Monte Carlo Protein Folding: Simulations of Met-Enkephalin with Solvent-Accessible Area Parameterizations

Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of Metropolis simulations of the brain peptide Met-Enkephalin. For the phenomenological energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied that had been proposed by previous authors. The simulations are compared with each other, with simulations with a distance dependent electrostatic permittivity $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and a recently proposed biased Metropolis technique are employed and their performances are evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other sets, selected configurations are minimized in search of the global energy minima. Unique minima are found for the vacuum and the $\epsilon(r)$ system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, autocorrelation times vary dramatically with the ASP parameters. Three ASP sets have much smaller autocorrelations at 300 K than the vacuum simulations, opening the possibility that simulations can be speeded up vastly by judiciously chosing details of the forceComment: 10 pages; published in "NIC Symposium 2004", eds. D. Wolf at el. (NIC, Juelich, 2004

Biochemical characterization of the Arctic char (<it>Salvelinus alpinus</it>) ovarian progestin membrane receptor

<p>Abstract</p> <p>Membrane progestin receptors are involved in oocyte maturation in teleosts. However, the maturation-inducing steroid (MIS) does not appear to be conserved among species and several progestins may fulfill this function. So far, complete biochemical characterization has only been performed on a few species. In the present study we have characterized the membrane progestin receptor in Arctic char (Salvelinus alpinu<it>s</it>) and show that the 17,20beta-dihydroxy-4-pregnen-3-one (17,20beta-P) receptor also binds several xenobiotics, thus rendering oocyte maturation sensitive to environmental pollutants. We identified a single class of high affinity (K_d, 13.8 ± 1.1 nM), low capacity (B_max, 1.6 ± 0.6 pmol/g ovary) binding sites by saturation and Scatchard analyses. Receptor binding displayed rapid association and dissociation kinetics typical of steroid membrane receptors, with t_1/2s of less than 1 minute. The 17,20beta-P binding also displayed tissue specificity with high, saturable, and specific 17,20beta-P binding detected in ovaries, heart and gills while no specific binding was observed in muscle, brain or liver. Changes in 17,20beta-P binding during oocyte maturation were consistent with its identity as the oocyte MIS membrane receptor. Incubation of fully-grown ovarian follicles with gonadotropin induced oocyte maturation, which was accompanied by a five-fold increase in 17,20beta-P receptor binding. In addition, competition studies with a variety of steroids revealed that receptor binding is highly specific for 17,20beta-P, the likely maturation-inducing steroid (MIS) in Arctic char. The relative-binding affinities of all the other progestogens and steroids tested were less than 5% of that of 17,20beta-P for the receptor. Several ortho, para derivatives of DDT also showed weak binding affinity for the 17,20beta-P receptor supporting the hypothesis that xenobiotics may bind steroid receptors on the oocyte's surface and might thereby interfere with oocyte growth and maturation.</p

Politics of codification in Meiji Japan (1868-1912) : Comparative perspective of position of customary law in Japanese civil code

Article

Slave: persons and property? : The Roman law on slavery and its reception in Western Europe and its overseas territories

In Roman law, slaves were regarded as objects that could be the property of somebody else. Since slaves were also human beings, an ingerent ambivalence was inextricably connected to the Roman conception of slavery. The Romans did not have any moral objections to slavery, however, and did not feel the need to grant slaves at least some legal capacity. Slaves were just res and, therefore, unable to conclude a contract or enter a marriage. The Roman law on slavery did not disppear from Western Europe with the Fall of the Western Roman Empire in the fifth century. Especially in Southern Euroean countries, where slavery persisted until well into the sixteenth century, the Roman notion of slaves as "things' was still adhered to by medieval lawyers. The ambivalence that was so strongly connected to this notion became, however, increasingly problematic under the influence of Chritian theology. As a respose to this, slaves were granted a certain as a 'legal person', but only in spiritual affairs. In the fifteenth century, Western European countries started to acquire overseas territories, where slavery became an important institution. The rules regulating slavery in most of these colonies were (again) directly influenced by the relevant Roman law provisions, In the overseas territories of Spain and France, the medieval approach to slavery was predominant, meaning that slaves were legally regarded as things, as in Roman law, but at the same time enjoyed some rights as persons, especially in spiritual matters. In the colonies of the Dutch Republic, the influence of Roman law was even stronger. Consequently, slaves remained legally just res

