THE CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN

Lesa J. Beamer¹, Stephen F. Carroll², and David Eisenberg³

¹Department of Biochemistry University of Missouri - Columbia Columbia, MO 65211
²XOMA Corporation Berkeley, CA 94710
³Molecular Biology Institute UCLA Los Angeles, CA 90095-1570

Gram-negative bacteria and their lipopolysaccharides (LPS) can trigger a powerful inflammatory response when present in the mammalian bloodstream. Recently, two related proteins that modulate the toxic effects of bacterial LPS and act in the innate immune response to the bacterial infection have been identified. One of these proteins, bactericidal/permeability-increasing protein (BPI), is found in a type of white blood cell called a polymorphonuclear neutrophil. BPI is potently bactericidal toward Gram-negative bacteria, shows high affinity binding to the lipid A portion of LPS, and neutralizes the inflammatory properties of LPS in vitro and in vivo [1]. These functions have been localized to N-terminal fragments of BPI, and a recombinant N-terminal BPI protein is under clinical investigation for treatment of bacterial infections. In contrast to BPI, the second protein (LPS-binding protein or LBP) is not bactericidal and it enhances the inflammatory properties of LPS.

Full-length (456 residues) human BPI was crystallized and its structure determined at 2.4 resolution by multiple isomorphous replacement with anomalous scattering [2]. The structure shows that BPI is a boomerang-shaped molecule formed from two similar domains related by a pseudo two-fold axis. Each domain contains a barrel composed of a beta-sheet and two alpha-helices arranged in a novel protein fold. Two extensive, apolar pockets on the concave surface of the boomerang each bind a molecule of phosphatidylcholine. The phospholipid binds with its acyl carbon chains buried in the hydrophobic core of the protein while the zwitterionic head group is exposed to solvent. These pockets may indicate a site of interaction between BPI and LPS, and could be involved in neutralizing its toxic effects.

The structure of BPI serves as a framework for understanding the related LPS-binding protein, LBP. Despite their different effects in vivo, BPI and LBP are closely related, sharing 45% amino acid identity. Multiple sequence alignments of BPI and LBP proteins indicate residues that form the lipid-binding pockets have been highly conserved, suggesting their functional importance [3]. In addition, several conserved positively charged residues are found to cluster at the tip of the N-terminal domain, and may be involved in electrostatic interactions with phosphate groups of LPS. The three-dimensional structure of BPI provides a model for design of site-directed mutants and the interpretation of biochemical data for these two important proteins.

1. Elsbach P and Weiss J, Bactericidal/permeability increasing protein and host defense against Gram-negative bacteria and endotoxin. Curr Opin Immunology 5: 103-107, 1993.
2. Beamer LJ, Carroll SF and Eisenberg D, Crystal structure of human BPI and two bound phospholipids at 2.4 resolution. Science 276: 1861-1864, 1997.
3. Beamer LJ, Carroll SF and Eisenberg D, The BPI/LBP family of proteins: A structural analysis of conserved regions. Protein Science 1998.