Substitution, cooperative, and solvent effects on π pnicogen bonds in the FH2P and FH2As complexes

Ab initio calculations have been carried out to study the substitution effect on the π pnicogen bond in ZH(2)P-C(2)HM (Z?=?H, H(3)C, NC, F; M?=?H, CH(3), Li) dimer, cooperative effect of the π pnicogen bond and hydrogen bond in XH-FH(2)Y-C(2)H(4) (X?=?HO, NC, F; Y?=?P and As) trimer, and solvent effect on the π pnicogen bond in FH(2)P-C(2)H(2), FH(2)P-C(2)H(4), FH(2)As-C(2)H(2), and FH(2)As-C(2)H(4) dimers. The interaction energy of π pnicogen bond increases in magnitude from -1.51?kcal?mol(-1) in H(3)P-C(2)H(2) dimer to -7.53?kcal?mol(-1) in FH(2)P-C(2)HLi dimer at the MP2/aug-cc-pVTZ level. The π pnicogen bond is enhanced by 12-30?% due to the presence of hydrogen bond in the trimer. The π pnicogen bond is also enhanced in solvents. The natural bond orbital analysis and symmetry adapted perturbation theory (SAPT) were used to unveil the source of substitution, cooperative, and solvent effects.     

cPLA2α and EHD1 interact and regulate the vesiculation of cholesterol-rich, GPI-anchored, protein-containing endosomes

The lipid modifier phospholipase A2 catalyzes the hydrolysis of phospholipids to inverted-cone-shaped lysophospholipids that contribute to membrane curvature and/or tubulation. Conflicting findings exist regarding the function of cytosolic phospholipase A2 (cPLA2) and its role in membrane regulation at the Golgi and early endosomes. However, no studies addressed the role of cPLA2 in the regulation of cholesterol-rich membranes that contain glycosylphosphatidylinositol-anchored proteins (GPI-APs). Our studies support a role for cPLA2α in the vesiculation of GPI-AP-containing membranes, using endogenous CD59 as a model for GPI-APs. On cPLA2α depletion, CD59-containing endosomes became hypertubular. Moreover, accumulation of lysophospholipids induced by a lysophospholipid acyltransferase inhibitor extensively vesiculated CD59-containing endosomes. However, overexpression of cPLA2α did not increase the endosomal vesiculation, implying a requirement for additional factors. Indeed, depletion of the "pinchase" EHD1, a C-terminal Eps15 homology domain (EHD) ATPase, also induced hypertubulation of CD59-containing endosomes. Furthermore, EHD1 and cPLA2α demonstrated in situ proximity (<40 nm) and interacted in vivo. The results presented here provide evidence that the lipid modifier cPLA2α and EHD1 are involved in the vesiculation of CD59-containing endosomes. We speculate that cPLA2α induces membrane curvature and allows EHD1, possibly in the context of a complex, to sever the curved membranes into vesicles.     

Drugging the undruggable: gabapentin,pregabalin and the calcium channel α2δ subunit

In the post-genomic era, the idea of using the sequence of a protein to determine its potential role as a drug target has gained currency. The goal of this approach to drug discovery is to use the sequence of a protein that is known to bind a specific ligand or drug, along with the known structure of the ligand binding site, to predict other similar proteins that are also “druggable”. Gabapentin (Neurontin) and pregabalin (Lyrica) are drugs currently in the clinic that were developed based on the hypothesis that generating non-hydrolyzable analogs of GABA would lead to the development of antiepileptic agents. While these compounds are indeed good anticonvulsants, their activity is surprisingly not due to activity in the GABAergic system. By purifying the protein to which gabapentin bound, and determining its identity as the α₂δ₁ subunit of voltage gated calcium channels, it was possible to make progress in developing new compounds with similar activities to gabapentin, including pregabalin. The recognition of the α₂δ₁ subunit as the receptor for these drugs also meant that related proteins, such as α₂δ₃, may be interesting targets for novel pain therapeutics.     

Phytochemicals: the good, the bad and the ugly?

