Bacterial ß-Barrel Outer Membrane Proteins: A Common Structural Theme Implicated in a Wide Variety of Functional Roles

Bacterial ß-Barrel Outer Membrane Proteins: A Common Structural Theme Implicated in a Wide Variety of Functional Roles

Pantelis G. Bagos (University of Central Greece and University of Athens, Greece) and Stavros J. Hamodrakas (University of Athens, Greece)
Copyright: © 2009 |Pages: 26
DOI: 10.4018/978-1-60566-076-9.ch010
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Abstract

ß-barrel outer membrane proteins constitute the second and less well-studied class of transmembrane proteins. They are present exclusively in the outer membrane of Gram-negative bacteria and presumably in the outer membrane of mitochondria and chloroplasts. During the last few years, remarkable advances have been made towards an understanding of their functional and structural features. It is now wellknown that ß-barrels are performing a large variety of biologically important functions for the bacterial cell. Such functions include acting as specific or non-specific channels, receptors for various compounds, enzymes, translocation channels, structural proteins, and adhesion proteins. All these functional roles are of great importance for the survival of the bacterial cell under various environmental conditions or for the pathogenic properties expressed by these organisms. This chapter reviews the currently available literature regarding the structure and function of bacterial outer membrane proteins. We emphasize the functional diversity expressed by a common structural motif such as the ß-barrel, and we provide evidence from the current literature for dozens of newly discovered families of transmembrane ß-barrels.
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Structural Features Of Β-Barrels

The β-barrel is a protein fold occurring in soluble proteins as well in transmembrane ones. A β-barrel may be considered as a β-sheet that twists and coils to form a closed barrel-shaped structure, which is stabilized by the hydrogen bonds formed by the sheet edges (first and last strands). The observed so far transmembrane β-barrels preferentially lay their axis along the membrane normal and are exclusively composed of meandering all-next-neighbor antiparallel β-strands, suggesting a repeating β-hairpin structural motif. It has been shown that any type of β-barrel can accurately be described solely by two parameters, namely the number of β-strands n and the shear number S. S is a measure of the stagger of the strands in the sheet. Theoretical analysis combined with available three dimensional structures proved that these two parameters determine all other features of the β-barrel (Murzin, Lesk et al. 1994; Murzin, Lesk et al. 1994). Currently, available high-resolution structures of transmembrane β-barrel proteins include β-barrels of varying features, with 8 ≤ n ≤ 22 and 8 ≤ S ≤ 24 (Table 1). Furthermore, it is worth mentioning that all transmembrane β-barrels observed so far consist of an even number of strands.

Key Terms in this Chapter

Porins: This is the oldest known and well-studied super-family of transmembrane beta-barrels. Porins are large enough to allow passive diffusion i.e., they act as channels that are specific to different types of molecules. They are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. The amino acid composition of the transmembrane beta strands is unique since polar and non-polar residues alternate along them. This way, the non-polar residues face outwards in order to interact with the non-polar lipid bilayer, while the polar residues face the barrel interior in order to interact with the aqueous channel. Porins typically control the diffusion of small metabolites like sugars, ions, and amino acids. The archetypical general diffusion porins of Gram-negative Bacteria are composed of 16-stranded beta-barrels and are active only as homo-trimers (trimeric porins). However, other families have been found deviating from this motif such as the sugar porins which are trimeric porins composed of 18-stranded beta-barrels or the monomeric porins composed of 14-stranded beta-barrels.

Beta-Barrel Outer Membrane Proteins: They constitute one of the two major structural classes of transmembrane proteins (the other being the alpha-helical membrane proteins). They have their membrane-spanning segments entirely composed of short amphipathic beta-strands that twist and coil in order to form a barrel (beta-barrel). They have been found up to now only in the outer membranes of Gram-negative Bacteria and presumably (based on low resolution experimental data) on the outer surfaces of mitochondria and chloroplasts. They perform a series of very important biological functions such as membrane transport, receptor activity, and enzyme function or have a structural role. The smallest known transmembrane beta-barrels are composed of 8 beta-strands, whereas the largest are composed of 24 beta-strands even though it is possible that barrels with a larger number exist.

Outer Membrane: The term refers to the external (outside) membranes of Gram-negative bacteria, chloroplasts and mitochondria. The outer membrane of Gram-negative bacteria has a unique and unusual structure. The outer leaflet of the membrane is composed of a complex lipopolysaccharide (LPS) whose lipid portion acts as an endotoxin. Another noticeable difference of the outer membrane (at least in Bacteria) is the fact that proteins that are embedded in it (integral membrane proteins), are having their membrane-spanning segments entirely composed of beta-strands (beta-barrel outer membrane proteins), as opposed to integral membrane proteins in any other membrane which have their membrane spanning segments formed by hydrophobic alpha-helices (alpha-helical membrane proteins).

Gram-Negative Bacteria: Traditionally, Bacteria are divided according to their behaviour to the Gram staining. Bacteria that are stained by the Gram’s method are commonly referred to as Gram-positive, whereas others (that are not stained) are referred to as Gram negative. Gram-negative Bacteria include a number of important classes such as proteobacteria, cyanobacteria, spirochaetes, green sulfur and green non-sulfur bacteria. They all share a common structure in their surface which is composed of a cytoplasmic membrane, a periplasmic space and an outer membrane.

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