Structural Alphabets for Protein Structure Classification: A Comparison Study

Finding structural similarities between proteins often helps reveal shared functionality, which otherwise might not be detected by native sequence information alone. Such similarity is usually detected and quantified by protein structure alignment. Determining the optimal alignment between two protein structures, however, remains a hard problem. An alternative approach is to approximate each three-dimensional protein structure using a sequence of motifs derived from a structural alphabet. Using this approach, structure comparison is performed by comparing the corresponding motif sequences or structural sequences. In this article, we measure the performance of such alphabets in the context of the protein structure classification problem. We consider both local and global structural sequences. Each letter of a local structural sequence corresponds to the best matching fragment to the corresponding local segment of the protein structure. The global structural sequence is designed to generate the best possible complete chain that matches the full protein structure. We use an alphabet of 20 letters, corresponding to a library of 20 motifs or protein fragments having four residues. We show that the global structural sequences approximate well the native structures of proteins, with an average coordinate root mean square of 0.69 Å over 2225 test proteins. The approximation is best for all α-proteins, while relatively poorer for all β-proteins. We then test the performance of four different sequence representations of proteins (their native sequence, the sequence of their secondary-structure elements, and the local and global structural sequences based on our fragment library) with different classifiers in their ability to classify proteins that belong to five distinct folds of CATH. Without surprise, the primary sequence alone performs poorly as a structure classifier. We show that addition of either secondary-structure information or local information from the structural sequence considerably improves the classification accuracy. The two fragment-based sequences perform better than the secondary-structure sequence but not well enough at this stage to be a viable alternative to more computationally intensive methods based on protein structure alignment.     

Dynamics and Variability of Early Morphogenesis in the Loach according to Observations of Individual Developmental Trajectories

The dynamics and variability of quantitative morphological characters (morphological variables), which undergo changes upon epiboly, were studied by means of vital observations and measurements of developing loach (Misgurnus fossilis L.) embryos within equal time intervals. None of morphological variables, which characterize the dynamics of blastoderm shape, had monotonous dependence on time. In each individual embryo, the intervals of changes in morphological variables in the “normal” direction corresponding to the change of their mean values during the normal course of epiboly alternated with arrests, as well as with the changes of morphological variables in the reverse direction. The dynamics of morphological variables in time, which reflect the sequence of morphological states of the same embryo, and those of individual variations (variations of morphological states of different embryos on the same temporal section) had identical structure. This suggests instability of individual trajectories of morphogenesis or, strictly speaking, their actual absence. It was shown for the first time on the basis of analysis of individual trajectories of morphogenesis that its dynamics corresponded to so-called “determined chaos,” which was previously discussed only as a theoretical possibility. The data obtained suggest that upon approach to the equatorial area of the embryo, the blastoderm marginal zone was elongated in the longitudinal direction and contracted across the axis of its movement. As a result, a positive feedback arises between the cooperated cell movement and the change of shape of the surface, over which the cells move. This leads, due to unstable radial symmetry of this movement, to the formation of embryonic shield.__________Translated from Ontogenez, Vol. 36, No. 3, 2005, pp. 211–221.Original Russian Text Copyright © 2005 by Cherdantsev, Tsvetkova.     

机械化保护性耕作条件下土壤质量的数值化评价

通过9年的长期田间定位试验研究了陕西关中平原中部冬小麦 夏玉米轮作条件下深松耕（ST）、旋耕（RT）、秸秆还（SR）、免耕（NTS）等保护性耕作措施及传统耕作（TT）对土壤理化性状和作物产量的影响,并采用主成分分析方法进行土壤质量的综合评价.结果表明：与传统耕作相比,保护性耕作模式提高了土壤肥力质量,改善了土壤物理环境条件;显著提高了土壤脲酶和碱性磷酸酶的活性;除秸秆覆盖免耕处理的玉米和小麦产量低于传统耕作外,其他保护性耕作措施均不同程度地提高了作物产量,其中小麦增产13%～28%,玉米增产3%～12%.与传统耕作相比,保护性耕作土壤质量指数提高了19.8%～44.0%.综合考虑经济效应和生态效益,隔年深松、秸秆粉碎联合旋耕作业以及秸秆覆盖联合深松作业不仅能增加作物产量还可改善土壤质量,可在研究区进行推广应用.     

Past intensification trajectories of livestock led to mixed social and environmental services

Recent studies highlighted the multiple positive and negative contributions of livestock to society. Livestock production, through its direct and indirect impacts on land use, is an important driver of services provision. Although a few studies provide an account on the multiple services in different livestock systems, there is still an important knowledge gap on the drivers that contribute to the differentiation of services provisioning across areas. We investigated the hypothesis that the current level of services has derived from past intensification trajectories of livestock. The objective of this study was to understand the influences of past changes in livestock, land-use and socio-economic variables on the current provision of social, environmental and cultural services by the livestock sector in France. We combined a long-term country-wide database on livestock intensification between 1938 and 2010 and a database on services provisioning in 2010. We used a set of multivariate methods to simultaneously analyse the changes in livestock intensification from 1938 to 2010 and the current level of services provisioning. Our analysis focused on a set of 60 French departments where livestock play a significant economic role in agricultural production. Our study revealed that the provision of services was spatially structured and based on three groups of departments, characterised by different rates of change in intensification variables. In the first group, ‘Intensive livestock areas’, the high level of employment in the livestock sector was mainly associated with high rates of change in monogastric stocking rates (+1045%) and milk productivity (+451%). In the second group, ‘Extensive livestock areas’, the high levels of environmental and cultural services were mainly associated with moderate rates of change in herbivores stocking rate (+95%) and the stability of grassland area (+13%). In the third group, ‘Transition areas’, the low provision of all services was associated with the decline in livestock due to crop expansion. This study provides knowledge to understand how past changes determined the current contribution of livestock areas in providing differentiated bundles of services, which might help steer the development of the current livestock sector towards more sustainable trajectories.     

