On the characterization and selection of diverse conformational ensembles with applications to flexible docking

To address challenging flexible docking problems, a number of docking algorithms pregenerate large collections of candidate conformers. To remove the redundancy from such ensembles, a central problem in this context is to report a selection of conformers maximizing some geometric diversity criterion. We make three contributions to this problem. First, we resort to geometric optimization so as to report selections maximizing the molecular volume or molecular surface area (MSA) of the selection. Greedy strategies are developed, together with approximation bounds. Second, to assess the efficacy of our algorithms, we investigate two conformer ensembles corresponding to a flexible loop of four protein complexes. By focusing on the MSA of the selection, we show that our strategy matches the MSA of standard selection methods, but resorting to a number of conformers between one and two orders of magnitude smaller. This observation is qualitatively explained using the Betti numbers of the union of balls of the selection. Finally, we replace the conformer selection problem in the context of multiple-copy flexible docking. On the aforementioned systems, we show that using the loops selected by our strategy can improve the result of the docking process.     

Positional cloning of a type 2 diabetes quantitative trait locus; tomosyn-2, a negative regulator of insulin secretion

We previously mapped a type 2 diabetes (T2D) locus on chromosome 16 (Chr 16) in an F2 intercross from the BTBR T (+) tf (BTBR) Lep(ob/ob) and C57BL/6 (B6) Lep(ob/ob) mouse strains. Introgression of BTBR Chr 16 into B6 mice resulted in a consomic mouse with reduced fasting plasma insulin and elevated glucose levels. We derived a panel of sub-congenic mice and narrowed the diabetes susceptibility locus to a 1.6 Mb region. Introgression of this 1.6 Mb fragment of the BTBR Chr 16 into lean B6 mice (B6.16(BT36-38)) replicated the phenotypes of the consomic mice. Pancreatic islets from the B6.16(BT36-38) mice were defective in the second phase of the insulin secretion, suggesting that the 1.6 Mb region encodes a regulator of insulin secretion. Within this region, syntaxin-binding protein 5-like (Stxbp5l) or tomosyn-2 was the only gene with an expression difference and a non-synonymous coding single nucleotide polymorphism (SNP) between the B6 and BTBR alleles. Overexpression of the b-tomosyn-2 isoform in the pancreatic β-cell line, INS1 (832/13), resulted in an inhibition of insulin secretion in response to 3 mM 8-bromo cAMP at 7 mM glucose. In vitro binding experiments showed that tomosyn-2 binds recombinant syntaxin-1A and syntaxin-4, key proteins that are involved in insulin secretion via formation of the SNARE complex. The B6 form of tomosyn-2 is more susceptible to proteasomal degradation than the BTBR form, establishing a functional role for the coding SNP in tomosyn-2. We conclude that tomosyn-2 is the major gene responsible for the T2D Chr 16 quantitative trait locus (QTL) we mapped in our mouse cross. Our findings suggest that tomosyn-2 is a key negative regulator of insulin secretion.     

Telomeric injury by KML001 in human T cells induces mitochondrial dysfunction through the p53-PGC-1α pathway

Telomere erosion and mitochondrial dysfunction are prominent features of aging cells with progressive declines of cellular functions. Whether telomere injury induces mitochondrial dysfunction in human T lymphocytes, the major component of adaptive host immunity against infection and malignancy, remains unclear. We have recently shown that disruption of telomere integrity by KML001, a telomere-targeting drug, induces T cell senescence and apoptosis via the telomeric DNA damage response (DDR). In this study, we used KML001 to further investigate the role and mechanism of telomere injury in mitochondrial dysregulation in aging T cells. We demonstrate that targeting telomeres by KML001 induces mitochondrial dysfunction, as evidenced by increased mitochondrial swelling and decreased mitochondrial membrane potential, oxidative phosphorylation, mitochondrial DNA content, mitochondrial respiration, oxygen consumption, glycolysis, and ATP energy production. Mechanistically, we found that the KML001-induced telomeric DDR activated p53 signaling, which in turn repressed the expression of peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α) and nuclear respiratory factor 1 (NRF-1), leading to T cell mitochondrial dysfunction. These results, forging a direct link between telomeric and mitochondrial biology, shed new light on the human T cell aging network, and demonstrate that the p53-PGC-1α-NRF-1 axis contributes to mitochondrial dysfunction in the setting of telomeric DDR. This study suggests that targeting this axis may offer an alternative, novel approach to prevent telomere damage-mediated mitochondrial and T cell dysfunctions to combat a wide range of immune aging-associated human diseases.Subject terms: Immunology, Diseases     

