Structural characterization of intact proteins is enhanced by prevalent fragmentation pathways rarely observed for peptides

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS3 of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.     

The Direct Synthesis of Hydrogen Peroxide Using Platinum‐Promoted Gold–Palladium Catalysts

The direct synthesis of hydrogen peroxide offers a potentially green route to the production of this important commodity chemical. Early studies showed that Pd is a suitable catalyst, but recent work indicated that the addition of Au enhances the activity and selectivity significantly. The addition of a third metal using impregnation as a facile preparation method was thus investigated. The addition of a small amount of Pt to a CeO₂‐supported AuPd (weight ratio of 1:1) catalyst significantly enhanced the activity in the direct synthesis of H₂O₂ and decreased the non‐desired over‐hydrogenation and decomposition reactions. The addition of Pt to the AuPd nanoparticles influenced the surface composition, thus leading to the marked effects that were observed on the catalytic formation of hydrogen peroxide. In addition, an experimental approach that can help to identify the optimal nominal ternary alloy compositions for this reaction is demonstrated.     

An investigation of site-selective gas-phase reactions of amino alcohols with dimethyl ether ions

The reactions of dimethyl ether ions with neutral amino alcohols were examined in both a quadrupole ion trap mass spectrometer and a triple quadrupole mass spectrometer. These ion-molecule reactions produced two types of ions: the protonated species [M+l]⁺ and a more complex product at [M+13]⁺. The abundance of the [M+13]⁺ ions relative to that of the [M+1]⁺ ions decreases with increasing formal interfunctional distance. Multistage collision-activated dissociation techniques were used to characterize the [M+13]⁺ product ions, their reactivities, and the mechanisms for their formation and dissociation. In addition, molecular semiempirical calculation methods were used to probe the thermochemistry of these reactions. Reaction at the amino alcohol nitrogen site is favored, and the resulting [M+13]⁺ addition products may cyclize for additional stabilization. Comparisons were made among the behavior of related compounds, such as alcohols, diols, amines, and diamines. The alcohols reacted only to form the protonated species, but the diols, amines, and diamines all formed significant amounts of [M+13]⁺ ions or related dissociation products.     

Convergent sequences of sparse graphs: A large deviations approach

Models based on sparse graphs are of interest to many communities: they appear as basic models in combinatorics, probability theory, optimization, statistical physics, information theory, and more applied fields of social sciences and economics. Different notions of similarity (and hence convergence) of sparse graphs are of interest in different communities. In probability theory and combinatorics, the notion of Benjamini‐Schramm convergence, also known as left‐convergence, is used quite frequently. Statistical physicists are interested in the the existence of the thermodynamic limit of free energies, which leads naturally to the notion of right‐convergence. Combinatorial optimization problems naturally lead to so‐called partition convergence, which relates to the convergence of optimal values of a variety of constraint satisfaction problems. The relationship between these different notions of similarity and convergence is, however, poorly understood. In this paper we introduce a new notion of convergence of sparse graphs, which we call Large Deviations or LD‐convergence, and which is based on the theory of large deviations. The notion is introduced by “decorating” the nodes of the graph with random uniform i.i.d. weights and constructing corresponding random measures on and . A graph sequence is defined to be converging if the corresponding sequence of random measures satisfies the Large Deviations Principle with respect to the topology of weak convergence on bounded measures on . The corresponding large deviations rate function can be interpreted as the limit object of the sparse graph sequence. In particular, we can express the limiting free energies in terms of this limit object. We then establish that LD‐convergence implies the other three notions of convergence discussed above, and at the same time establish several previously unknown relationships between the other notions of convergence. In particular, we show that partition‐convergence does not imply left‐ or right‐convergence, and that right‐convergence does not imply partition‐convergence. © 2016 Wiley Periodicals, Inc. Random Struct. Alg., 51, 52–89, 2017     

All directed BIBDs with k = 3 exist

A directed BIBD with parameters ($\text{υ, b, r, k, λ}{}^1$) is a BIBD with parameters ($\text{υ, b, r, k, 2λ}{}^1$) in which each ordered pair of varieties occurs together in exactly $\text{λ}{}^1$ blocks. It is shown that $\text{λ}{}^1\text{υ(υ ? 1) ≡ 0}$ (mod 3) is a necessary and sufficient condition for the existence of a directed ($\text{υ, b, r, k, λ}{}^1$) BIBD with k = 3.     

