Application of the random coil index to studying protein flexibility

Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to quantitatively estimate model-free order parameters and flexibility in protein structural ensembles using only backbone chemical shifts. Because of its potential utility, we have undertaken a more detailed investigation of the RCI method in an attempt to ascertain its underlying principles, its general utility, its sensitivity to chemical shift errors, its sensitivity to data completeness, its applicability to other proteins, and its general strengths and weaknesses. Overall, we find that the RCI method is very robust and that it represents a useful addition to traditional methods of studying protein flexibility. We have implemented many of the findings and refinements reported here into a web server that allows facile, automated predictions of model-free order parameters, MD RMSF and NMR RMSD values directly from backbone ¹H, ¹³C and ¹⁵N chemical shift assignments. The server is available at . Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

最小Hamilton路算法在蛋白质结构预测中的应用

本文对蛋白质loop结构进行了反向研究,即对由n个残基构成的loop已知其空间结构,求匹配的n个氨基酸残基序列.把loop的3D信息转化为一个加权完全图Kn模型,然后求加权Kn图的最小Hamilton路.这条H路对应与寻找一个氨基酸残基序列,使该序列能够折叠成这个立体结构模型.根据Bayesian定律得到一个加权表,应用对loop的预测问题,取得预期的结果.     

Approaching a functional measure of vulnerability in marine ecosystems

Ecosystem vulnerability is a major concern for management purposes, especially when directed toward conservation and sustainable exploitation. We estimate the relative vulnerability of selected marine-ecosystems in the Gulf of Mexico through simulation experiments based on trophic models. The same perturbation pattern was applied to different functional groups at different trophic levels. Perturbation consisted of increasing biomass extraction for a single group up to 98% at a constant rate over 50 years. The ratio Ascendency to Capacity of Development, A/C, was estimated as a measure of ecosystem order. The maximum negative difference respect to the initial A/C represents the gain of entropy. The slope of the relationship between entropy gained and the trophic level provides an estimate of the relative vulnerability of the ecosystem. This was applied to five ecosystems in the Gulf of Mexico: Florida coral reef; Mexican coastal lagoon, Terminos Lagoon; and three continental shelves, the northern Gulf of Mexico, USA; Yucatan and the Campeche Sound, Mexico. The pattern of vulnerability among ecosystems is related to ecosystem complexity. The coral reef exhibited a lower slope, corresponding to higher vulnerability, which is related to higher connectivity, production efficiency, and net ecosystem production. Increasingly higher slopes, corresponding to lower vulnerability, followed a gradient from the coral reef to the continental shelves to the least vulnerable system, the coastal lagoon. Middle trophic levels contribute to higher vulnerability. This interpretation is supported by the concept of energy flows within trophic networks. The relevance of these findings for management is discussed.     

Liposomal membranes XI. A suggestion to structural characteristics of acido-thermophilic bacterial membranes

To understand the role of ω-cyclohexyl fatty acid residue of lipids in acido-thermophilic bacterial membranes, three unusual phosphatidylcholines, 1,2-di-11-cyclohexylundecanoyl-l-α-phosphatidylcholine (11_CYPC), 1,2-di-13-cyclohexyltridecanoyl-l-α-phosphatidylcholine (13_CYPC), and 1–13-cyclohexyltridecanoyl-2–11-cyclohexylundecanoyl-l-α-phosphatidylcholine (1–13_CY-2–11_CYPC) were prepared and the steady-state fluorescence anisotropy of 1,6-diphenylhexatriene (DPH) in the hydrophobic domain of these liposomal bilayers was determined. Compared with the case of dipalmitoyl (DPPC) or dimyristoyl phosphatidylcholine (DMPC), introducing the ω-cyclohexyl moiety onto lecithins makes the bilayers fluid below the phase transition temperature, while immobilizes them above the phase transition temperatures. The properties of the unusual phosphatidylcholine liposomes suggested by the steady-state fluorescence anisotropy investigation were in good agreement with those obtained from the thermotropic and permeability investigations. Results obtained are discussed from the view point of the role and function of lipid membranes of acido-thermophilic bacteria which contain unusual fatty acids.     

Sscillatory Cortical Activity during Visual Hallucinations

From a theoretical point of view we investigate cortical activity patterns causing dynamic visual hallucinations. For this reason we analyze an oscillatory instability of the dynamics ofthe activator-inhibitor model of Ermentrout and Cowan.Such an oscillatory instability occurs as a result of several disease mechanisms.We explicitly derive the order parameter equation. By means of the averaging theorem, we obtain the averaged order parameter equation.The latter enables us to determine stable and unstable bifurcating cortical activity patterns analytically in lowest order.Depending on model parameters as well as on initial conditions two types of cortical activity patterns occur: travelling waves and blinking rolls, i.e.standing waves oscillating with the same frequency and with a phase shift of /2. In contrast to cortical activitypatterns caused by non-oscillatory instabilitiesanalyzed by Ermentrout and Cowan and by the author the travelling waves and the blinking rolls lead to a variety of dynamic visual hallucinations which are discussed indetail.     

An Empirical Power Comparison of Three Tests of Exponentiality Under Mixture- and Outlier-Models

We present the results of an empirical power study of three prominent goodness-of-fit tests for exponentiality due to Shapiro and Wilk (1972), Durbin (1975), and Tiku (1980) by considering the mixture- and the outlier- exponential models as alternatives. This study is on similar lines as those of Dyer and Harbin (1981) and Balakrishnan (1983). We show that Tiku's test is on the whole considerably more powerful than the other two tests.     

Study of biocomplexity in an aquatic ecosystem through ascendency

The ascendancy concept aims at quantitatively describing the growth and development of an ecosystem as whole. Growth is an increase in the total system throughflow, while development is taken to be a rise in the average mutual information inherent in the network flow structure. As an ecosystem matures and goes through a series of successional stages, its ascendancy exhibits a propensity to increase. In any ecosystem the equilibrium condition may gradually turn into a chaotic situation for different reasons. In this paper a model is proposed of an aquatic ecosystem comprising of three groups, viz., phytoplankton, zooplankton and fish. Rate parameters are changed according to the change of the size of the organisms. The model is run in different conditions with gradual decrement of the body sizes of zooplankton. Allometric principle of the relationship of body size of zooplankton and two rate parameters (growth rate and half saturation constant) are incorporated in this model. According to allometric principle gradual decrement of body sizes of zooplankton consequently increases the grazing rate and decreases the half-saturation constant of this organisms. The system exhibits different states (equilibrium point--stable limit cycle--doubling and ultimately chaos) by gradual increase of zooplankton grazing rate and decrease of half-saturation constant. This paper tests the high level of ascendancy of the systems at the edge of oscillation before starting of the chaos. This high level of throughflow and mutual information, i.e. Ascendency supports the hypothesis that the system can coordinate the most complex behavior and shows maximum biocomplexity in this situation.