Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100?ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.     

Interaction of photoperiod and nutritive state in female reproduction of Lymnaea stagnalis

Summary

A study was made of the interaction of the photoperiod and the availability of food in influencing egg laying of the freshwater snail Lymnaea stagnalis. At a long day photoperiod (LD = 16 h light/8 h dark) egg laying of fed snails had increased compared with that of fed animals kept at a medium day photoperiod (MD = 12 h light/12 h dark). In MD snails oviposition ceased within a week of the beginning of a starvation period. This is most probably due to a reduction in the activities of the neuroendocrine caudodorsal cells which secrete an ovulation hormone. In contrast, in starved LD snails a low rate of ovipository activity continued, indicating that a lowered frequency of caudodorsal cell release cycles occurred under these conditions. The decreased mean size (number of eggs) of the egg masses in starved LD snails indicates that the activities of the endocrine dorsal bodies, which control vitellogenesis and synthetic activities in the female accessory sex organs, had decreased.

All MD snails survived, but nearly all LD snails died during the course of the experiment. Determinations of the mantle glycogen stores of LD snails suggest that the high mortality of LD snails is due to exhaustion of the animal's energy reserves.     

State ethnicization and the crisis of leadership succession among Israel's Druze

States often ethnicize ethnic groups for their own purposes. In doing so, however, they unleash contradictory processes. While the state facilitates the integration of individuals into modern state structures on the basis of personal achievement, it will also traditionalize collective identity by promoting a recognized leader or headman. Over time ethnic reformers will challenge such state ethnicization and attempt to organize the community to achieve more autonomy, using state legislation to achieve these reforms. Paradoxically, this attempt, if successful, will not only encroach upon state power but also curtail the choice of the individual in the ethnic group to define his or her own ethnicity. The following article analyses the Israeli Druze's relationship to the State of Israel and the controversy among the Druze over the group's international organization. It analyses at what point state ethnicization gives way to ethnic autonomy at the expense of state power, and explores its implications on the development of civil society within the ethnic community. The diminution of state ethnicization in a democracy need not necessarily entail the empowerment of the ethnic group but rather the individual who belongs to it.     

Chocolate cities: A brief note from a race and capitalism perspective

Marcus Hunter and Zandria Robinson have provided us with an innovative methodology for analysing “maps” of African Americans’ lived political, social and cultural experiences past and present. Their powerful innovation is creating maps of the black experience based on black people’s lived experience. They argue that carefully tracing spatially blacks’ political, social and cultural patterns over time leads one to the conclusion that the shared experiences of blacks throughout the polity (and indeed throughout the Diaspora) have far more in common than not. I argue that we can better understand not only the maps that black people have created, but also chocolate cities themselves by using an analytical framework that integrates the analysis of the lived experience of black people with a structural analysis that interrogates the articulation of white supremacy, capitalism and patriarchy. This framework is related to the developing research into racial capitalism that is now being conducted globally.     

The mobilization of the ethnic vote: A thesis with some Scottish and Welsh evidence*

This article provides a historical and comparative analysis of post‐imperial migrations of ethnic unmixing. It examines the post‐Soviet migration of ethnic Russians to Russia in the light of the migrations of other once‐dominant ‘new minorities’ engendered by transitions from multinational empire to incipient nation‐states: Balkan Muslims during and after the disintegration of the Ottoman Empire, Hungarians after the collapse of the Habsburg Empire, and Germans after the collapse of the Habsburg Empire and the German Kaiserreich.     

The case in international law for Canada's extension of fisheries jurisdiction beyond 200 miles

In March 1995, Canadian fisheries authorities boarded and arrested the Spanish fishing vessel, Estai, outside the Canadian 200‐mile zone on the Grand Banks, an event that served to focus world attention on a dispute that had its origins in the failure of the 1982 United Nations Convention on the Law of the Sea to implement an effective conservation and management regime for fish stocks on the high seas, particularly with respect to fish stocks that straddle coastal states’ exclusive economic zones. This article examines the origins of the dispute, including the allegations relating to overfishing of North Atlantic Fisheries Organization‐recommended quotas, the background to the vessel's arrest, and the subsequent confrontation that occurred, both at diplomatic levels and on the high seas, between Canada and the European Union. An analysis is made of the case in international law for Canada's extension of jurisdiction beyond 200 miles pursuant to the provisions of Section 5 of the Coastal Fisheries Protection Act. Finally, the article examines the implications of the recently concluded Agreement on the Conservation and Management of Straddling Fish Stocks and Highly Migratory Fish Stocks for disputes of the kind that arose in the present case.     

