The neurotrophin receptor (NTR) has what appears to be a death domain homology, but the death function of the domain has not been convincingly demonstrated. One important question is whether the sequence at the C-terminus of NTR encodes a structurally homologous domain. The specific aims of this project have been 1) to obtain and analyze an accurate multiple alignment based on secondary structure prediction and the single known three-dimensional structure, and 2) to model the structure of the neurotrophin receptor death domain by homology. This model could be used to plan experimental mutagenesis of the NTR death domain. The Computer Graphics Laboratory has provided access to software and hardware capability for analysis of available sequence data on death domains. Structure-based alignments have taken advantage of the solution NMR structure of one of these death domains, Fas (CD95). This structure represents a novel protein fold composed of six helices. Multiple alignments of all available death domain sequences (including species homologs) suggest that high structural variation can exist that is still consistent with apoptotic induction. The aligned region of NTR is not more divergent than other functionally characterized domains are from each other. In other words, extensive sequence variation exists among functional deth domains, and the NTR sequence falls well within this variation. This analysis also revealed that differences between the NTR domain and its known functional relatives occur primarily in loops connecting the six helices or in the highly divergent helix 1. One unexpected finding was that a three amino acid deletion in the widely used rat NTR cloned sequence appears to fall in the hinge region between helix 1 and helix 2. We are proceeding with development of a molecular model of the NTR death doman using molecular modeling tools, including utilities, database access, MidasPlus and other modeling packages. This project continues characterization of the structure and function of the NTR death domain.