate the use of synthetic surfactants and solvents. Moreover, the use of colloidal particles as stabilizers provides emulsions with original properties compared to surfactant‐stabilized emulsions, microemulsions, and micellar systems. Despite these specific advantages, the application of Pickering emulsions to catalysis has been rarely explored. This Minireview describes very recent examples of hybrid and composite amphiphilic materials for the design of interfacial catalysts in Pickering emulsions with special emphasis on their assets and challenges for industrially relevant biphasic reactions in fine chemistry, biofuel upgrading, and depollution.