Autophosphorylation Is a Mechanism of Inhibition in Twitchin Kinase

Titin-like kinases are muscle-specific kinases that regulate mechanical sensing in the sarcomere. Twitchin kinase (TwcK) is the best-characterized member of this family, both structurally and enzymatically. TwcK activity is auto-inhibited by a dual intrasteric mechanism, in which N- and C-terminal tail extensions wrap around the kinase domain, blocking the hinge region, the ATP binding pocket and the peptide substrate binding groove. Physiologically, kinase activation is thought to occur by a stretch-induced displacement of the inhibitory tails from the kinase domain. Here, we now show that TwcK inhibits its catalysis even in the absence of regulatory tails, by undergoing auto-phosphorylation at mechanistically important elements of the kinase fold. Using mass spectrometry, site-directed mutagenesis and catalytic assays on recombinant samples, we identify residues T212, T301, T316 and T401 as primary auto-phosphorylation sites in TwcK in vitro. Taken together, our results suggest that residue T316, located in the peptide substrate binding P + 1 loop, is the dominantly regulatory site in TwcK. Based on these findings, we conclude that TwcK is regulated through a triple-inhibitory mechanism consisting of phosphorylation and intrasteric blockage, which is responsive not only to mechanical cues but also to biochemical modulation. This implies that mechanically stretched conformations of TwcK do not necessarily correspond to catalytically active states, as previously postulated. This further suggests a phosphorylation-dependent desensitization of the TwcK-mediated mechanoresponse of the sarcomere in vivo.     

Impact of the green tea ingredient epigallocatechin gallate and a short pentapeptide (Ile-Ile-Ala-Glu-Lys) on the structural organization of mixed micelles and the related uptake of cholesterol

Background

High levels of blood cholesterol are conventionally linked to an increased risk of developing cardiovascular disease (Grundy, 1986). Here we examine the molecular mode of action of natural products with known cholesterol-lowering activity, such as for example the green tea ingredient epigallocatechin gallate and a short pentapeptide, Ile-Ile-Ala-Glu-Lys.

On the encoding of movement vectors by honeybees. Are distance and direction represented independently?

Honeybees flying repeatedly over the same trajectory link it to an associated visual stimulus such that on viewing the stimulus they perform a trajectory in the habitual direction. To test if trajectory length can also be linked to a visual stimulus, bees were trained to fly through a multi-comparmented maze. Bees flew through a multi-compartmented maze. In one compartment a short trajectory could be linked to a stripe pattern oriented at 45° to the horizontal. In another compartment a longer trajectory could be linked to 135° stripes. Bees made both associations: their trajectories were short when viewing 45° stripes and longer when viewing 135° stripes. 90° stripes evoked trajectories of intermediate length.To test if distance and direction are linked independently to stripe orientation, a bee's trajectory was linked to 135° stripes in one compartment and to 45° stripes in another. These trajectories were the same length but differed in their horizontal direction by 60° or by 120°. 90° stripes evoked trajectories of intermediate direction which were shorter than those elicited by either training pattern. Bees were also trained to generate one long and one short trajectory with directions 120° apart. The trajectories elicited by 90° stripes were then biased towards the direction of the long training vector. Length and direction are not treated separately. The rules for combining trajectories resemble those of vector averaging.     

Effect of initial size on daily growth and survival in freshwater Chondrostoma nasus larvae: a field survey

Effects of initial size on the growth and survival of a freshwater fish, Chondrostoma nasus , were tested in a field survey, where individually tagged larvae were introduced into a potential nursery habitat. Characteristics of individual daily growth trajectories were utilized as a basis to explain growth, as well as survival patterns, in relation to ontogeny. Initial size only affected growth rates during the larval phase. Survival patterns could not be explained solely based on size-selective mortality processes because prey–predator interactions played a major role as well. This is confirmed by the Lande–Arnold selection model because directional, as well as stabilizing gradients, showed significant values. Thus, for the 0+ year freshwater fish, inherited size-specific effects were a significant advantage for growth performance and survival in early ontogeny. As fish grew older, however, other effects such as compensatory growth and prey–predator interactions apparently gained in importance.     

Similarities and distinctions in Y chromosome gene pool of Western Slavs

Analysis of Y chromosome Y‐STRs has proven to be a useful tool in the field of population genetics, especially in the case of closely related populations. We collected DNA samples from 169 males of Czech origin, 80 males of Slovakian origin, and 142 males dwelling Northern Poland. We performed Y‐STR analysis of 12 loci in the samples collected (PowerPlex Y system from Promega) and compared the Y chromosome haplotype frequencies between the populations investigated. Also, we used Y‐STR data available from the literature for comparison purposes. We observed significant differences between Y chromosome pools of Czechs and Slovaks compared to other Slavic and European populations. At the same time we were able to point to a specific group of Y‐STR haplotypes belonging to an R1a haplogroup that seems to be shared by Slavic populations dwelling in Central Europe. The observed Y chromosome diversity may be explained by taking into consideration archeological and historical data regarding early Slav migrations. Am J Phys Anthropol 142:540–548, 2010. © 2010 Wiley‐Liss, Inc.