NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein–protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus–cell and cell–cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein–protein interaction surface.     

Carbon dioxide induced separation of ionic liquids and water

Both hydrophobic and hydrophilic room-temperature ionic liquids can be separated from aqueous solutions with relatively low-pressure gaseous carbon dioxide.     

SciFinder-guided rational design of fluorescent carbon dots for ratiometric monitoring intracellular pH fluctuations under heat shock

Intracellular pH plays a significant role in various biological processes, including cell proliferation, apoptosis, metabolism, enzyme activity and homeostasis. In this work, a novel design strategy for the preparation of pH responsive carbon dots (CDs-pH) for ratiometric intracellular imaging was reported. By using SciFinder database, fluorescent CDs-pH with the required pK_a value of 6.84 were rationally designed, which is vital important for precise sensing of intracellular pH. As a result, the synthesized CDs-pH demonstrated robust ability to test pH fluctuations within the physiological range of 5.4-7.4. The CDs-pH was further utilized for fluorescent ratiometric imaging of pH in living HeLa cells, effectively avoided the influence of autofluorescence from native cellular species. Moreover, real-time monitoring of intracellular pH fluctuation under heat shock was successfully realized. This SciFinder-guided design strategy is simple and flexible, which has a great potential to be used for the development of other types of CDs for various applications.     

Alpha,beta-unsaturated imines from titanium hydroamination and functionalization by rhodium C-H activation

Titanium pyrrolyl complexes are effective catalysts for the synthesis of alpha,beta-unsaturated imines, which can be further functionalized using Rh-catalyzed alkene or alkyne insertion into the beta-C-H bond.     

Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors

We used luminescent CdSe-ZnS core-shell quantum dots (QDs) as energy donors in fluorescent resonance energy transfer (FRET) assays. Engineered maltose binding protein (MBP) appended with an oligohistidine tail and labeled with an acceptor dye (Cy3) was immobilized on the nanocrystals via a noncovalent self-assembly scheme. This configuration allowed accurate control of the donor-acceptor separation distance to a range smaller than 100 A and provided a good model system to explore FRET phenomena in QD-protein-dye conjugates. This QD-MBP conjugate presents two advantages: (1) it permits one to tune the degree of spectral overlap between donor and acceptor and (2) provides a unique configuration where a single donor can interact with several acceptors simultaneously. The FRET signal was measured for these complexes as a function of both degree of spectral overlap and fraction of dye-labeled proteins in the QD conjugate. Data showed that substantial acceptor signals were measured upon conjugate formation, indicating efficient nonradiative exciton transfer between QD donors and dye-labeled protein acceptors. FRET efficiency can be controlled either by tuning the QD photoemission or by adjusting the number of dye-labeled proteins immobilized on the QD center. Results showed a clear dependence of the efficiency on the spectral overlap between the QD donor and dye acceptor. Apparent donor-acceptor distances were determined from efficiency measurements and corresponding F?rster distances, and these results agreed with QD bioconjugate dimensions extracted from structural data and core size variations among QD populations.     

Dual-core optofluidic chip for independent particle detection and tunable spectral filtering

We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.     

A slowly relaxing rigid biradical for efficient dynamic nuclear polarization surface-enhanced NMR spectroscopy: expeditious characterization of functional group manipulation in hybrid materials

A new nitroxide-based biradical having a long electron spin-lattice relaxation time (T(1e)) has been developed as an exogenous polarization source for DNP solid-state NMR experiments. The performance of this new biradical is demonstrated on hybrid silica-based mesostructured materials impregnated with 1,1,2,2-tetrachloroethane radical containing solutions, as well as in frozen bulk solutions, yielding DNP enhancement factors (ε) of over 100 at a magnetic field of 9.4 T and sample temperatures of ~100 K. The effects of radical concentration on the DNP enhancement factors and on the overall sensitivity enhancements (Σ(?)) are reported. The relatively high DNP efficiency of the biradical is attributed to an increased T(1e), which enables more effective saturation of the electron resonance. This new biradical is shown to outperform the polarizing agents used so far in DNP surface-enhanced NMR spectroscopy of materials, yielding a 113-fold increase in overall sensitivity for silicon-29 CPMAS spectra as compared to conventional NMR experiments at room temperature. This results in a reduction in experimental times by a factor >12,700, making the acquisition of (13)C and (15)N one- and two-dimensional NMR spectra at natural isotopic abundance rapid (hours). It has been used here to monitor a series of chemical reactions carried out on the surface functionalities of a hybrid organic-silica material.