MolCom: a method to compare protein molecules based on 3-D structural and chemical similarity.

This paper describes an improved method for conducting global feature comparisons of protein molecules in three dimensions and for producing a new form of multiple structure alignment. Our automated MolCom method incorporates an octtree strategy to partition and examine molecular properties in three-dimensional space at multiple levels of analysis. The MolCom method's multiple alignment is in the form of an octtree which locates regions in three-dimensional space where correspondence between molecules is identified based on a dynamic set of molecular features. MolCom offers a practical solution to the inherent compromise between computational complexity and analytical detail. MolCom is currently the only method that can analyze and compare a series of defined physicochemical properties using multiple, simultaneous levels of resolution. It is also the only method that provides a consensus structure outlining precisely where the similarity exists in three-dimensional space. Using a modest-sized collection of structural properties, separate experiments were conducted to calibrate MolCom and to verify that the spatial analyses and resulting structure alignments accurately identified both similar and dissimilar structures. The accuracy of MolCom was found to be over 99% and the similarity scores correlated strongly with the z-scores of the Alignment by Incremental Combinatorial Extension of the Optimal Path method.

Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair.

Trypanosome RNA editing utilizes a seven polypeptide complex that includes two RNA ligases, band IV and band V. We now find that band IV protein contributes to the structural stability of the editing complex, so its lethal genetic knock-out could reflect structural or catalytic requirements. To assess the catalytic role in editing, we generated cell lines which inducibly replaced band IV protein with an enzymatically inactive but structurally conserved version. This induction halts cell growth, showing that catalytic activity is essential. These induced cells have impaired in vivo editing, specifically of RNAs requiring uridylate (U) deletion; unligated RNAs cleaved at U-deletion sites accumulated. Additionally, mitochondrial extracts of cells with reduced band IV activity were deficient in catalyzing U-deletion, specifically at its ligation step, but were not deficient in U-insertion. Thus band IV ligase is needed to seal RNAs in U-deletion. U-insertion does not appear to require band IV, so it might use the other ligase of the editing complex. Furthermore, band IV ligase was also found to serve an RNA repair function, both in vitro and in vivo.

MK801, an NMDA antagonist, blocks acquisition of a spatial task but does not block maternal experience effects.

Two studies were conducted to determine the effect on learning and memory of MK801, an N-methyl-D-aspartate (NMDA) antagonist that acts through noncompetitive blockade of the ion channel associated with the NMDA receptor. In the first study we found a dose-dependent impairment in the acquisition of a modified radial-arm maze task, resulting from injections (IP) of MK801 10 minutes prior to training. The retention of that learning, as measured by the amount of training required for reacquisition on the following day, was unaffected by the drug. In contrast, in the second study, MK801 did not block the experience-based facilitation of maternal responding seen 8 days after one hour of exposure to pups: experienced dams showed facilitated onset of maternal behavior, relative to inexperienced dams, regardless of the drug they received. However, injections of MK-801, either just before or just after the maternal experience, did lead to some deficits in maternal responding on the first day of testing. We have previously shown that these maternal experience effects are blocked by injections (ICV, SC) of cycloheximide, a protein synthesis inhibitor. These results suggest that the NMDA system does not mediate all, if any, of cycloheximide's effects on maternal experience and, furthermore, that the NMDA system may mediate some but not all forms of learning.