Design and development of novel N-(pyrimidin-2-yl)-1,3,4-oxadiazole hybrids to treat cognitive dysfunctions

Novel hybrids bearing a 2-aminopyrimidine (2-AP) moiety linked to substituted 1,3,4-oxadiazoles were designed, synthesized and biologically evaluated. Among the developed compounds, 28 noncompetitively inhibited human acetylcholinesterase (hAChE; pIC₅₀?=?6.52; Ki?=?0.17?µM) and showed potential in vitro antioxidant activity (60.0%) when evaluated using the Ellman’s and DPPH assays, respectively. Compound 28 competitively displaced propidium iodide (PI) from the peripheral anionic site (PAS) of hAChE (17.6%) and showed high blood-brain barrier (BBB) permeability, as observed in the PAMPA-BBB assay. Additionally, compound 28 inhibited hAChE-induced Aβ aggregation in a concentration-dependent manner according to the thioflavin T assay and was devoid of neurotoxic liability towards SH-SY5Y cell lines, as demonstrated by the MTT assay. The behavioral studies of compound 28 in mice showed a significant reversal of scopolamine-induced amnesia, as observed in Y-maze and passive avoidance tests. Furthermore, compound 28 exhibited significant AChE inhibition in the brain in ex vivo studies. An evaluation of oxidative stress biomarkers revealed the antioxidant potential of 28. Moreover, in silico molecular docking and dynamics simulation studies were used as a computational tool to evaluate the interactions of compound 28 with the active site residues of hAChE.     

Selective oxidative stress induces dual damage to telomeres and mitochondria in human T cells

Oxidative stress caused by excess reactive oxygen species (ROS) accelerates telomere erosion and mitochondrial injury, leading to impaired cellular functions and cell death. Whether oxidative stress‐mediated telomere erosion induces mitochondrial injury, or vice versa, in human T cells—the major effectors of host adaptive immunity against infection and malignancy—is poorly understood due to the pleiotropic effects of ROS. Here we employed a novel chemoptogenetic tool that selectively produces a single oxygen (¹O₂) only at telomeres or mitochondria in Jurkat T cells. We found that targeted ¹O₂ production at telomeres triggered not only telomeric DNA damage but also mitochondrial dysfunction, resulting in T cell apoptotic death. Conversely, targeted ¹O₂ formation at mitochondria induced not only mitochondrial injury but also telomeric DNA damage, leading to cellular crisis and apoptosis. Targeted oxidative stress at either telomeres or mitochondria increased ROS production, whereas blocking ROS formation during oxidative stress reversed the telomeric injury, mitochondrial dysfunction, and cellular apoptosis. Notably, the X‐ray repair cross‐complementing protein 1 (XRCC1) in the base excision repair (BER) pathway and multiple mitochondrial proteins in other cellular pathways were dysregulated by the targeted oxidative stress. By confining singlet ¹O₂ formation to a single organelle, this study suggests that oxidative stress induces dual injury in T cells via crosstalk between telomeres and mitochondria. Further identification of these oxidation pathways may offer a novel approach to preserve mitochondrial functions, protect telomere integrity, and maintain T cell survival, which can be exploited to combat various immune aging‐associated diseases.     

