A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction

We present a new structurally derived pair-to-pair substitution matrix (P2PMAT). This matrix is constructed from a very large amount of integrated high quality multiple sequence alignments (Blocks) and protein structures. It evaluates the likelihoods of all 160,000 pair-to-pair substitutions. P2PMAT matrix implicitly accounts for evolutionary conservation, correlated mutations, and residue-residue contact potentials. The usefulness of the matrix for structural predictions is shown in this article. Predicting protein residue-residue contacts from sequence information alone, by our method (P2PConPred) is particularly accurate in the protein cores, where it performs better than other basic contact prediction methods (increasing accuracy by 25-60%). The method mean accuracy for protein cores is 24% for 59 diverse families and 34% for a subset of proteins shorter than 100 residues. This is above the level that was recently shown to be sufficient to significantly improve ab initio protein structure prediction. We also demonstrate the ability of our approach to identify native structures within large sets of (300-2000) protein decoys. On the basis of evolutionary information alone our method ranks the native structure in the top 0.3% of the decoys in 4/10 of the sets, and in 8/10 of sets the native structure is ranked in the top 10% of the decoys. The method can, thus, be used to assist filtering wrong models, complementing traditional scoring functions.     

Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase

Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo–As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway, which is essential for catalysis, is not modified upon inhibition. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our predictions with binding sites in Protein Data Bank and found significantly more binding events occur at sites we predicted. Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases.     

Tree growth,mortality, and above-ground biomass accumulation in a holm oak forest under a five-year experimental field drought

A holm oak forest was exposed to an experimental drought during 5 years to elucidate the growth responses of the dominant species Quercus ilex, Arbutus unedo and Phillyrea latifolia. Soil water availability was partially reduced, about 15% as predicted for this area for the next decades by GCM and ecophysiological models, by plastic strips intercepting rainfall and by ditch exclusion of water runoff. The stem diameter increment was highly correlated with annual rainfall in all species, and drought treatment strongly reduced the diameter increment of Q. ilex (41%) and specially of A. unedo (63%), the species showing higher growth rates. Stem mortality rates were highly correlated with previous stem density, but drought treatment increased mortality rates in all species. Q. ilex showed the highest mortality rates (9% and 18% in control and drought plots, respectively), and P. latifolia experienced the lowest mortality rates (1% and 3% in control and drought plots, respectively). Drought strongly reduced the increment of live aboveground biomass during these 5 years (83%). A. unedo and Q. ilex experienced a high reduction in biomass increment by drought, whereas P. latifolia biomass increment was insensitive to drought. The different sensitivity to drought of the dominant species of the holm oak forest may be very important determining their future development and distribution in a drier environment as expected in Mediterranean areas for the next decades. These drier conditions could thus have strong effects on structure (species composition) and functioning (carbon uptake and biomass accumulation) of these Mediterranean forests.     

Concise review of the genus Asparagopsis Montagne, 1840

Journal of Applied Phycology - Asparagopsis (Bonnemaisoniaceae, Rhodophyta) species are distributed in most temperate and tropical waters of the world, where they are considered an iconic invader....     

Calling louder and longer: how bats use biosonar under severe acoustic interference from other bats

Active-sensing systems such as echolocation provide animals with distinct advantages in dark environments. For social animals, however, like many bat species, active sensing can present problems as well: when many individuals emit bio-sonar calls simultaneously, detecting and recognizing the faint echoes generated by one''s own calls amid the general cacophony of the group becomes challenging. This problem is often termed ‘jamming’ and bats have been hypothesized to solve it by shifting the spectral content of their calls to decrease the overlap with the jamming signals. We tested bats’ response in situations of extreme interference, mimicking a high density of bats. We played-back bat echolocation calls from multiple speakers, to jam flying Pipistrellus kuhlii bats, simulating a naturally occurring situation of many bats flying in proximity. We examined behavioural and echolocation parameters during search phase and target approach. Under severe interference, bats emitted calls of higher intensity and longer duration, and called more often. Slight spectral shifts were observed but they did not decrease the spectral overlap with jamming signals. We also found that pre-existing inter-individual spectral differences could allow self-call recognition. Results suggest that the bats’ response aimed to increase the signal-to-noise ratio and not to avoid spectral overlap.     

The role of forest structure and human occupation in structuring mammal assemblages in oligotrophic ecosystems of Central Amazonia

Large mammals are vulnerable to extinction, and respond directly to ecological gradients within the forest and to the intensity of forest product use by humans. In this study, we evaluated the effects of differences in forest structure and human occupation history on the composition of medium and large‐sized mammal assemblages of the terra‐firme forests of the Anavilhanas National Park, one of the most oligotrophic Amazonian ecosystems. Mammal surveys were conducted along 11 linear transects of 4 km, six of which were located in areas once inhabited by people and managed until the year that the park was created (over 30 years ago), and five in areas that were not inhabited at that time. We detected 469 individuals of 26 species during diurnal and nocturnal sampling, and 11 additional species outside transects. Human occupation history was strongly related to forest structure components. Fruit biomass, canopy cover and tree size were strongly associated with uninhabited areas, and influenced the structure of mammal assemblages. A direct relationship between diet category and species size was observed. Large frugivore‐herbivores and carnivores were more closely associated with areas with more fruit, larger trees and greater canopy cover. In contrast, small arboreal frugivore‐omnivores associated more closely with open canopy and smaller trees. Our study indicated that the effects of human occupation history on forest structure are still evident three decades after the removal of local people from the park. This long‐term effect can be explained by the low resilience of the Anavilhanas environments, demonstrating the fragility of mammal assemblages in face of anthropogenic variation in forest structure in the oligotrophic ecosystems of the Negro River basin.