Structural and functional characterization of BaiA,an enzyme involved in secondary bile acid synthesis in human gut microbe

Despite significant influence of secondary bile acids on human health and disease, limited structural and biochemical information is available for the key gut microbial enzymes catalyzing its synthesis. Herein, we report apo‐ and cofactor bound crystal structures of BaiA2, a short chain dehydrogenase/reductase from Clostridium scindens VPI 12708 that represent the first protein structure of this pathway. The structures elucidated the basis of cofactor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the cofactor binding site seems crucial in determining cofactor specificity. Limited flexibility of Glu42 results in imminent steric and electrostatic hindrance with 2′‐phosphate group of NADP(H). Consistent with crystal structures, steady state kinetic characterization performed with both BaiA2 and BaiA1, a close homolog with 92% sequence identity, revealed specificity constant (k_cat/K_M) of NADP⁺ at least an order of magnitude lower than NAD⁺. Substitution of Glu42 with Ala improved specificity toward NADP⁺ by 10‐fold compared to wild type. The cofactor bound structure uncovered a novel nicotinamide‐hydroxyl ion (NAD⁺‐OH^?) adduct contraposing previously reported adducts. The OH^? of the adduct in BaiA2 is distal to C4 atom of nicotinamide and proximal to 2′‐hydroxyl group of the ribose moiety. Moreover, it is located at intermediary distances between terminal functional groups of active site residues Tyr157 (2.7 Å) and Lys161 (4.5 Å). Based on these observations, we propose an involvement of NAD⁺‐OH^? adduct in proton relay instead of hydride transfer as noted for previous adducts. Proteins 2014; 82:216–229. © 2013 Wiley Periodicals, Inc.     

Curcumin Alters the Salt Bridge-containing Turn Region in Amyloid β(1–42) Aggregates

Amyloid β (Aβ) fibrillar deposits in the brain are a hallmark of Alzheimer disease (AD). Curcumin, a common ingredient of Asian spices, is known to disrupt Aβ fibril formation and to reduce AD pathology in mouse models. Understanding the structural changes induced by curcumin can potentially lead to AD pharmaceutical agents with inherent bio-compatibility. Here, we use solid-state NMR spectroscopy to investigate the structural modifications of amyloid β(1–42) (Aβ₄₂) aggregates induced by curcumin. We find that curcumin induces major structural changes in the Asp-23–Lys-28 salt bridge region and near the C terminus. Electron microscopy shows that the Aβ₄₂ fibrils are disrupted by curcumin. Surprisingly, some of these alterations are similar to those reported for Zn²⁺ ions, another agent known to disrupt the fibrils and alter Aβ₄₂ toxicity. Our results suggest the existence of a structurally related family of quasi-fibrillar conformers of Aβ₄₂, which is stabilized both by curcumin and by Zn^2+.     

Ionic liquids as solvents for biopolymers: Acylation of starch and zein protein

Biopolymers such as starch and zein protein were found to be soluble at 80 °C in ionic liquids such as 1-butyl-3-methylimidazolium chloride (BMIMCl) and 1-butyl-3-methylimidazolium dicyanamide (BMIMdca) in concentrations up to 10% (w/w). Higher concentrations of biopolymers in these novel solvents resulted in solutions with too high viscosity to stir. Solutions of both starch and zein in BMIMCl were acylated with anhydrides in presence of pyridine to give acetyl starch and benzoyl zein with various degrees of substitution. Without pyridine the acylation reaction did not proceed. ¹H NMR and IR spectroscopies were used to determine the degree of substitution of starch. Viscosity studies indicated that the starch underwent slight reduction in molecular weight during the course of acylation. Starch was also soluble in other non-conventional solvents such as choline chloride/oxalic acid and choline chloride/ZnCl₂. However, zein was insoluble in these solvents.     

Sucrose metabolism of perennial ryegrass in relation to cold acclimation

Sugar metabolism is one of the important factors involved in winter hardiness and since the discovery of sucrose biosynthesis, considerable advances have been made in understanding its regulation and crucial role. This investigation examined the changes in activities of sucrose metabolizing enzymes and sugar content during cold hardening of perennial ryegrass (Lolium perenne L.). Changes in acid invertase (AI), sucrose synthase (SS) and sucrose phosphate synthase (SPS) along with all the three soluble sugars glucose, fructose and sucrose were measured in leaves and stem base tissue during cold acclimation. Although fructans were the predominant carbohydrate the changes in glucose, fructose and sucrose were significant. All the three soluble sugars in both leaf and stem tissues started to decrease from the first day and continued up to day 7 and thereafter started to increase until day 28. AI in the soluble fraction showed a higher activity than that in the cell wall bound fraction. In both the leaf and stem bases soluble AI activity increased during the first week and after that it started to decrease gradually. On the other hand both the SS and SPS increased gradually throughout the acclimation period. Sucrose content was negatively correlated with AI and positively correlated with SS and SPS accounting well for the relation between the substrate and enzyme activity. These results suggest that AI, SS and SPS in ryegrass are regulated by cold acclimation and play an important role in sugar accumulation and acquisition of freezing tolerance.     

