Byrneweiss3821

Changes in the structure of double-stranded (ds) DNA with temperature affect processes in thermophilic organisms and are important for nanotechnological applications. Here we investigate temperature-dependent conformational changes of dsDNA at the scale of several helical turns and at the base pair step level, inferred from extensive all-atom molecular dynamics simulations of DNA at temperatures from 7 to 47 °C. Our results suggest that, contrary to twist, the overall bending of dsDNA without A-tracts depends only very weakly on temperature, due to the mutual compensation of directional local bends. Investigating DNA length as a function of temperature, we find that the sum of distances between base pair centers (the wire length) exhibits a large expansion coefficient of ∼2 × 10-4 °C-1, similar to values reported for thermoplastic materials. However, the wire length increase with temperature is absorbed by expanding helix radius, so the length measured along the helical axis (the spring length) seems to suggest a very small negative thermal expansion coefficient. These compensatory mechanisms contribute to thermal stability of DNA structure on the biologically relevant scale of tens of base pairs and longer.Analysis of proteins and complexes under native mass spectrometric (MS) and solution conditions was typically performed using time-of-flight (ToF) analyzers, due to their routine high m/z transmission and detection capabilities. However, over recent years, the ability of Orbitrap-based mass spectrometers to transmit and detect a range of high molecular weight species is well documented. Herein, we describe how a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (15 T FT-ICR MS) is more than capable of analyzing a wide range of ions in the high m/z scale (>5000), in both positive and negative instrument polarities, ranging from the inorganic cesium iodide salt clusters; a humanized IgG1k monoclonal antibody (mAb; 148.2 kDa); a IgG1-mertansine drug conjugate (148.5 kDa, drug-to-antibody ratio; DAR 2.26); anIgG1-siRNA conjugate (159.1 kDa; ribonucleic acid to antibody ratio; RAR 1); the membrane protein aquaporin-Z (97.2 kDa) liberated from a C8E4 detergent micelle; the empty MSP1D1-nanodisc (142.5 kDa) and the tetradecameric chaperone protein complex GroEL (806.2 kDa; GroEL dimer at 1.6 MDa). We also investigate different regions of the FT-ICR MS that impact ion transmission and desolvation. Finally, we demonstrate how the transmission of these species and resultant spectra are highly consistent with those previously generated on both quadrupole-ToF (Q-ToF) and Orbitrap instrumentation. PKM2-IN-1 ic50 This report serves as an impactful example of how FT-ICR mass analyzers are competitive to Q-ToFs and Orbitraps for high mass detection at high m/z.Proteins often have multiple switching domains that are coupled to each other and to the binding of ligands in order to realize signaling functions. Here we investigate the C2A domain of Synaptotagmin-1 (Syt-1), a calcium sensor in the neurotransmitter release machinery and a model system for the large family of C2 membrane binding domains. We combine extensive molecular dynamics (MD) simulations with Markov modeling in order to model conformational switching domains, their states, and their dependence on bound calcium ions. Then, we use transfer entropy to characterize how the switching domains are coupled via directed or allosteric mechanisms and give rise to the calcium sensing function of the protein. Our proposed switching mechanism contributes to the understanding of the neurotransmitter release machinery. Furthermore, the methodological approach we develop serves as a template to analyze conformational switching domains and the broad study of their coupling in macromolecular machines.Application of the aroma extract dilution analysis (AEDA) on an extract/distillate from raw shiitake mushrooms revealed 32 odorants among which 3-(methylthio)propanal (cooked potato), 1-octen-3-one, and 1-octen-3-ol (both mushroom-like) showed the highest flavor dilution (FD) factors. An isotope enrichment experiment with raw shiitake tissue and either 13C18-linoleic acid or 2H4-1-octen-3-ol confirmed that both 1-octen-3-ol and 1-octen-3-one are direct degradation products of the fatty acid, but it could be proven for the first time that the ketone is not formed by an oxidation of the alcohol. After pan-frying, 42 odor-active compounds appeared among which 3-hydroxy-4,5-dimethylfuran-2(5H)-one (savory), 1,2,4,5-tetrathiane (burnt, sulfury), 4-hydroxy-2,5-dimethylfuran-3(2H)-one (caramel-like), phenylacetic acid (honey-like), 3-(methylthio)-propanal, and trans-4,5-epoxy-(E)-2-decenal (metallic) showed the highest FD factors. To get a deeper insight into their aroma contribution, 19 key odorants were quantitated in the raw shiitake and twenty-one in the pan-fried mushrooms by stable isotope dilution assays, and new methods for the quantitation of four sulfur compounds were developed. A calculation of odor activity values (OAV; ratio of concentration to odor threshold) showed that 1-octen-3-one was by far the most important odorant in raw shiitake. During pan-frying, in particular, four aroma compounds were significantly increased, i.e., 4-hydroxy-2,5-dimethylfuran-3(2H)-one, dimethyl trisulfide, 1,2,4,5-tetrathiane, and 1,2,3,5,6-pentathiepane. The overall aroma profile of pan-fried shiitake could very well be mimicked by an aroma recombinate consisting of 15 reference aroma compounds in the concentrations determined in the pan-fried mushrooms. Further results showed that the sulfur compounds were even higher in rehydrated dry shiitake as compared to the pan-fried mushrooms.Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. link2 The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source postprocessing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures in both strong-confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. We also propose and validate a new order parameter for identifying the building blocks of quasi-one-dimensional ice. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture built with nix and employing a YAML-Lua scripting pipeline. The software has been designed to be user-friendly and extensible. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one- and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogeneous ice nucleation on a silver-exposed β-AgI surface, homogeneous ice nucleation, flat monolayer square ice formation, and freezing of an ice nanotube.DNA mutations can result from replication errors due to different forms of DNA damage, including low-abundance DNA adducts induced by reactions with electrophiles. The lack of strategies to measure DNA adducts within genomic loci, however, limits our understanding of chemical mutagenesis. The use of artificial nucleotides incorporated opposite DNA adducts by engineered DNA polymerases offers a potential basis for site-specific detection of DNA adducts, but the availability of effective artificial nucleotides that insert opposite DNA adducts is extremely limited, and furthermore, there has been no report of a quantitative strategy for determining how much DNA alkylation occurs in a sequence of interest. In this work, we synthesized an artificial nucleotide triphosphate that is selectively inserted opposite O6-carboxymethyl-guanine DNA by an engineered polymerase and is required for DNA synthesis past the adduct. We characterized the mechanism of this enzymatic process and demonstrated that the artificial nucleotide is a marker for the presence and location in the genome of O6-carboxymethyl-guanine. Finally, we established a mass spectrometric method for quantifying the incorporated artificial nucleotide and obtained a linear relationship with the amount of O6-carboxymethyl-guanine in the target sequence. In this work, we present a strategy to identify, locate, and quantify a mutagenic DNA adduct, advancing tools for linking DNA alkylation to mutagenesis and for detecting DNA adducts in genes as potential diagnostic biomarkers for cancer prevention.Creating high-density durable bifunctional active sites in an air electrode is essential but still challenging for a long-life rechargeable zinc-air battery with appealing power density. Herein, we discover a general strategy mediated by metastable rock salt oxides for achieving high-density well-defined transition-metal nanocrystals encapsulated in N-doped carbon shells (M@NC) which are anchored on a substrate by a porous carbon network as highly active and durable bifunctional catalytic sites. link3 Small-size (15 ± 5 nm) well-dispersed Co2Fe1@NC in a high density (metal loading up to 54.0 wt %) offers the zinc-air battery a record power density of 423.7 mW cm-2. The dual protection from the complete graphitic carbon shells and the anchoring of the outer carbon network make Co2Fe1@NC chemically and mechanically durable, giving the battery a long cycling life. Systematic in-situ temperature-dependent characterizations as well as DFT modeling rationalize the rock salt oxide-mediated process and its indispensable role in achieving high-density nanosized M@NC. These findings open up opportunities for designing efficient electrocatalysts for high-performance Zn-air batteries and diverse energy devices.A high-consequence chemical emergency is a major public health concern. In the United States, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health pioneers discovery and early development of critical medical countermeasures against chemical threats.Polypeptide micelles are widely used as biocompatible nano-platforms, but often suffer from their poor structural stability. Unimolecular polypeptide micelles can effectively address the structure instability issue, but their synthesis with uniform struc-ture, well controlled and desired sizes remains challenging. Herein, we report the convenient preparation of spherical unimolecular micelles through dendritic polyamine-initiated ultrafast ring-opening polymerization of N-carboxyanhydride (NCA). Synthetic polypeptides with exceptionally high MWs (up to 85 MDa) and low dispersity (Ð less then 1.05) can be readily obtained, which are the biggest synthetic polypeptides ever reported. The degree of polymerization was controlled in a vast range (25 - 3200), giving access to nearly monodisperse unimolecular micelles with predict-able sizes. Many NCA monomers can be polymerized using this ultrafast polymerization method, which enables the incorporation of various structural and functional moieties to the unimolecular micelles.