The bacterial porin superfamily: sequence alignment and structure prediction

• Published in: Molecular microbiology Vol. 5; no. 9; p. 2153
• Main Authors: Jeanteur, D, Lakey, J H, Pattus, F
• Format: Journal Article
• Language: English
• Published: England 01.09.1991
• Subjects: Amino Acid Sequence; Bacterial Outer Membrane Proteins - chemistry; Bacterial Outer Membrane Proteins - genetics; Biological Transport; Escherichia coli - chemistry; Escherichia coli - genetics; Gram-Negative Bacteria - chemistry; Gram-Negative Bacteria - genetics; Molecular Sequence Data; Phylogeny; Porins; Protein Conformation; Rhodobacter capsulatus - chemistry; Rhodobacter capsulatus - genetics; Sequence Homology, Nucleic Acid; Surface Properties
• ISSN: 0950-382X
• DOI: 10.1111/j.1365-2958.1991.tb02145.x

The porins of Gram-negative bacteria are responsible for the 'molecular sieve' properties of the outer membrane. They form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Owing to the strong hydrophilicity of their amino acid sequence and the nature of their secondary structure (beta strands), conventional hydropathy methods for predicting membrane topology are useless for this class of protein. The large number of available porin amino acid sequences was exploited to improve the accuracy of the prediction in combination with tools detecting amphipathicity of secondary structure. Using the constraints of beta-sheet structure these porins are predicted to contain 16 membrane-spanning strands, 14 of which are common to the two (enteric and the neisserial) porin subfamilies.