Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.

A method is presented that uses beta-strand interactions at both the sequence and the atomic level, to predict beta-structural motifs of protein sequences. A program called Wrap-and- Pack implements this method and is shown to recognize beta-trefoils, an important class of globular beta-structures, in the Protein Data Bank with 92% specificity and 92.3% sensitivity in cross-validation. It is demonstrated that Wrap-and-Pack learns each of the ten known SCOP beta-trefoil families, when trained primarily on beta-structures that are not beta-trefoils, together with three-dimensional structures of known beta-trefoils from outside the family. Wrap-and-Pack also predicts many proteins of unknown structure to be beta-trefoils. The computational method used here may generalize to other beta-structures for which strand topology and profiles of residue accessibility are well conserved.     

Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks

In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.     

Responses of Mature and Aged Sympathetic Neurons to Laminin and NGF: An in Vitro Study

Whilst the potent effects of NGF and laminin on developing neurons are well documented, relatively little is known about the effects of, or altered availability of or altered responsiveness to, these substances on the growth of adult neurons. We have therefore examined this question using explant cultures of sympathetic neurons from the superior cervical ganglion (SCG) of mature and aged rats. Explants were grown on substrata containing different doses of laminin, either with or without added NGF in culture medium containing FCS. Individually, laminin and NGF had relatively small effects on neurite outgrowth and length, which tended to be reduced in old neurons. In contrast, laminin in the presence of exogenous NGF exerted a powerful effect on nerve growth which was substantially greater than the sum of the effects of the individual factors. This synergy was evident in all experimental groups and was greatest in old explants at high doses of laminin, where growth was comparable to that of mature neurons. The dose-response curve of old neurons to laminin in the presence of added NGF indicated reduced responsiveness. These results suggest that variations in the availability of laminin and/or exogenous NGF, together with altered patterns of neuronal responsiveness, may contribute to impaired neuronal plasticity in old age.     

Activation of inositol phospholipid breakdown in HL60 cells by P2-purinergic receptors for extracellular ATP. Evidence for mediation by both pertussis toxin-sensitive and pertussis toxin-insensitive mechanisms

The mechanisms whereby P2-purinergic receptors for extracellular ATP are coupled to the inositol phospholipid-signaling system were studied in the HL60 human promyelocytic leukemia cell line. Brief pretreatment of either undifferentiated or differentiated HL60 cells with various activators of protein kinase C Ca2+/phospholipid-dependent enzyme (e.g. phorbol myristate acetate) produced a 50-fold decrease in the potency of extracellular ATP to induce mobilization of intracellular Ca2+. The ATP-induced increase in rate of inositol trisphosphate (InsP3) accumulation in these 4-beta-phorbol 12-myristate-13-acetate-treated cells was characterized by a 40% decrease in the maximal rate of InsP3 accumulation. Incubation of the cells with NaF also induced mobilization of the same Ca2+ stores released in response to extracellular ATP; this provided indirect evidence that the transmembrane signaling actions of P2-purinergic receptors may be mediated by GTP-binding regulatory proteins. This latter possibility was further supported by the finding that treatment of either undifferentiated or differentiated HL60 cells with pertussis toxin produced a significant, but partial, inhibition of ATP-induced signaling actions. These included: 1) a 60-70% decrease in the maximum rate of InsP3 accumulation, and 2) a 1.5 log unit increase in the half-maximally effective [ATP] required for mobilization of intracellular Ca2+. In cells treated with both pertussis toxin and 4-beta-phorbol 12-myristate-13-acetate, there was an 80% decrease in maximal rate of ATP-induced InsP3 accumulation and near-complete inhibition of ATP-induced Ca2+ mobilization. Significantly, the residual, pertussis toxin-insensitive portion of ATP-induced signaling was observed in the same samples of differentiated HL60 cells wherein pertussis toxin treatment produced complete abolition of InsP3 accumulation and Ca2+ mobilization in response to occupation of chemotactic peptide receptors. These results indicate that the activation of inositol phospholipid breakdown by P2-purinergic receptors in HL60 cells may be mediated by both pertussis toxin-sensitive and toxin-insensitive mechanisms; this suggests that these myeloid progenitor cells may express two distinct types of GTP-binding proteins coupled to phospholipase C.