The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes

Abstract

Many outer membrane proteins (OMPs) in Gram-negative bacteria possess known beta-barrel three-dimensional (3D) structures. These proteins, including channel-forming transmembrane porins, are diverse in sequence but exhibit common structural features. We here report computational analyses of six outer membrane proteins of known 3D structures with respect to (1) secondary structure, (2) hydropathy, and (3) amphipathicity. Using these characteristics, as well as the presence of an N-terminal targeting sequence, a program was developed allowing prediction of integral membrane beta-barrel proteins encoded within any completely sequenced prokaryotic genome. This program, termed the beta-barrel finder (BBF) program, was used to analyze the proteins encoded within the Escherichia coli genome. Out of 4290 sequences examined, 118 (2.8%) were retrieved. Of these, almost all known outer membrane proteins with established beta-barrel structures as well as many probable outer membrane proteins were identified. This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes.

Fig. 1.

Hydropathy and amphipathicity plots for OmpF of the GBP family. The PDB code for OmpF is 2OMF. Solid lines indicate hydropathy; dotted lines indicate amphipathicity; dashed lines indicate predicted β-structures. The format of presentation used here is also used in Figures 2–6 ▶ ▶ ▶ ▶ ▶.

Fig. 2.

Hydropathy and amphipathicity plots for OmpA of the OOP family. The PDB code for OmpA is 1BXW.

Fig. 3.

Hydropathy and amphipathicity plots for LamB of the SP family. The PDB code for LamB is 1MAL.

Fig. 4.

Hydropathy and amphipathicity plots for FhuA of the OMR family. The PDB code for FhuA is 1BY3.

Fig. 5.

Hydropathy and amphipathicity plots for OmpX. The PDB code for OmpX is 1QJ8.

Fig. 6.

Hydropathy and amphipathicity plots for phospholipase A. The PDB code for Phospholipase A is 1QD5.