GPCR-OKB: the G protein coupled receptor oligomer knowledge base

Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and computational methodologies, we developed the GPCR-Oligomerization Knowledge Base (GPCR-OKB). GPCR-OKB is a system that supports browsing and searching for GPCR oligomer data. Such data were manually derived from the literature. While focused on GPCR oligomers, GPCR-OKB is seamlessly connected to GPCRDB, facilitating the correlation of information about GPCR protomers and oligomers

Continuum bound states K-long, D_{1}(2420), D_{s1}(2536) and their partners K-short, D_{1}(2400), D*_{sJ}(2463)

The very recently observed $D^{\ast}_{sJ}(2463)$ meson is described as a $J^{P}=1^{+}$ $c\bar{s}$ bound state in a unitarised meson model, owing its existence to the strong OZI-allowed $^{3}P_{0}$ coupling to the nearby $S$-wave $D^{\ast}K$ threshold. By the same non-perturbative mechanism, the narrow axial-vector $D_{s1}(2536)$ resonance shows up as a quasi-bound-state partner embedded in the $D^{\ast}K$ continuum. With the same model and parameters, it is also shown that the preliminary broad $1^{+}$ $D_{1}(2400)$ resonance and the established narrow $1^{+}$ $D_{1}(2420)$ may be similar $c\bar{n}$ partners, as a result of the strong OZI-allowed $^{3}P_{0}$ coupling to the nearby $S$-wave $D^{\ast}\pi$ threshold. The continuum bound states $D_{1}$(2420) and $D_{s1}(2536)$ are found to be mixtures of 33% $^{3}P_{1}$ and 67% $^{1}P_{1}$, whereas their partners $D_{1}(2400)$ and $D^{\ast}_{sJ}(2463)$ have more or less the opposite $^{2S+1}P_1$-state content, but additionally with some $D^{\ast}\pi$ or $D^{\ast}K$ admixture, respectively. The employed mechanism also reproduces the ratio of the $K_{L}$-$K_{S}$ mass difference and the $K_{S}$ width, by describing $K_{L}$ as a bound state embedded in the $\pi\pi$ continuum. The model's results for $J^{P}=1^{+}$ states containing one $b$ quark are also discussed.Comment: 11 pages, plain LaTeX, v2:relation to work of Kokoski and Godfrey in conclusions and more references v3:B-states included. More reference

On the regularization scheme and gauge choice ambiguities in topologically massive gauge theories

It is demonstrated that in the (2+1)-dimensional topologically massive gauge theories an agreement of the Pauli-Villars regularization scheme with the other schemes can be achieved by employing pairs of auxiliary fermions with the opposite sign masses. This approach does not introduce additional violation of discrete (P and T) symmetries. Although it breaks the local gauge symmetry only in the regulator fields' sector, its trace disappears completely after removing the regularization as a result of superrenormalizability of the model. It is shown also that analogous extension of the Pauli-Villars regularization in the vector particle sector can be used to agree the arbitrary covariant gauge results with the Landau ones. The source of ambiguities in the covariant gauges is studied in detail. It is demonstrated that in gauges that are softer in the infrared region (e.g. Coulomb or axial) nonphysical ambiguities inherent to the covariant gauges do not arise.Comment: Latex, 13 pages. Replaced mainly to change preprint references to journal one

Phenomenological Model and Phase Behavior of Saturated and Unsaturated Lipids and Cholesterol

We present a phenomenological theory for the phase behavior of ternary mixtures of cholesterol and saturated and unsaturated lipids, one which describes both liquid and gel phases, and illuminates the mechanism of the behavior. In a binary system of the lipids, the two phase separate when the saturated chains are well ordered, as in the gel phase, simply due to packing effects. In the liquid phase the saturated ones are not sufficiently well ordered for separation to occur. The addition of cholesterol, however, increases the saturated lipid order to the point that phase separation is once again favorable. For the system above the main chain transition of the saturated lipid, we can obtain phase diagrams in which there is liquid-liquid phase separation in the ternary system but not in any of the binary ones, while below that temperature we obtain the more common phase diagram in which a gel phase, rich in saturated lipid, appears in addition to the two liquid phases.Comment: 16 pages, 2 figure

