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α-Helical membrane-active antimicrobial peptides (AMPs) are known to act via a range of mechanisms, including the formation of barrel-stave and toroidal pores and the micellisation of the membrane (carpet mechanism). Different mechanisms imply that the peptides adopt different 3D-structures when bound at the water-membrane interface, a highly amphipathic environment. Here, an evolutionary algorithm is used to predict the 3D-structure of a range of α-helical membrane-active AMPs at the water-membrane interface by optimising amphipathicity. This amphipathic structure prediction (ASP) is capable of distinguishing between curved and linear peptides solved experimentally, potentially allowing the activity and mechanism of action of different membrane-active AMPs to be predicted. The ASP algorithm is accessible via a web interface at http://atb.uq.edu.au/asp/.
This article was published in the following journal.
Name: FEBS letters
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Bacteriocins produced by species of PEDIOCOCCUS. They range from 3.5-4.6 kDa in mass, contain a conserved YGNGVXCXK motif and beta sheet at their N-terminals, and a more diverse hydrophobic or amphiphilic C-terminal alpha helical domain. They function as antimicrobial peptides against several pathogenic species of GRAM POSITIVE BACTERIA, including LISTERIA MONOCYTOGENES and are useful as FOOD PRESERVATIVES.
A family of small peptides expressed primarily by MUCOUS MEMBRANE EPITHELIAL CELLS in vertebrates. Their structure is highly conserved and is defined by a three-leaved (trefoil) domain of 42 or 43 amino acids; it includes six cysteines that create the trefoil structure through disulfide bridges. Trefoil peptides may form dimers with each other, or associate with MUCINS and other factors. They are important for maintaining epithelial integrity and for protection from noxious agents.
A group of anaerobic, rod-shaped bacteria that show up as pink (negative) when treated by the Gram-staining method.
A genus of gram-negative, curved and spiral-shaped bacteria found in stagnant, freshwater environments. These organisms are motile by bipolar tufts of flagella having a long wavelength and about one helical turn. Some species of Spirillum cause a form of RAT-BITE FEVER.
Small cationic peptides that are an important component, in most species, of early innate and induced defenses against invading microbes. In animals they are found on mucosal surfaces, within phagocytic granules, and on the surface of the body. They are also found in insects and plants. Among others, this group includes the DEFENSINS, protegrins, tachyplesins, and thionins. They displace DIVALENT CATIONS from phosphate groups of MEMBRANE LIPIDS leading to disruption of the membrane.