614 research outputs found
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis
Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipeline, we see large increases in the domain coverage of sequences. We have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now resolve domain overlaps to provide highly comprehensive composite multi-domain architectures. To make these data more accessible for comparative genome analyses, we have developed novel search algorithms for searching genomes to identify related multi-domain architectures. In addition to providing domain family annotations, we have now developed a pipeline for 3D homology modelling of domains in Gene3D. This has been applied to the human genome and will be rolled out to other major organisms over the next year
The occupation of a box as a toy model for the seismic cycle of a fault
We illustrate how a simple statistical model can describe the quasiperiodic
occurrence of large earthquakes. The model idealizes the loading of elastic
energy in a seismic fault by the stochastic filling of a box. The emptying of
the box after it is full is analogous to the generation of a large earthquake
in which the fault relaxes after having been loaded to its failure threshold.
The duration of the filling process is analogous to the seismic cycle, the time
interval between two successive large earthquakes in a particular fault. The
simplicity of the model enables us to derive the statistical distribution of
its seismic cycle. We use this distribution to fit the series of earthquakes
with magnitude around 6 that occurred at the Parkfield segment of the San
Andreas fault in California. Using this fit, we estimate the probability of the
next large earthquake at Parkfield and devise a simple forecasting strategy.Comment: Final version of the published paper, with an erratum and an
unpublished appendix with some proof
Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions
Background
Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals.
Results
Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall.
Conclusions
The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions
Resummed small-x and first-moment evolution of fragmentation functions in perturbative QCD
We study the splitting functions for the evolution of fragmentation
distributions and the coefficient functions for single-hadron production in
semi-inclusive electron-positron annihilation in massless perturbative QCD for
small values of the momentum fraction and scaling variable x, where their
fixed-order approximations are completely destabilized by huge double
logarithms of the form alpha_s^n 1/x ln^(2n-a) x. Complete analytic all-order
expressions in Mellin-N space are presented for the resummation of these terms
at the next-to-next-to-leading logarithmic accuracy. The poles for the first
moments, related to the evolution of hadron multiplicities, and the small-x
instabilities of the next-to-leading order splitting and coefficient functions
are removed by this resummation, which leads to an oscillatory small-x
behaviour and functions that can be used at N=1 and down to extremely small
values of x. First steps are presented towards extending these results to the
higher accuracy required for an all-x combination with the state-of-the-art
next-to-next-to-leading order large-x results.Comment: 21 pages, LaTeX, 4 figures (.eps). FORM file of main results included
in sourc
Ligand binding to an Allergenic Lipid Transfer Protein Enhances Conformational Flexibility resulting in an Increase in Susceptibility to Gastroduodenal Proteolysis
Non-specific lipid transfer proteins (LTPs) are a family of lipid-binding molecules that are widely distributed across flowering plant species, many of which have been identified as allergens. They are highly resistant to simulated gastroduodenal proteolysis, a property that may play a role in determining their allergenicity and it has been suggested that lipid binding may further increase stability to proteolysis. It is demonstrated that LTPs from wheat and peach bind a range of lipids in a variety of conditions, including those found in the gastroduodenal tract. Both LTPs are initially cleaved during gastroduodenal proteolysis at three major sites between residues 39â40, 56â57 and 79â80, with wheat LTP being more resistant to cleavage than its peach ortholog. The susceptibility of wheat LTP to proteolyic cleavage increases significantly upon lipid binding. This enhanced digestibility is likely to be due to the displacement of Tyr79 and surrounding residues from the internal hydrophobic cavity upon ligand binding to the solvent exposed exterior of the LTP, facilitating proteolysis. Such knowledge contributes to our understanding as to how resistance to digestion can be used in allergenicity risk assessment of novel food proteins, including GMOs
- âŠ