MultiCoil: a program for predicting two- and three-stranded coiled coils

Dominant negative mutants of TRAF3 reveal an important role for the coiled coil domains in cell death signaling by the lymphotoxin-beta receptor

Ligation of the lymphotoxin-beta receptor (LTbetaR) recruits tumor necrosis factor receptor-associated factor-3 (TRAF3) and initiates cell death in HT29 adenocarcinoma cells. The minimal receptor binding domain (TRAF-C) defined by two hybrid analyses is not sufficient for direct recruitment to the ligated receptor. A series of TRAF3 deletion mutants reveal that a subregion of the coiled coil motif is required for efficient recruitment to the LTbetaR. Furthermore, the ability of TRAF3 to self-associate maps to an adjacent subregion. A TRAF3 deletion mutant that lacks the N-terminal zinc RING and zinc finger motifs, but retains the coiled coil and TRAF-C motifs, competitively displaces endogenous TRAF3 from the LTbetaR. A second TRAF3 mutant that lacks the receptor binding domain, yet contains the TRAF3 self-association domain, prevents TRAF3 homodimers from being recruited to the LTbetaR. Both of these mutants have a dominant negative effect on cell death and demonstrate that the recruitment of TRAF3 oligomers is necessary to initiate signal transduction that activates the cell death pathway.

An iterative method for improved protein structural motif recognition

We present an iterative algorithm that uses randomness and statistical techniques to improve existing methods for recognizing protein structural motifs. Our algorithm is particularly effective in situations where large numbers of sufficiently diverse examples of the motif are not known. These are precisely the situations that pose significant difficulties for previously known methods. We have implemented our algorithm and we demonstrate its performance on the coiled coil motif. We test our program LearnCoil on the domain of 3-stranded coiled coils and subclasses of 2-stranded coiled coils. We show empirically that for these motifs, our method overcomes the problem of limited data.