Phytochemicals are constitutive metabolites that enable plants to overcome temporary or continuous threats integral to their environment, while also controlling essential functions of growth and reproduction. All of these roles are generally advantageous to the producing organisms but the inherent biological activity of such constituents often causes dramatic adverse consequences in other organisms that may be exposed to them. Nevertheless, such effects may be the essential indicator of desirable properties, such as therapeutic potential, especially when the mechanism of bioactivity can be delineated. Careful observation of cause and effect, followed by a coordinated approach to identify the responsible entities, has proved extremely fruitful in discovering roles for phytochemical constituents. The process is illustrated by selected examples of plants poisonous to animals and include the steroidal alkaloid toxin of Veratrum californicum (Western false hellebore), piperidine alkaloids of Lupinus species (lupines), and polyhydroxy indolizidine, pyrrolizidine and nortropane alkaloids of Astragalus and Oxytropis species (locoweeds), Castanospermum australe (Moreton Bay chestnut) and Ipomoea species (morning glories).     

DE-loop mutations affect ��2 microglobulin stability, oligomerization, and the low-pH unfolded form

β2 microglobulin (β2m) is the light chain of class‐I major histocompatibility complex (MHC‐I). Its accumulation in the blood of patients affected by kidney failure leads to amyloid deposition around skeletal joints and bones, a severe condition known as Dialysis Related Amyloidosis (DRA). In an effort to dissect the structural determinants of β2m aggregation, several β2m mutants have been previously studied. Among these, three single‐residue mutations in the loop connecting strands D and E (W60G, W60V, D59P) have been shown to affect β2m amyloidogenic properties, and are here considered. To investigate the biochemical and biophysical properties of wild‐type (w.t.) β2m and the three mutants, we explored thermal unfolding by Trp fluorescence and circular dichroism (CD). The W60G mutant reveals a pronounced increase in conformational stability. Protein oligomerization and reduction kinetics were investigated by electrospray‐ionization mass spectrometry (ESI‐MS). All the mutations analyzed here reduce the protein propensity to form soluble oligomers, suggesting a role for the DE‐loop in intermolecular interactions. A partially folded intermediate, which may be involved in protein aggregation induced by acids, accumulates for all the tested proteins at pH 2.5 under oxidizing conditions. Moreover, the kinetics of disulfide reduction reveals specific differences among the tested mutants. Thus, β2m DE‐loop mutations display long‐range effects, affecting stability and structural properties of the native protein and its low‐pH intermediate. The evidence presented here hints to a crucial role played by the DE‐loop in determining the overall properties of native and partially folded β2m.     

Endothelial NO and O2− production rates differentially regulate oxidative,nitroxidative, and nitrosative stress in the microcirculation

Endothelial dysfunction causes an imbalance in endothelial NO and O₂⁻ production rates and increased peroxynitrite formation. Peroxynitrite and its decomposition products cause multiple deleterious effects including tyrosine nitration of proteins, superoxide dismutase (SOD) inactivation, and tissue damage. Studies have shown that peroxynitrite formation during endothelial dysfunction is strongly dependent on the NO and O₂⁻ production rates. Previous experimental and modeling studies examining the role of NO and O₂⁻ production imbalance on peroxynitrite formation showed different results in biological and synthetic systems. However, there is a lack of quantitative information about the formation and biological relevance of peroxynitrite under oxidative, nitroxidative, and nitrosative stress conditions in the microcirculation. We developed a computational biotransport model to examine the role of endothelial NO and O₂⁻ production on the complex biochemical NO and O₂⁻ interactions in the microcirculation. We also modeled the effect of variability in SOD expression and activity during oxidative stress. The results showed that peroxynitrite concentration increased with increase in either O₂⁻ to NO or NO to O₂⁻ production rate ratio (Q_O2⁻/Q_NO or Q_NO/Q_O2⁻, respectively). The peroxynitrite concentrations were similar for both production rate ratios, indicating that peroxynitrite-related nitroxidative and nitrosative stresses may be similar in endothelial dysfunction or inducible NO synthase (iNOS)-induced NO production. The endothelial peroxynitrite concentration increased with increase in both Q_O2⁻/Q_NO and Q_NO/Q_O2⁻ ratios at SOD concentrations of 0.1–100 μM. The absence of SOD may not mitigate the extent of peroxynitrite-mediated toxicity, as we predicted an insignificant increase in peroxynitrite levels beyond Q_O2⁻/Q_NO and Q_NO/Q_O2⁻ ratios of 1. The results support the experimental observations of biological systems and show that peroxynitrite formation increases with increase in either NO or O₂⁻ production, and excess NO production from iNOS or from NO donors during oxidative stress conditions does not reduce the extent of peroxynitrite mediated toxicity.     

