Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies

Secondary structure topology in this article refers to the order and the direction of the secondary structures, such as helices and strands, with respect to the protein sequence. Even when the locations of the secondary structure Cα atoms are known, there are still (N!2^N)(M!2^M) different possible topologies for a protein with N helices and M strands. This work explored the question if the native topology is likely to be identified among a large set of all possible geometrically constrained topologies through an evaluation of the residue contact energy formed by the secondary structures, instead of the entire chain. We developed a contact pair specific and distance specific multiwell function based on the statistical characterization of the side chain distances of 413 proteins in the Protein Data Bank. The multiwell function has specific parameters to each of the 210 pairs of residue contacts. We illustrated a general mathematical method to extend a single well function to a multiwell function to represent the statistical data. We have performed a mutation analysis using 50 proteins to generate all the possible geometrically constrained topologies of the secondary structures. The result shows that the native topology is within the top 25% of the list ranked by the effective contact energies of the secondary structures for all the 50 proteins, and is within the top 5% for 34 proteins. As an application, the method was used to derive the structure of the skeletons from a low resolution density map that can be obtained through electron cryomicroscopy. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

On the approaches applied in formulation of a kinetic model of photosystem II: Different approaches lead to different simulations of the chlorophyll a fluorescence transients

Chlorophyll a fluorescence rise (O-J-I-P transient) was in literature simulated using models describing reactions occurring solely in photosystem II (PSII) and plastoquinone (PQ) pool as well as using complex models which described, in addition to the above, also subsequent electron transport occurring beyond the PQ pool. However, there is no consistency in general approach how to formulate a kinetic model and how to describe particular reactions occurring even in PSII only. In this work, simple kinetic PSII models are considered always with the same electron carriers and same type of reactions but some reactions are approached in different ways: oxygen evolving complex is considered bound to PSII or “virtually” separated from PSII; exchange of doubly reduced secondary quinone PSII electron acceptor, Q_B, with PQ molecule from the PQ pool is described by one second order reaction or by two subsequent reactions; and all possible reactions or only those which follow in logical order are considered. By combining all these approaches, eight PSII models are formulated which are used for simulations of the chlorophyll a fluorescence transients. It is shown that the different approaches can lead to qualitatively different results. The approaches are compared with other models found elsewhere in the literature and therefore this work can help the readers to better understand the other models and their results.     

Morphological variation in a secondary contact between divergent lineages of brown trout (Salmo trutta) from the Iberian Peninsula

The aim of this study was to analyze the morphological variation of brown trout (Salmo trutta) in the Duero basin, an Atlantic river basin in the Iberian Peninsula, where a spatial segregation of two divergent lineages was previously reported, based on isozyme, microsatellite and mtDNA data. In these studies, two divergent pure regions (Pisuerga and Lower-course) and several hybrid populations between them were identified. Morphological variation was evaluated in 11 populations representative of the genetic differentiation previously observed in the Duero basin, using multivariate analysis on 12 morphometric and 4 meristic traits. A large differentiation between populations was observed (interpopulation component of variance: 41.8%), similar to that previously detected with allozymes and microsatellites. Morphometric differentiation was also reflected by the high classification success of pure and hybrid individuals to their respective populations, using multivariate discriminant functions (94.1% and 79.0%, respectively). All multivariate and clustering analyses performed demonstrated a strong differentiation between the pure regions. The hybrid populations, though showing large differentiation among them, evidenced an intermediate position between the pure samples. Head and body shape traits were the most discriminant among the morphometric characters, while pectoral rays and gillrakers were the most discriminant among the meristic traits. These results confirmed the high divergence of the brown trout from the Duero basin and suggest some traits on which selection could be acting to explain the spatial segregation observed.     

How Many 3D Structures Do We Need to Train a Predictor？

It has been shown that the progress in the determination of membrane protein structure grows exponentially, with approximately the same growth rate as that of the water-soluble proteins. In order to investigate the effect of this, on the performance of prediction algorithms for both α-helical and β-barrel membrane proteins, we conducted a prospective study based on historical records. We trained separate hidden Markov models with different sized training sets and evaluated their performance on topology pred...     

Unripe red fruits may be aposematic

The unripe fruits of certain species are red. Some of these species disperse their seeds by wind (Nerium oleander, Anabasis articulata), others by adhering to animals with their spines (Emex spinosa) or prickles (Hedysarum spinosissimum). Certainly neither type uses red coloration as advertisement to attract the seed dispersing agents. Fleshy-fruited species (Rhamnus alaternus, Rubus sanguineus and Pistacia sp.), which disperse their seeds via frugivores, change fruit color from green to red while still unripe and then to black or dark blue upon ripening. The red color does not seem to function primarily in dispersal (unless red fruits form advertisement flags when there are already black ripe fruits on the plant) because the red unripe fruits of these species are poisonous, spiny, or unpalatable. The unripe red fruits of Nerium oleander are very poisonous, those of Rhamnus alaternus and Anabasis articulata are moderately poisonous, those of Rubus sanguineus are very sour, those of Pistacia sp. contain unpalatable resin and those of Emex spinosa and Hedysarum spinosissimum are prickly. We propose that these unripe red fruits are aposematic, protecting them from herbivory before seed maturation.     

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structural complexity and can be used to increase the overall structural diversity of initial pools for in vitro selection experiments. Random Filtering selectively increases the number of five-way junctions in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure distribution, whether uniform or otherwise. We show that using our computationally designed DNA pool greatly improves access to highly complex sequence structures for SELEX experiments (without losing our ability to select for common one-way and two-way junction sequences).