Health Risk Assessment Due to Groundwater Arsenic Contamination: Children Are at High Risk

Health risk assessment due to groundwater As contamination was conducted in two As-prone panchayats, Rampur Diara (RD) and Haldichapra (HC) of the Maner block of the Patna district, Bihar (India). All 100% of the water samples surveyed were found to be contaminated with As with a mean value of 52 μg/L (n = 10) in RD and 231 μg/L (n = 10) in HC, both exceeding the World Health Organization (WHO) guideline of 10 μg/L and the Bureau of Indian Standards (BIS) standard of 50 μg/L, respectively. The average calculated per capita consumption of As through drinking water in RD ranged from 120 μg/day for 5–10-year-old children to 320 μg/day for adults older than 41 years, while in HC the average calculated As through consumption ranged from 580 μg/day for 5–10-year-old children to 1470 μg/day for adults older than 41 years. Hazard quotients were calculated to be between 12.1 to 41.6 for the RD population and 58.3 to 192.5 for the HC population, both exceeding the typical toxic risk index 1. In addition, cancer risk of 19 per 1000 was found for RD children and 87 per 1000 for HC children. Visible symptoms of Arsenicosis were also observed in the area.     

Differential Activity of Stanniocalcin in Male and Female Fresh Water Teleost Mastacembelus armatus (Lacepede) during Gonadal Maturation

The present study was carried out to analyze the differences in the activity of hormone stanniocalcin (STC) between male and female fishes of Mastacembelus armatus during their gonadal cycle. A large variation in nuclear diameter of cells of corpuscles of Stannius (CS) were recorded in relation to testicular cycle as well as ovarian cycle which indicates that the cellular activity varied with different phases of reproductive cycle in both male and female fish. Similar changes in nuclear diameter of CS cells were also observed after 17alpha-methyltestosterone administration in males and 17 β-estradiol administrations in females. A positive correlation was observed between plasma STC levels, gonadosomatic index (GSI) and the sex steroids in both sexes, suggesting that STC has a role in the processes involved in gonadal development. In addition females showed remarkable changes in plasma calcium level during gonadal cycle while no such change for males were observed. In females the plasma calcium level estimated during different phases of reproductive cycle indicates positive correlation between plasma level of calcium and gonad growth. Thus hyperactivity of CS cells was noted in both male and female fishes during gonadal cycle along with the differences in the activity of STC as well. In female it may act as hypocalcemic factor and bring the level of calcium to normal which increases during preparatory and pre spawning phases to fulfill the increased demand of calcium for vitellogenesis. However data of male fishes indicated that plasma STC concentration varied widely during gonadal cycle but showed no consistent relationship to plasma calcium level.     

Structural basis for promoter DNA recognition by the response regulator OmpR

OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR–DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc–DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this “druggable” target.     

Novel red colour emitting Ca0.995Mg2(SO4)3:0.5Eu2+ phosphor under ultraviolet,blue, and green excitation for plant growth LEDs

In the recent few years, Eu²⁺- and Mn⁴⁺-activated phosphors are widely used as potential colour converters for indoor plant cultivation lighting application due to their marvellous luminescence characteristics as well as low cost. In this investigation, we synthesized novel red colour-emitting Ca_(2−x)Mg₂(SO₄)₃:xmol% Eu²⁺ (x = 0–1.0 mol%) phosphors via a solid-state reaction method in a reducing atmosphere. The photoluminescence (PL) excitation spectra of synthesized phosphors exhibited a broad excitation band with three excitation bands peaking at 349 nm, 494 nm, and 554 nm. Under these excitations, emission spectra exhibited a broad band in the red colour region at ~634 nm. The PL emission intensity was measured for different concentrations of Eu²⁺. The maximum Eu²⁺ doping concentration in the Ca₂Mg₂(SO₄)₃ host was observed for 0.5 mol%. According to Dexter theory, it was determined that dipole–dipole interaction was responsible for the concentration quenching. The luminous red colour emission of the sample was confirmed using Commission international de l'eclairage colour coordinates. The results of PL excitation and emission spectra of the prepared phosphors were well matched with excitation and emission wavelengths of phytochrome P_R. Therefore, from the entire investigation and obtained results it was concluded that the synthesized Ca_0.995Mg₂(SO₄)₃:0.5mol%Eu²⁺ phosphor has huge potential for plant cultivation application.