New Exactly Solvable Two-Dimensional Quantum Model Not Amenable to Separation of Variables

The supersymmetric intertwining relations with second order supercharges allow to investigate new two-dimensional model which is not amenable to standard separation of variables. The corresponding potential being the two-dimensional generalization of well known one-dimensional P\"oschl-Teller model is proven to be exactly solvable for arbitrary integer value of parameter $p:$ all its bound state energy eigenvalues are found analytically, and the algorithm for analytical calculation of all wave functions is given. The shape invariance of the model and its integrability are of essential importance to obtain these results.Comment: 23 page

One-loop effective action in N=2{\cal N}=2 supersymmetric massive Yang-Mills theory

We consider the ${\cal N}=2$ supersymmetric theory of the massive Yang-Mills field formulated in the ${\cal N}=2$ harmonic superspace. The various gauge-invariant forms of writing the mass term in the action (in particular, using the Stueckelberg superfield), which result in dual formulations of the theory, are presented. We develop a gauge-invariant and explicitly supersymmetric scheme of the loop off-shell expansion of the superfield effective action. In the framework of this scheme, we calculate gauge-invariant and explicitly ${\cal N}=2$ supersymmetric one-loop counterterms including new counterterms depending on the Stueckelberg superfield. Component structure of one of these counterterms is analyzed.Comment: 18, pages, Accepted for publication in Theor. Math. Phy

Lipids modulate the conformational dynamics of a secondary multidrug transporter

Direct interactions with lipids have emerged as key determinants of the folding, structure and function of membrane proteins, but an understanding of how lipids modulate protein dynamics is still lacking. Here, we systematically explored the effects of lipids on the conformational dynamics of the proton-powered multidrug transporter LmrP from Lactococcus lactis, using the pattern of distances between spin-label pairs previously shown to report on alternating access of the protein. We uncovered, at the molecular level, how the lipid headgroups shape the conformational-energy landscape of the transporter. The model emerging from our data suggests a direct interaction between lipid headgroups and a conserved motif of charged residues that control the conformational equilibrium through an interplay of electrostatic interactions within the protein. Together, our data lay the foundation for a comprehensive model of secondary multidrug transport in lipid bilayers

Structural characteristics of endometrial receptivity at chronic endometritis

Purpose - evaluation of endometrial receptivity in women with chronic endometritis based on the study of structural features of the surface epithelium, the expression pattern of steroid hormones and leykemia-inhibitory factor in the 'implantation window.' The analysis of the morphological status of the endometrium in 76 patients (study group) with chronic endometritis and 20 gynecologically healthy women (control group) was carried out. It was established that patients with chronic endometritis observed disorder endometrial receptivity, including damage to the surface epithelium of the mucous membrane of the uterus, impaired maturation pinopodes the time 'implantation window', decreased expression of leukemia-inhibitory factor, and this hyperexpression estrogen receptors. This could be the basis of violations of reproductive function in women with chronic endometritis.Цель - оценка рецептивности эндометрия у женщин с хроническим эндометритом на основании изучения структурных особенностей поверхностного эпителия, характера экспрессии к стероидным гормонам и лейкемия-ингибирующему фактору в период «окна имплантации». Проведен анализ морфологического состояния эндометрия у 76 пациенток (основная группа) с хроническим эндометритом и 20 гинекологически здоровых женщин (группа сравнения). Установлено. что у пациенток с хроническим эндометритом наблюдается расстройство рецептивности эндометрия, включающее повреждение поверхностного эпителия слизистой оболочки матки, нарушение созревания пиноподий к моменту «окна имплантации», снижение экспрессии лейкемия-ингибирующего фактора и гиперэкспрессию рецепторов к эстрогенам. Это может лежать в основе нарушения репродуктивной функции у женщин с хроническим эндометритом