New oxygen isotope evidence for the origin of mesosiderites and main group pallasites

High precision oxygen isotope analyses reveal that the silicate portion of mesosiderites are indistinguishable from the HEDs and suggest a common origin. However, the main group pallasites have a distinct signature, and therefore different source

Northwest Africa 5790. Top Sequence of the Nakhlite Pile

NWA 5790 is a recently discovered nakhlite. Its mineralogy, petrology and geochemistry suggest that it is the topmost sequence of the nakhlite lava pile

Sm-Nd Isotopic Studies of Two Nakhlites, NWA 5790 and Nakhla

NWA 5790 is a Martian meteorite recently found in the Mauritania part of the Saharan desert and is classified as a nakhlite, containing a small amount of interstitial plagioclase. Unlike other Martian meteorites ( e.g., shergottites), nakhlites have been only moderately shocked and their original igneous textures are still well-preserved. In this report, we present Sm-Nd isotopic data for NWA 5790 and Nakhla, a rare "fall" nakhlite, correlate their ages with those of other nakhlites and discuss their petrogenesis

A Classification Table for Achondrites

Classifying chondrites is relatively easy and the criteria are well documented. It is based on mineral compositions, textural characteristics and more recently, magnetic susceptibility. It can be more difficult to classify achondrites, especially those that are very similar to terrestrial igneous rocks, because mineralogical, textural and compositional properties can be quite variable. Achondrites contain essentially olivine, pyroxenes, plagioclases, oxides, sulphides and accessory minerals. Their origin is attributed to differentiated parents bodies: large asteroids (Vesta); planets (Mars); a satellite (the Moon); and numerous asteroids of unknown size. In most cases, achondrites are not eye witnessed falls and some do not have fusion crust. Because of the mineralogical and magnetic susceptibility similarity with terrestrial igneous rocks for some achondrites, it can be difficult for classifiers to confirm their extra-terrestrial origin. We -as classifiers of meteorites- are confronted with this problem with every suspected achondrite we receive for identification. We are developing a "grid" of classification to provide an easier approach for initial classification. We use simple but reproducible criteria based on mineralogical, petrological and geochemical studies. We presented the classes: acapulcoites, lodranites, winonaites and Martian meteorites (shergottite, chassignites, nakhlites). In this work we are completing the classification table by including the groups: angrites, aubrites, brachinites, ureilites, HED (howardites, eucrites, and diogenites), lunar meteorites, pallasites and mesosiderites. Iron meteorites are not presented in this abstract

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

Analysis of protein–ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind (http://bioinfo3d.cs.tau.ac.il/MultiBind), performs multiple alignment of protein binding sites. It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules. The output is a detailed list of the shared physico-chemical binding site properties. The second webserver, MAPPIS (http://bioinfo3d.cs.tau.ac.il/MAPPIS), aims to analyze protein–protein interactions. It performs multiple alignment of protein–protein interfaces (PPIs), which are regions of interaction between two protein molecules. MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein–protein associations. The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB

Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way

Understanding the mechanisms of protein–protein interaction is a fundamental problem with many practical applications. The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes. A set of protein complexes composed of non-homologous domains interacting with homologous partners at equivalent binding sites was collected in 2006, offering an opportunity to investigate this point. We considered 433 pairs of protein–protein complexes from the ABAC database (AB and AC binary protein complexes sharing a homologous partner A) and analyzed the extent of physico-chemical similarity at the atomic and residue level at the protein–protein interface. Homologous partners of the complexes were superimposed using Multiprot, and similar atoms at the interface were quantified using a five class grouping scheme and a distance cut-off. We found that the number of interfacial atoms with similar properties is systematically lower in the non-homologous proteins than in the homologous ones. We assessed the significance of the similarity by bootstrapping the atomic properties at the interfaces. We found that the similarity of binding sites is very significant between homologous proteins, as expected, but generally insignificant between the non-homologous proteins that bind to homologous partners. Furthermore, evolutionarily conserved residues are not colocalized within the binding sites of non-homologous proteins. We could only identify a limited number of cases of structural mimicry at the interface, suggesting that this property is less generic than previously thought. Our results support the hypothesis that different proteins can interact with similar partners using alternate strategies, but do not support convergent evolution