Laser-induced fluorescence imaging of subsurface tissue structures with a volume holographic spatial-spectral imaging system

A three-dimensional imaging system incorporating multiplexed holographic gratings to visualize fluorescence tissue structures is presented. Holographic gratings formed in volume recording materials such as a phenanthrenquinone poly(methyl methacrylate) photopolymer have narrowband angular and spectral transmittance filtering properties that enable obtaining spatial-spectral information within an object. We demonstrate this imaging system's ability to obtain multiple depth-resolved fluorescence images simultaneously.     

Tracking regression and progression of atherosclerosis in human carotid arteries using high-resolution magnetic resonance imaging

BACKGROUND AND PURPOSE: Magnetic resonance imaging (MRI) can accurately and reproducibly measure the volume of atherosclerotic plaque in human carotid arteries. Atherosclerotic plaques may either progress or regress over time, depending on individual risk factors and treatment regimens. This study was designed to determine if regression or progression of human carotid atherosclerosis in patients receiving statin therapy over 24 months can be detected by high-resolution MRI. METHODS: In 11 subjects who had undergone unilateral carotid endarterectomy and were on statin therapy, volumes for total carotid artery, concentric wall (normal wall), eccentric wall (plaque), and lumen were quantified at 0, 16 and 24 months using a 1.5-T human imager equipped with 6-cm phased array coils. RESULTS: The interobserver mean coefficient of variation (CV) was lowest for the lumen volume (3.1%) and highest for the plaque volume (9.8%). The interscan mean CV was lowest for the total artery volume (3.2%) and highest for the plaque volume (9.9%). As much as 26% regression and 35% progression were observed in individual subject's carotid artery eccentric wall (plaque) volumes over time. Mean eccentric wall volume increased 5% by 16 months and 8% by 24 months. Mean total wall volume increased slightly at both 16 and 24 months (+1.2% and +1.8%). CONCLUSIONS: High-resolution MRI provides a noninvasive reproducible method of tracking changes in carotid atherosclerosis. This pilot study detected changes in individual subjects at both 16 and 24 months. MRI tracking of changes in atherosclerotic plaques should prove useful in assessing vascular disease risk and monitoring the efficacy of interventions designed to induce regression or retard progression.     

Inhomogeneous Distribution of Cationic Surfactants around Anionic Molecular Clusters

An interesting phenomenon is reported when uranyl peroxide nanoclusters U₆₀ (Li_48+mK₁₂(OH)_m[UO₂(O₂)(OH)]₆₀ (H₂O)_n, m≈20 and n≈310) interact with a small number of cationic surfactant molecules. Cationic surfactant molecules do not distribute evenly around the U₆₀ clusters during the interaction as expected. Instead, a small fraction of U₆₀ clusters attract almost all the surfactant molecules, leading to the self-assembly into supramolecular structures by using surfactant–U₆₀ complexes as building locks, and later further aggregate and precipitate based on hydrophobic interaction, whereas the rest of the clusters remained unbounded soluble macroions in bulk dispersion. This phenomenon nicely demonstrates a unique feature of macroion solutions. Considering that Debye–Hückel approximation is no longer valid in such solutions, the competition between the local electrostatic interaction and hydrophobic interaction becomes important to regulate the solution behaviors of macroions.     

Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases

The human KDM7 subfamily histone H3 Nϵ-methyl lysine demethylases PHF8 (KDM7B) and KIAA1718 (KDM7A) have different substrate selectivities and are linked to genetic diseases and cancer. We describe experimentally based computational studies revealing that flexibility of the region linking the PHD finger and JmjC domains in PHF8 and KIAA1718 regulates interdomain interactions, the nature of correlated motions, and ultimately H3 binding and demethylation site selectivity. F279S an X-linked mental retardation mutation in PHF8 is involved in correlated motions with the iron ligands and second sphere residues. The calculations reveal key roles of a flexible protein environment in productive formation of enzyme-substrate complexes and suggest targeting the flexible KDM7 linker region is of interest from a medicinal chemistry perspective.