Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH₄OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin–TBA complex and 1 M NH₄OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin–TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein–DNA complexes.

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Solvent effects on the intramolecular charge transfer character of N,N-diaryl dihydrophenazine catalysts for organocatalyzed atom transfer radical polymerization

The nature of intramolecular charge transfer (CT) of N,N-diaryl dihydrophenazine photocatalysts (PCs) in different solvents is explored in context of their performance in organocatalyzed atom transfer radical polymerization (O-ATRP). PCs having a computationally predicted lowest energy excited state exhibiting CT character can operate a highly controlled O-ATRP in a wide range of solvent polarities, from non-polar hexanes to highly polar N,N-dimethylacetamide. For PCs having a computationally predicted lowest energy excited state not possessing CT character, their ability to operate a controlled O-ATRP is decreased. This study confirms the importance of CT character in the excited state for N,N-diaryl dihydrophenazine PCs, and a deeper understanding of the activity of CT PCs has enabled the synthesis of polymers of low dispersity (<1.10) in a controlled fashion. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3017–3027     

Understanding Behavior of Polycaprolactone–Gelatin Blends under High Pressure CO<Subscript>2</Subscript>

Polycaprolactone (PCL) is widely used in biomedical applications as electrospun fibers or porous foams. As PCL is synthetic polymer, many researchers have explored blends of PCL–gelatin to combine mechanical and bioactive properties of individual components. High pressure carbon dioxide (CO2) has been studied to foam and impregnate many biocompatible polymers. In case of PCL–gelatin blends, certain compositions can be swelled reversibly under high pressure CO₂ without permanent deformation. This allows successful impregnation of PCL–gelatin blends under CO₂. This study summarizes effect of different treatments adopted during impregnation process including high pressure CO2 on several blend compositions of PCL–gelatin blends. Stress relaxation, polymer melting and dissolution were observed during several treatments which affects porosity and scaffold structure significantly. Results summarized in this study will aid in optimum selection of PCL–gelatin blend composition for biomedical applications. Furthermore, CO₂ solubility in polymers is restricted due to thermodynamic limitations but can be altered in the presence of a co-solvent to produce better foams. PCL can be foamed using supercritical CO₂. However, CO₂ foaming of PCL–gelatin blend becomes challenging to simultaneous swelling of PCL and compression of gelatin providing blend structural stability. This study has demonstrated ability of supercritical CO₂ to foam PCL–gelatin blends in presence of water to create porous structure. These foams were subjected post-fabrication crosslinking and supercritical CO₂ without losing porosity of foams. Thus, creating a strategy to use environmentally benign processes to fabricate, crosslink and impregnate porous scaffolds for biomedical applications.     

Computational study of pH‐responsive di‐lanthanide complexes

Lanthanide complexes have found extensive use as luminescent probes for biological and medical investigations. Recently, a di‐europium complex that exhibits pH‐dependent luminescence‐decay was reported, and the ligand in that complex includes a large number of ionizable sites. To better understand the pH‐dependence of luminescence‐decay of this complex, the pK _a's of all tautomers of the di‐Lu³⁺ version of this complex were calculated computationally. The calculated Boltzmann‐averaged pK _a's of the complex are 5.85, ?0.21, and ?1.47 for the di‐Lu³⁺ complex in its first, second, and third protonation states, respectively. These pK _a values across protonation states indicate that changes in luminescence‐decay rate at physiologically relevant pH may be related to first protonation event of the complex exclusively.     

One step synthesis of indirubins by reductive coupling of isatins with KBH4

One step synthesis of the natural product indirubin by reductive coupling of isatin with KBH₄ is described and a possible mechanism for the reaction is proposed. Eleven indirubin derivatives were obtained easily from the corresponding substituted isatin.     

An eco‐epidemiological predator–prey model where predators distinguish between susceptible and infected prey

A predator–prey model with disease amongst the prey and ratio‐dependent functional response for both infected and susceptible prey is proposed and its features analysed. This work is based on previous mathematical models to analyse the important ecosystem of the Salton Sea in Southern California and New Mexico where birds (particularly pelicans) prey on fish (particularly tilapia). The dynamics of the system around each of the ecologically meaningful equilibria are presented. Natural disease control is considered before studying the impact of the disease in the absence of predators and the interaction of predators and healthy prey and the disease effects on predators in the absence of healthy prey. Our theoretical results are confirmed by numerical simulation. Copyright © 2016 John Wiley & Sons, Ltd.     

Bayesian Model Assessment in Joint Modeling of Longitudinal and Survival Data With Applications to Cancer Clinical Trials

Joint models for longitudinal and survival data are routinely used in clinical trials or other studies to assess a treatment effect while accounting for longitudinal measures such as patient-reported outcomes. In the Bayesian framework, the deviance information criterion (DIC) and the logarithm of the pseudo-marginal likelihood (LPML) are two well-known Bayesian criteria for comparing joint models. However, these criteria do not provide separate assessments of each component of the joint model. In this article, we develop a novel decomposition of DIC and LPML to assess the fit of the longitudinal and survival components of the joint model, separately. Based on this decomposition, we then propose new Bayesian model assessment criteria, namely, ΔDIC and ΔLPML, to determine the importance and contribution of the longitudinal (survival) data to the model fit of the survival (longitudinal) data. Moreover, we develop an efficient Monte Carlo method for computing the conditional predictive ordinate statistics in the joint modeling setting. A simulation study is conducted to examine the empirical performance of the proposed criteria and the proposed methodology is further applied to a case study in mesothelioma. Supplementary materials for this article are available online.     

Dirichlet product for boolean functions

Boolean functions play an important role in many symmetric cryptosystems and are crucial for their security. It is important to design boolean functions with reliable cryptographic properties such as balancedness and nonlinearity. Most of these properties are based on specific structures such as Möbius transform and Algebraic Normal Form. In this paper, we introduce the notion of Dirichlet product and use it to study the arithmetical properties of boolean functions. We show that, with the Dirichlet product, the set of boolean functions is an Abelian monoid with interesting algebraic structure. In addition, we apply the Dirichlet product to the sub-family of coincident functions and exhibit many properties satisfied by such functions.