Major histocompatibility complex (MHC) molecules are a key element of the cellular immune response. Encoded by the MHC they are a family of highly polymorphic peptide receptors presenting peptide antigens for the surveillance by T cells. We have shown that certain organic compounds can amplify immune responses by catalyzing the peptide loading of human class II MHC molecules HLA-DR. Here we show now that they achieve this by interacting with a defined binding site of the HLA-DR peptide receptor. Screening of a compound library revealed a set of adamantane derivatives that strongly accelerated the peptide loading rate. The effect was evident only for an allelic subset and strictly correlated with the presence of glycine at the dimorphic position ␤86 of the HLA-DR molecule. The residue forms the floor of the conserved pocket P1, located in the peptide binding site of MHC molecule. Apparently, transient occupation of this pocket by the organic compound stabilizes the peptide-receptive conformation permitting rapid antigen loading. This interaction appeared restricted to the larger Gly ␤86 pocket and allowed striking enhancements of T cell responses for antigens presented by these "adamantyl-susceptible" MHC molecules. As catalysts of antigen loading, compounds targeting P1 may be useful molecular tools to amplify the immune response. The observation, however, that the ligand repertoire can be affected through polymorphic sites form the outside may also imply that environmental factors could induce allergic or autoimmune reactions in an allele-selective manner.

A series of multiple nanosecond molecular dynamics simulations has been carried out for a dipalmitoylphosphatidylcholine lipid bilayer system in water solution, with ubiquinone (UQ) freely moving inside the bilayer. The focus is on the mobility and the preferential positions of the quinone molecule. Two different tail lengths have been used in the simulations to investigate the effect of the long tail, attached to the quinone-ring. The lateral diffusion rate in the nanosecond time scale, obtained for 2,3-dimethoxy-5-ethyl-6-methyl-1,4-benzoquinone (short tail, denoted UQ-et) was at 60 °C found to be roughly the same as that for the lipids. The headgroup of UQ-et preferred a location between the 4th and the 10th carbon atom in the palmitic chains of the lipids. For UQ-10 (10 unit long isoprenoid tail), two preferred positions of the headgroup were found in separate simulations with different initial configurations for the quinone; one close to the lipid headgroups, the other in the membrane midplane. Transitions between these two positions were absent and were presumably restricted by the barrier formed by the relatively ordered high-density region of the palmitic tails close to the lipid headgroups. The lateral diffusion of UQ-10 in the investigated time regime was found in the range of 10-7−10-6 cm2/s and strongly dependent on its relative position inside the membrane; in the midplane position its diffusion was more than three times faster than the diffusion of the lipids, while it was comparable with that of the lipids when the UQ-10 head was close to the membrane surface.

Antimicrobial, cationic peptides are abundant throughout nature as part of many organisms' defence against microorganisms. They exhibit a large variety of sequences and structural motifs and are thought to act by rupturing the bacterial membrane. Several models based on biophysical experiments have been proposed for their mechanism of action. Here we present the NMR-determined structure of the cyclic, cationic antimicrobial peptide cyclo(RRWWRF) both free in aqueous solution and bound to detergent micelles. The peptide has a rather flexible but ordered structure in water. A distinct structure is formed when the peptide is bound to a detergent micelle. The structures in neutral and negatively charged micelles are nearly identical but differ from that in aqueous solution. The orientation of the amino acid side chains creates an amphipathic molecule with the peptide backbone forming the hydrophilic part. The orientation of the peptide in the micelle was determined by using NOEs and paramagnetic agents. The peptide is oriented mainly parallel to the micelle surface in both detergents. Substitution of the arginine and tryptophan residues is known to influence the antimicrobial activity. Therefore the structure of the micelle-bound analogues cyclo(RRYYRF), cyclo(KKWWKF) and cyclo(RRNalNalRF) were also determined. They exhibit remarkable similarities in backbone conformation and side-chain orientation. The structure of these peptides allows the side-chain properties to be correlated to biological activity.

Antimicrobial peptides have gained a lot of interest in recent years due to their potential use as a new generation of antibiotics. It is believed that this type of relatively short, amphipathic, cationic peptide targets the bacterial membrane, and destroys the chemical gradients over the membrane via formation of stable or transient pores. Here we use the NMR structure of cyclo(RRWWRF) in a series of molecular dynamics simulations in membranes at various peptide/lipid ratios. We observe that the NMR structure of the peptide is still stable after 100 ns simulation. At a peptide/lipid ratio of 2:128, the membrane is only a little affected compared to a pure dipalmitoylphosphatidylcholine lipid membrane, but at a ratio of 12:128, the water-lipid interface becomes more fuzzy, the water molecules can reach deeper into the hydrophobic core, and the water penetration free-energy barrier changes. Moreover, we observe that the area per lipid decreases and the deuterium order parameters increase in the presence of the peptide. We suggest that the changes in the hydrophobic core, together with the changes in the headgroups, result in an imbalance of the membrane and that it is thus not an efficient hydrophobic barrier in the presence of the peptides, independent of pore formation.

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