PROSITE documentation PDOC00498

General diffusion Gram-negative porins signature

The outer membrane of Gram-negative bacteria acts as a molecular filter for hydrophilic compounds. Proteins, known as porins [1], are responsible for the 'molecular sieve' properties of the outer membrane. Porins form large water-filled channels which allows the diffusion of hydrophilic molecules into the periplasmic space. Some porins form general diffusion channels that allows any solutes up to a certain size (that size is known as the exclusion limit) to cross the membrane, while other porins are specific for a solute and contain a binding site for that solute inside the pores (these are known as selective porins). As porins are the major outer membrane proteins, they also serve as receptor sites for the binding of phages and bacteriocins.

General diffusion porins generally assemble as trimer in the membrane and the transmembrane core of these proteins is composed exclusively of β strands [2]. It has been shown [3] that a number of general porins are evolutionary related, these porins are:

• Enterobacteria phoE.
• Enterobacteria ompC.
• Enterobacteria ompF.
• Enterobacteria nmpC.
• Bacteriophage PA-2 LC.
• Neisseria PI.A.
• Neisseria PI.B.

As a signature pattern we selected a conserved region, located in the C-terminal part of these proteins, which spans two putative transmembrane β strands.