Conventional and newly developed bioheat transport models in vascularized tissues: A review

Heat transfer in a biological system is a complex process and its analysis is difficult. Heterogeneous vascular architecture, blood flow in the complex network of arteries and veins, varying metabolic heat generation rates and dependence of tissue properties on its physiological condition contribute to this complexity. The understanding of heat transfer in human body is important for better insight of thermoregulatory mechanism and physiological conditions. Its understanding is also important for accurate prediction of thermal transport and temperature distribution during biomedical applications. During the last three decades, many attempts have been made by researchers to model the complex thermal behavior of the human body. These models, viz., blood perfusion, countercurrent, thermal phase-lag, porous-media, perturbation, radiation, etc. have their corresponding strengths and limitations. Along with their biomedical applications, this article reviews various contextual issues associated with these models. After brief discussion of early bioheat models, the newly developed bioheat models are discussed in detail. Dependence of these models on biological properties, viz., thermophysical and optical properties are also discussed.     

Zn(++) binding disrupts the Asp(23)-Lys(28) salt bridge without altering the hairpin-shaped cross-β Structure of Aβ(42) amyloid aggregates

Observations like high Zn²⁺ concentrations in senile plaques found in the brains of Alzheimer''s patients and evidences emphasizing the role of Zn²⁺ in amyloid-β (Aβ)-induced toxicity have triggered wide interest in understanding the nature of Zn²⁺-Aβ interaction. In vivo and in vitro studies have shown that aggregation kinetics, toxicity, and morphology of Aβ aggregates are perturbed in the presence of Zn²⁺. Structural studies have revealed that Zn²⁺ has a binding site in the N-terminal region of monomeric Aβ, but not much is precisely known about the nature of binding of Zn²⁺ with aggregated forms of Aβ or its effect on the molecular structure of these aggregates. Here, we explore this aspect of the Zn²⁺-Aβ interaction using one- and two-dimensional ¹³C and ¹⁵N solid-state NMR. We find that Zn²⁺ causes major structural changes in the N-terminal and the loop region connecting the two β-sheets. It breaks the salt bridge between the side chains of Asp²³ and Lys²⁸ by driving these residues into nonsalt-bridge-forming conformations. However, the cross-β structure of Aβ₄₂ aggregates remains unperturbed though the fibrillar morphology changes distinctly. We conclude that the salt bridge is not important for defining the characteristic molecular architecture of Aβ₄₂ but is significant for determining its fibrillar morphology and toxicity.     

Design for rectangular hyperbolic crop–weed competition

Fitting curves to data rather than doing multiple pairwise comparisons necessitates consideration of design. For the rectangular hyperbolic model of crop‐weed competition, emphasising extreme weed densities is shown to be efficient relative to experiments using a traditional design.     

9-Phenyl acridine exhibits antitumour activity by inducing apoptosis in A375 cells

Several acridine derivatives have been screened for their therapeutic potential and some are already established as antiprotozoan, antibacterial or anticancer agents. However, phenyl derivative at C-9 position of acridine had remained unexplored for their biological activity so far. In this report, we present our findings with 9-phenyl acridine (ACPH) as an anticancer agent. Both A375 and HeLa, two human cancer cell lines, were more sensitive to ACPH than normal cells namely human lymphocytes and also Chinese hamster V79 cells. ACPH also led to regression of tumour volume in mice. In A375 cells, we have shown that it caused DNA damage and blocked cell cycle progression at G(2)-M phase. Treatment with ACPH led to lowering of mitochondrial potential, upregulation of bax, release of cytochrome C and activation of caspase 3. As a new agent showing lower toxicity to normal cells and greater sensitivity towards cancerous cell line, ACPH shows promise as an effective cancer chemotherapeutic agent. ACPH treatment resulted in apoptotic death of cells through mitochondria-mediated caspase-dependent pathway.     

Obesity,a major risk factor for immunity and severe outcomes of COVID-19

An influenza-like virus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for COVID-19 disease and spread worldwide within a short time. COVID-19 has now become a significant concern for public health. Obesity is highly prevalent worldwide and is considered a risk factor for impairing the adaptive immune system. Although diabetes, hypertension, cardiovascular disease (CVD), and renal failure are considered the risk factors for COVID-19, obesity is not yet well-considered. The present study approaches establishing a systemic association between the prevalence of obesity and its impact on immunity concerning the severe outcomes of COVID-19 utilizing existing knowledge. Overall study outcomes documented the worldwide prevalence of obesity, its effects on immunity, and a possible underlying mechanism covering obesity-related risk pathways for the severe outcomes of COVID-19. Overall understanding from the present study is that being an immune system impairing factor, the role of obesity in the severe outcomes of COVID-19 is worthy.     

A comparative spectroscopic and calorimetric investigation of the interaction of amsacrine with heme proteins,hemoglobin and myoglobin

The binding of the anilido aminoacridine derivative amsacrine with the heme proteins, hemoglobin, and myoglobin, was characterized by various spectroscopic and calorimetric methods. The binding affinity to hemoglobin was (1.21?±?.05) × 10⁵ M^?1, while that to myoglobin was three times higher (3.59?±?.15) × 10⁵ M^?1. The temperature-dependent fluorescence study confirmed the formation of ground-state complexes with both the proteins. The stronger binding to myoglobin was confirmed from both spectroscopic and calorimetric studies. The binding was exothermic in both cases at the three temperatures studied, and was favored by both enthalpy and entropy changes. Circular dichroism results, three-dimensional (3D) and synchronous fluorescence studies confirmed that the binding of amsacrine significantly changed the secondary structure of hemoglobin, while the change in the secondary structure of myoglobin was much less. New insights, in terms of structural and energetic aspects of the interaction of amsacrine with the heme proteins, presented here may help in understanding the structure-activity relationship, therapeutic efficacy, and drug design aspects of acridines.