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41.
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. 相似文献
42.
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale 总被引:1,自引:0,他引:1
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. 相似文献
43.
Eran Amichai Gaddi Blumrosen Yossi Yovel 《Proceedings. Biological sciences / The Royal Society》2015,282(1821)
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. 相似文献
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle 总被引:1,自引:0,他引:1
Suen G Teiling C Li L Holt C Abouheif E Bornberg-Bauer E Bouffard P Caldera EJ Cash E Cavanaugh A Denas O Elhaik E Favé MJ Gadau J Gibson JD Graur D Grubbs KJ Hagen DE Harkins TT Helmkampf M Hu H Johnson BR Kim J Marsh SE Moeller JA Muñoz-Torres MC Murphy MC Naughton MC Nigam S Overson R Rajakumar R Reese JT Scott JJ Smith CR Tao S Tsutsui ND Viljakainen L Wissler L Yandell MD Zimmer F Taylor J Slater SC Clifton SW Warren WC Elsik CG Smith CD Weinstock GM Gerardo NM Currie CR 《PLoS genetics》2011,7(2):e1002007
Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses. 相似文献
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Scott D. Betts Todd M. Hachigian Eran Pichersky Charles F. Yocum 《Plant molecular biology》1994,26(1):117-130
The psbO gene of cyanobacteria, green algae and higher plants encodes the precursor of the 33 kDa manganese-stabilizing protein (MSP), a water-soluble subunit of photosystem II (PSII). Using a pET-T7 cloning/expression system, we have expressed in Escherichia coli a full-length cDNA clone of psbO from Arabidopsis thaliana. Upon induction, high levels of the precursor protein accumulated in cells grown with vigorous aeration. In cells grown under weak aeration, the mature protein accumulated upon induction. In cells grown with moderate aeration, the ratio of precursor to mature MSP decreased as the optical density at induction increased. Both forms of the protein accumulated as inclusion bodies from which the mature protein could be released under mildly denaturing conditions that did not release the precursor. Renatured Arabidopsis MSP was 87% as effective as isolated spinach MSP in restoring O2 evolution activity to MSP-depleted PSII membranes from spinach; however, the heterologous protein binds to spinach PSIIs with about half the affinity of the native protein. We also report a correction to the previously published DNA sequence of Arabidopsis psbO (Ko et al., Plant Mol Biol 14 (1990) 217–227). 相似文献
49.
Two recombinant His-tagged proteins, a plant 4-coumarate:coenzyme A ligase (EC 6.2.1.12) and a bacterial benzoate:coenzyme A ligase (EC 6.2.1.25), were expressed in Escherichia coli and purified in a single step using Ni-chelating chromatography. Purified enzymes were used to synthesize cinnamoyl-coenzyme A (CoA), p-coumaroyl-CoA, feruloyl-CoA, caffeoyl-CoA, and benzoyl-CoA. Conversions up to 95% were achieved. Using a rapid solid-phase extraction procedure, the target CoA esters were isolated with yields of up to 80%. Structures were confirmed by analytical comparison with chemically synthesized reference compounds and electrospray ionization-mass spectrometry. The recombinant enzymes were stable for several months at -80 degrees C, thus providing a reliable and facile method to produce these delicate biological intermediates. 相似文献
50.
Gal?Haspel Eran?Gefen Amos?Ar J.?Gustavo?Glusman Frederic?LibersatEmail author 《Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology》2005,191(6):529-534
Unlike predators, which immediately consume their prey, parasitoid wasps incapacitate their prey to provide a food supply for their offspring. We have examined the effects of the venom of the parasitoid wasp Ampulex compressa on the metabolism of its cockroach prey. This wasp stings into the brain of the cockroach causing hypokinesia. We first established that larval development, from egg laying to pupation, lasts about 8 days. During this period, the metabolism of the stung cockroach slows down, as measured by a decrease in oxygen consumption. Similar decreases in oxygen consumption occurred after pharmacologically induced paralysis or after removing descending input from the head ganglia by severing the neck connectives. However, neither of these two groups of cockroaches survived more than six days, while 90% of stung cockroaches survived at least this long. In addition, cockroaches with severed neck connectives lost significantly more body mass, mainly due to dehydration. Hence, the sting of A. compressa not only renders the cockroach prey helplessly submissive, but also changes its metabolism to sustain more nutrients for the developing larva. This metabolic manipulation is subtler than the complete removal of descending input from the head ganglia, since it leaves some physiological processes, such as water retention, intact. 相似文献