The polybasic insert,the RBD of the SARS-CoV-2 spike protein,and the feline coronavirus – evolved or yet to evolve

Recent research on the SARS-CoV-2 pandemic has exploded around the furin-cleavable polybasic insert PRRAR↓S, found within the spike protein. The insert and the receptor-binding domain, (RBD), are vital clues in the Sherlock Holmes-like investigation into the origin of the virus and in its zoonotic crossover. Based on comparative analysis of the whole genome and the sequence features of the insert and the RBD domain, the bat and the pangolin have been proposed as very likely intermediary hosts. In this study, using the various databases, in-house developed tools, sequence comparisons, structure-guided docking, and molecular dynamics simulations, we cautiously present a fresh, theoretical perspective on the SARS-CoV-2 virus activation and its intermediary host. They are a) the SARS-CoV-2 has not yet acquired a fully optimal furin binding site or this seemingly less optimal sequence, PRRARS, has been selected for survival; b) in structural models of furin complexed with peptides, PRRAR↓S binds less well and with distinct differences as compared to the all basic RRKRR↓S; c) these differences may be exploited for the design of virus-specific inhibitors; d) the novel polybasic insert of SARS-CoV-2 may be promiscuous enough to be cleaved by multiple enzymes of the human airway epithelium and tissues which may explain its unexpected broad tropism; e) the RBD domain of the feline coronavirus spike protein carries residues that are responsible for high-affinity binding of the SARS-CoV-2 to the ACE 2 receptor; f) en route zoonotic transfer, the virus may have passed through the domestic cat whose very human-like ACE2 receptor and furin may have played some role in optimizing the traits required for zoonotic transfer.     

Replication and recombination functions associated with the yeast plasmid, 2μ circle

By examining both the transformation efficiency of yeast of various plasmids containing defined regions of the 2μ circle genome and the characteristics of the resultant transformants, we have identified several regions of the 2μ circle genome which are involved in 2μ circle replication or recombination. First, by identifying those DNA fragments from the molecule which promote high frequency transformation of yeast, we have localized the origin of replication to a sequence partially within the large unique region, which, as determined by subsequent deletion analysis, extends from the middle of the inverted repeat region into the contiguous unique region. Second, by examining the relative efficiency of replication in yeast of hybrid plasmids containing either the entire 2μ circle genome or a fragment of 2μ circle encompassing the origin of replication, we have determined that efficient use of the 2μ circle origin requires some function or functions encoded in the molecule at a site away from the origin. Third, by examining the ability of a mutant 2μ circle molecule to undergo intramolecular recombination in yeast, we have identified a 2μ circle gene which codes for a product required for this process.     

Mitochondrial Morphogenesis,Dendrite Development,and Synapse Formation in Cerebellum Require both Bcl-w and the Glutamate Receptor δ2

Bcl-w belongs to the prosurvival group of the Bcl-2 family, while the glutamate receptor δ2 (Grid2) is an excitatory receptor that is specifically expressed in Purkinje cells, and required for Purkinje cell synapse formation. A recently published result as well as our own findings have shown that Bcl-w can physically interact with an autophagy protein, Beclin1, which in turn has been shown previously to form a protein complex with the intracellular domain of Grid2 and an adaptor protein, nPIST. This suggests that Bcl-w and Grid2 might interact genetically to regulate mitochondria, autophagy, and neuronal function. In this study, we investigated this genetic interaction of Bcl-w and Grid2 through analysis of single and double mutant mice of these two proteins using a combination of histological and behavior tests. It was found that Bcl-w does not control the cell number in mouse brain, but promotes what is likely to be the mitochondrial fission in Purkinje cell dendrites, and is required for synapse formation and motor learning in cerebellum, and that Grid2 has similar phenotypes. Mice carrying the double mutations of these two genes had synergistic effects including extremely long mitochondria in Purkinje cell dendrites, and strongly aberrant Purkinje cell dendrites, spines, and synapses, and severely ataxic behavior. Bcl-w and Grid2 mutations were not found to influence the basal autophagy that is required for Purkinje cell survival, thus resulting in these phenotypes. Our results demonstrate that Bcl-w and Grid2 are two critical proteins acting in distinct pathways to regulate mitochondrial morphogenesis and control Purkinje cell dendrite development and synapse formation. We propose that the mitochondrial fission occurring during neuronal growth might be critically important for dendrite development and synapse formation, and that it can be regulated coordinately by multiple pathways including Bcl-2 and glutamate receptor family members.     

