Program in Biophysics and Dept. of Genetics, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115
In gram-negative bacteria, three families of export pumps with a shared organization have been identified: the resistance-nodulation-division family, the major facilitator superfamily, and the family of ATP-binding cassette transporters. Each export system is thought to be composed of an inner membrane transporter, an outer membrane channel, and an accessory protein termed a membrane fusion protein (MFP). The MFPs, which are 350-550 residue proteins with weak sequence similarity, are believed to facilitate simultaneous efflux across both membranes by linking the transporter with an outer membrane channel. Because the MFP family is a large collection of proteins that share low sequence similarity and a common function, it is an attractive subject for pattern recognition algorithms. In order to investigate the function of the MFPs in the export process, the motif-detection algorithms of ASSET (Neuwald & Green, 1994, J. Mol. Biol. 239: 698) and the Gibbs Motif Sampler (Neuwald et. al, 1995, Prot. Sci. 4: 1618) were used along with other sequence analysis strategies. A conserved motif was detected by both methods, occurring two to three times in each MFP sequence. The motif was refined and then searched against the database of proteins sequences, allowing the identification of several novel MFP family members, and the discovery of the motif in otherwise unrelated families of proteins, some members of which have known structure. Examination of these structures provides some insight into the mechanism by which membrane apposition may be achieved.