Equality of Men and Women in Article 24 of the Japanese Constitution (1947) : The Role of Beate Sirota (1923–2012) and Beyond

Beate Sirota has been described as the ‘heroine of Japanese women’s rights’, because of her considerable contribution regarding the inclusion of a forceful provision on the rights of women in the new Constitution of Japan formulated in 1947. She performed this task as a member of the Government Section of the Supreme Commander for the Allied Powers (SCAP), a position held by General Douglas MacArthur. Her role was serendipitous because the US occupying forces did not initially intend to conduct a thorough revision of the Meiji Constitution (1890). Moreover, Sirota was not a constitutional scholar, let alone an expert on the rights of women. However, after she got involved in the drafting of a new constitution, her intimate knowledge of the position of women in Japanese society due to spending her youth in Japan proved useful. She proposed elaborate and detailed provisions on women’s rights (Article 24) in the draft of the new constitution to counter the expected resistance. Since its introduction, the provision has been a firm anchor for the proponents of the emancipation of women in Japan. This paper aims to examine the determining factors and circumstances of Article 24 of the Constitution of Japan, Sirota’s role in its realisation, and the aftermath.Article

Coarse-Grained Simulations of Membranes under Tension

We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area per lipid, the monolayer overlap, the nematic order, and pressure profiles. Both the low-temperature regime, where the membranes are in a gel phase, and the high-temperature regime, where they are in the fluid phase, are considered. In the gel state, the membrane is hardly influenced by tension. In the fluid state, high tensions lead to structural changes in the membrane, which result in different compressibility regimes. The ripple state, which is found at tension zero in the transition regime between the fluid and the gel phase, disappears under tension and gives way to an interdigitated phase. We also study the membrane fluctuations in the fluid phase. In the low tension regime the data can be fitted nicely to a suitably extended elastic theory. At higher tensions the elastic fit consistently underestimates the strength of long-wavelength fluctuations. Finally, we investigate the influence of tension on the effective interaction between simple transmembrane inclusions and show that tension can be used to tune the hydrophobic mismatch interaction between membrane proteins.Comment: 14 pages, 14 figures, accepted for publication in The Journal of Chemical Physic

Integrable Models and Confinement in (2+1)-Dimensional Weakly-Coupled Yang-Mills Theory

We generalize the (2+1)-dimensional Yang-Mills theory to an anisotropic form with two gauge coupling constants $e$ and $e^{\prime}$. In an axial gauge, a regularized version of the Hamiltonian of this gauge theory is $H_{0}+{e^{\prime}}^{2}H_{1}$, where $H_{0}$ is the Hamiltonian of a set of (1+1)-dimensional principal chiral nonlinear sigma models. We treat $H_{1}$ as the interaction Hamiltonian. For gauge group SU(2), we use form factors of the currents of the principal chiral sigma models to compute the string tension for small $e^{\prime}$, after reviewing exact S-matrix and form-factor methods. In the anisotropic regime, the dependence of the string tension on the coupling constant is not in accord with generally-accepted dimensional arguments.Comment: Now 37 pages, Section 5 moved to an appendix, more motivation given in the introduction, a few more typos correcte

Imaging morphological details and pathological differences of red blood cells using tapping-mode AFM

The surface topography of red blood cells (RBCs) was investigated under nearphysiological conditions using atomic force microscopy (AFM). An immobilization protocol was established where RBCs are coupled via molecular bonds of the membrane glycoproteins to wheat germ agglutinin (WGA), which is covalently and flexibly tethered to the support. This results in a tight but noninvasive attachment of the cells. Using tappingmode AFM, which is known as gentle imaging mode and therefore most appropriate for soft biological samples like erythrocytes, it was possible to resolve membrane skeleton structures without major distortions or deformations of the cell surface. Significant differences in the morphology of RBCs from healthy humans and patients with systemic lupus erythematosus (SLE) were observed on topographical images. The surface of RBCs from SLE patients showed characteristic circularshaped holes with approx. 200 nm in diameter under physiological conditions, a possible morphological correlate to previously published changes in the SLE erythrocyte membrane