N2 fixation,and the relative contribution of fixed N,in corals from Curaçao and Hawaii

Coral Reefs - Corals from Hawaii (Montipora capitata) and the Caribbean (brown and orange morphs of Montastraea cavernosa) have previously been shown to harbor symbiotic bacteria capable of fixing...     

Serum LH,progesterone and estradiol-17β levels throughout the ovarian cycle,during the early stage of pregnancy and after the parturition and the abortion in the common marmoset,Callithrix jacchus

In the ovarian cycle of common marmosets, serum progesterone began to increase at two to three days after estradiol-17β or LH surge, attained a peak of 25–70 ng/ml and then declined to a level of under 2 ng/ml before the ensuing rise in estradiol-17β and LH. Serum estradiol-17β increased to 700–5,500 pg/ml during the luteal phase, synchronizing with progesterone. It is suggested that the corpus luteum secreted estradiol-17β as well as progesterone. The cycle length as determined from the interval between successive LH surges was approximately 28 days. During the luteal phase, the levels of progesterone and estradiol-17β were higher than in Old World monkeys and women, but marmosets were not accompanied by any clinical symptoms due to excessive progesterone and estradiol-17β. This suggests that such unresponsiveness to progesterone and estradiol-17β in marmosets reflects the small amount of estradiol-17β receptor and presumably also the lower function of the post receptor system. Recovery of the post-partum ovarian cycle in two marmosets differed from that observed in Old World monkeys and women. The first LH surge was found on the ninth and tenth day after parturition and the first ovulation led to the next pregnancy. This suggests that the suckling stimulus of newborns in the common marmoset does not cause any delay in recovery of the ovarian cycle. In three cases of abortion, the recovery of the ovarian cycle was almost the same as that in the case of normal parturition: the first LH surge appeared on the 10th, 14th, and 34th day after abortion.     

Localization of aquaporin-2, renal morphology and urine composition in the bottlenose dolphin and the Baird’s beaked whale

This study examined the distribution pattern of aquaporin-2 (AQP2), relative medullary thickness (RMT) and urine properties in the bottlenose dolphin Tursiops truncatus and Baird’s beaked whale Berardius bairdii. Immunohistochemical studies revealed that AQP2 was localized in the collecting tubules/ducts of both species’ renicules, as in terrestrial mammals. The collecting ducts with AQP2 were thinner and arranged more densely in the dolphin than in the whale. RMT values in the renicule were moderate in both species, but were significantly higher in the dolphin (6.0 ± 0.9) than the whale (4.9 ± 0.7). Urine of the bottlenose dolphin is comparatively concentrated (osmolality: 1715.7 ± 279.4 mOsm kg⁻¹, Na⁺: 490.1 ± 87.9 mmol l⁻¹, Cl⁻: 402.7 ± 79.6 mmol l⁻¹, K⁺: 80.7 ± 25.8 mmol l⁻¹, urea nitrogen: 703.5 ± 253.9 mmol l⁻¹), while urine of the dead Baird’s beaked whale is less concentrated (osmolality: 837.5 ± 293.8 mOsm kg⁻¹, Na⁺: 192.9 ± 81.5 mmol l⁻¹, Cl⁻: 159.9 ± 71.4 mmol l⁻¹, K⁺: 44.3 ± 29.5 mmol l⁻¹, urea nitrogen: 270.7 ± 120.3 mmol l⁻¹). These data suggest it is possible that the differences in these renal morphological features may be related in some way to the difference in urine composition between the species, although further studies are necessary. M. Suzuki and N. Endo are equal contributors to this study.     

Immunological investigations on the evolution of β2 II and III,IgD and inter-α-trypsininhibitor

Summary In continuation of earlier experiments on a group of 20 human plasma proteins the immunological cross-reactions between human and animal ₂-glycoprotein II, ₂ III, IgD and inter--trypsininhibitor have been investigated in an attempt to elucidate the evolution of these proteins, for which only few chemical data are available. Human ₂-glycoproteins II and III cross-react with their counterparts in the sera of gorilla gorilla, pongo pygmaeus, macaca nemestrina (group II of our nomenclature), human inter--trypsininhibitor with gorilla gorilla, pongo pygmaeus and IgD (-chain) only with gorilla gorilla sera (group I). No reaction was observed with sera of papio anubis, cebus albifrons and galago crassicaudatus as well as with sera of several non-primate mammals. No antigenic heterogeneity was demonstrable by comparative analysis in any of these 4 proteins. The results are discussed briefly in comparison with findings reported on other plasma proteins.