Responses of epidermal cell turgor pressure and photosynthetic activity of leaves of the atmospheric epiphyte Tillandsia usneoides (Bromeliaceae) after exposure to high humidity

It has been well-established that many epiphytic bromeliads of the atmospheric-type morphology, i.e., with leaf surfaces completely covered by large, overlapping, multicellular trichomes, are capable of absorbing water vapor from the atmosphere when air humidity increases. It is much less clear, however, whether this absorption of water vapor can hydrate the living cells of the leaves and, as a consequence, enhance physiological processes in such cells. The goal of this research was to determine if the absorption of atmospheric water vapor by the atmospheric epiphyte Tillandsia usneoides results in an increase in turgor pressure in leaf epidermal cells that subtend the large trichomes, and, by using chlorophyll fluorescence techniques, to determine if the absorption of atmospheric water vapor by leaves of this epiphyte results in increased photosynthetic activity. Results of measurements on living cells of attached leaves of this epiphytic bromeliad, using a pressure probe and of whole-shoot fluorescence imaging analyses clearly illustrated that the turgor pressure of leaf epidermal cells did not increase, and the photosynthetic activity of leaves did not increase, following exposure of the leaves to high humidity air. These results experimentally demonstrate, for the first time, that the absorption of water vapor following increases in atmospheric humidity in atmospheric epiphytic bromeliads is mostly likely a physical phenomenon resulting from hydration of non-living leaf structures, e.g., trichomes, and has no physiological significance for the plant's living tissues.     

Very rapid phosphorylation kinetics suggest a unique role for Lhcb2 during state transitions in Arabidopsis

Light‐harvesting complex II (LHCII) contains three highly homologous chlorophyll‐a/b‐binding proteins (Lhcb1, Lhcb2 and Lhcb3), which can be assembled into both homo‐ and heterotrimers. Lhcb1 and Lhcb2 are reversibly phosphorylated by the action of STN7 kinase and PPH1/TAP38 phosphatase in the so‐called state‐transition process. We have developed antibodies that are specific for the phosphorylated forms of Lhcb1 and Lhcb2. We found that Lhcb2 is more rapidly phosphorylated than Lhcb1: 10 sec of ‘state 2 light’ results in Lhcb2 phosphorylation to 30% of the maximum level. Phosphorylated and non‐phosphorylated forms of the proteins showed no difference in electrophoretic mobility and dephosphorylation kinetics did not differ between the two proteins. In state 2, most of the phosphorylated forms of Lhcb1 and Lhcb2 were present in super‐ and mega‐complexes that comprised both photosystem (PS)I and PSII, and the state 2‐specific PSI–LHCII complex was highly enriched in the phosphorylated forms of Lhcb2. Our results imply distinct and specific roles for Lhcb1 and Lhcb2 in the regulation of photosynthetic light harvesting.     

Pin1 inhibitors: Pitfalls,progress and cellular pharmacology

Compelling data supports the hypothesis that Pin1 inhibitors will be useful for the therapy of cancer: Pin1 deficient mice resist the induction of breast cancers normally evoked by expression of MMTV-driven Ras or Erb2 alleles. While Pin1 poses challenges for drug discovery, several groups have identified potent antagonists by structure based drug design, significant progress has been made designing peptidic inhibitors and a number of natural products have been found that blockade Pin1, notably epigallocatchechin gallate (EGCG), a major flavonoid in green tea. Here we critically discuss the modes of action and likely specificity of these compounds, concluding that a suitable chemical biology tool for probing the function of Pin1 has yet to be found. We conclude by outlining some open questions regarding the target validation of Pin1 and the prospects for identification of improved inhibitors in the future.