Dolanberger5478

Estimation of binding free energies is one of the central aims of simulations of biomolecular complexes. We explore the accuracy and efficiency of setups based on nonequilibrium pulling simulations applied to the estimation of binding affinities of DNA-binding proteins. Absolute binding free energies are calculated over a range of temperatures and compared to results obtained previously using an equilibrium method. We show that realistic binding affinities can be obtained with the presented nonequilibrium approach, which also entails lower computational requirements. Errors of the binding free energy estimates are investigated and are shown to be comparable to those observed previously. Bounds are provided on the convergence of the errors with respect to the number of pulling simulations performed and with respect to the applied pull rate.Phosphorylation is a widespread posttranslational protein modification and is important in various biological processes. However, milk fat globule membrane (MFGM) phosphoproteins have not been explored systematically in human milk. Here, we used quantitative phosphoproteomics to analyze phosphorylation sites in human MFGM proteins and their differences at different stages of lactation; 305 phosphorylation sites on 170 proteins and 269 phosphorylation sites on 170 proteins were identified in colostrum and mature MFGM, respectively. Among these, 71 phosphorylation sites on 48 proteins were differentially expressed between the different stages of lactation. Osteopontin in human MFGM was the most heavily phosphorylated protein, with a total of 39 identified phosphorylation sites. Our results shed light on phosphorylation sites, composition, and biological functions of MFGM phosphoproteins in human colostrum and mature milk, and provide novel insights into the crucial roles of protein phosphorylation during infant development.The synthesis of conjugated Möbius molecules remains elusive since twisted and macrocyclic structures are low-entropy species sporting their own synthetic challenges. Here we report the synthesis of a Möbius macrocycle in 84% yield via alkyne metathesis of 2,13-bis(propynyl)[5]helicene. MALDI-MS, NMR spectroscopy, and X-ray diffraction indicated a trimeric product of twofold symmetry with PPM/MMP configurations in the helicene subunits. Alternatively, a threefold-symmetric PPP/MMM structure was determined by DFT calculations to be more thermodynamically stable, illustrating remarkable kinetic selectivity for this alkyne metathesis cyclooligomerization. Computational studies provided insight into the kinetic selectivity, demonstrating a difference of 15.4 kcal/mol between the activation barriers for the PPM/MMP and PPP/MMM diastereodetermining steps. Computational (ACID and EDDB) and experimental (UV-vis and fluorescence spectroscopy and cyclic voltammetry) studies revealed weak conjugation between the alkyne and adjacent helicene groups as well as the lack of significant global aromaticity. Separation of the PPM and MMP enantiomers was achieved via chiral HPLC at the analytical scale.The properties of nanoplasmonic structures depend strongly on their geometry, creating the need for high-precision control and characterization. Here, by exploiting the low activation energy of gold atoms on nanoparticle surfaces, we show how laser irradiation reshapes nanoparticle dimers. Time-course dark-field microspectroscopy allows this process to be studied in detail for individual nanostructures. Three regimes are identified facet growth, formation of a conductive bridge between particles, and bridge growth. Electromagnetic simulations confirm the growth dynamics and allow measurement of bridge diameter, found to be highly reproducible and also self-limiting. Correlations in spectral resonances for the initial and final states give insight into the energy barriers for bridge growth. Dark-field microscopy shows that coalescence of multiple gaps in nanoparticle clusters can be digitally triggered, with each gap closing after discrete increases in irradiation power. Such control is important for light-induced nanowire formation or trimming of electronic and optoelectronic devices.A novel nucleic acid isothermal amplification method based on saltatory rolling circle amplification (SRCA) for rapid and visual detection of Alicyclobacillus acidoterrestris in apple juice was established. Fourteen A. acidoterrestris strains and 44 non-A. acidoterrestris strains were used to confirm the specificity. The sensitivity of SRCA was 4.5 × 101 CFU/mL by observing the white precipitate with the naked eye, while it was 4.5 × 100 CFU/mL by fluorescence visualization. The detection limit of SRCA in artificially inoculated apple juice was 7.1 × 101 and 7.1 × 100 CFU/mL via visualization of the white precipitate and fluorescence, respectively. Estradiol Benzoate Compared with the traditional PCR method, SRCA exhibited at least a 100-fold higher sensitivity and 100-fold lower detection limit. Seventy samples were investigated for A. acidoterrestris contamination, and the results showed 100% sensitivity, 97.01% specificity, and 97.14% accuracy compared with those by the conventional microbiological cultivation method. Overall, this method is a potentially useful tool for visual and rapid detection of A. acidoterrestris.The fatty acid (FA) composition and content of whole milk (3.25% fat) from organic, omega-3 (n-3) FA fortified, and conventional retail brands available in the northeastern U.S. were assessed monthly via gas chromatography. Among the retail labels, organic milk stood out as it contained a distinct and more healthful FA profile, consistently comprising a higher content of unique bioactive FAs (short-chain FAs, odd- and branched-chain FAs, vaccenic acid, and conjugated linoleic acids) per serving, particularly during the warm season. The total content of saturated FAs did not differ by retail label. While organic and n-3 fortified milk contained a similar content of total n-3 FAs, the proportion of individual n-3 FAs differed significantly (organic milk 183 n-3; n-3 fortified milk 206 n-3) as a result of the production system and process, respectively. Overall, per serving, the FA profile of organic milk may provide added nutritional and health benefits.