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Zusammentassung In Fortführung früherer Versuche über eine Gruppe von 20 menschlichen Plasmaproteinen wurden die immunologischen Kreuzreaktionen zwischen menschlichem und tierischem ₂-Glycoprotein II, ₂-Glycoprotein III, IgD und Inter--Trypsininhibitor untersucht. Damit wurde versucht, Informationen über die Evolution dieser Eiweiße zu gewinnen, von denen bisher erst wenige chemische Daten vorliegen.Die menschlichen ₂-Glycoprotein II und III zeigen Kreuzreaktionen mit ihren Homologen in den Seren von Gorilla gorilla, Pongo pygmaeus und Macaca nemestrina (Gruppe II unserer Nomenklatur), der Inter--Trypsininhibitor des Menschen mit denjenigen von Gorilla gorilla und Pongo pygmaeus und IgD (-Kette) nur mit denjenigen von Gorillaserum (Gruppe I). Mit den Seren von Papio anubis, Cebus albifrons und Galago crassicaudatus sowie von einigen Mammalia außerhalb der Primaten wurden keine Kreuzreaktionen gefunden. Bei allen vier Eiweißen war durch vergleichende Analyse kein Nachweis einer antigenen Heterogenität möglich. Die Ergebnisse werden kurz im Zusammenhang mit Befunden bei anderen Plasmaproteinen diskutiert.

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(Chief: Prof. Dr. E. Krah)     

Chemotaxis of the unicellular green algaDunaliella salina and the ciliatedTetrahymena pyriformis—effects of glycine,lysine, and alanine,and their oligopeptides

Chemotactic properties of amino acids (L-alanine, glycine and L-lysine) and their oligopeptides (10^–6M) and binding sites to these ligands were investigated in two unicellular models, the heterotrophicTetrahymena pyriformis and the auxotrophicDunaliella salina. Chemotaxis ofDunaliella induced by simple amino acids and their derivatives demonstrated that binding sites (receptors) for food molecules are not only present in the membrane but are also able to induce their basic physiological response. InTetrahymena, substances with special molecular structure and properties (polar, hydrophilic character of the signal peptide chain)-5-L-Lys, 5-Glywere required for chemoattraction, other peptides tested, lacking the required structure, were repellent. Divergences in chemotaxis and binding assays of both species suggest that trends of functional and binding parameters do not run parallel at this level of evolution.     

The relationship between B-cell lymphoma 2, interleukin-1β, interleukin-17, and interleukin-33 and the development of diabetic nephropathy

Molecular Biology Reports - Diabetic nephropathy (DN) is among the main complications of diabetes mellitus and has been a major factor of renal failure. This study was designed to address the...     

Discovery, synthesis and SAR of azinyl- and azolylbenzamides antagonists of the P2X₇ receptor

The discovery, of a series of 2-Cl-5-heteroaryl-benzamide antagonists of the P2X(7) receptor via parallel medicinal chemistry is described. Initial analogs suffered from poor metabolic stability and low Vd(ss). Multi parametric optimization led to identification of pyrazole 39 as a viable lead with excellent potency and oral bioavailability. Further attempts to improve the low Vd(ss) of 39 via introduction of amines led to analogs 40 and 41 which maintained the favorable pharmacology profile of 39 and improved Vd(ss) after iv dosing. But these analogs suffered from poor oral absorption, probably driven by poor permeability.     

Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining： relevance to cancer, aging, and the immune system

Nonhomologous DNA end joining （NHEJ） is the primary pathway for repair of double-strand DNA breaks in human cells and in multicellular eukaryotes. The causes of double-strand breaks often fragment the DNA at the site of damage, resulting in the loss of information there. NHEJ does not restore the lost information and may resect additional nucleotides during the repair process. The ability to repair a wide range of overhang and damage configurations reflects the flexibility of the nuclease, polymerases, and ligase of NHEJ. The flexibility of the individual components also explains the large number of ways in which NHEJ can repair any given pair of DNA ends. The loss of information locally at sites of NHEJ repair may contribute to cancer and aging, but the action by NHEJ ensures that entire segments of chromosomes are not lost.