Biological activities of 1,1,6-trisubstituted indanes: beyond magainin 2

Membrane orientation of MSI-78 measured by sum frequency generation vibrational spectroscopy

Antimicrobial peptides (AMPs) selectively disrupt bacterial cell membranes to kill bacteria whereas they either do not or weakly interact with mammalian cells. The orientations of AMPs in lipid bilayers mimicking bacterial and mammalian cell membranes are related to their antimicrobial activity and selectivity. To understand the role of AMP-lipid interactions in the functional properties of AMPs better, we determined the membrane orientation of an AMP (MSI-78 or pexiganan) in various model membranes using sum frequency generation (SFG) vibrational spectroscopy. A solid-supported single 1,2-dipalmitoyl-an-glycero-3-[phospho-rac-(1-glycerol)] (DPPG) bilayer or 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG) bilayer was used as a model bacterial cell membrane. A supported 1,2-dipalmitoyl-an-glycero-3-phosphocholine (DPPC) bilayer or a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer was used as a model mammalian cell membrane. Our SFG results indicate that the helical MSI-78 molecules are associated with the bilayer surface with ∼70° deviation from the bilayer normal in the negatively charged gel-phase DPPG bilayer at 400 nM peptide concentration. However, when the concentration was increased to 600 nM, MSI-78 molecules changed their orientation to make a 25° tilt from the lipid bilayer normal whereas multiple orientations were observed for an even higher peptide concentration in agreement with toroidal-type pore formation as reported in a previous solid-state NMR study. In contrary, no interaction between MSI-78 and a zwitterionic DPPC bilayer was observed even at a much higher peptide concentration (∼12,000 nM). These results demonstrate that SFG can provide insights into the antibacterial activity and selectivity of MSI-78. Interestingly, the peptide exhibits a concentration-dependent membrane orientation in the lamellar-phase POPG bilayer and was also found to induce toroidal-type pore formation. The deduced lipid flip-flop from SFG signals observed from lipids also supports MSI-78-induced toroidal-type pore formation.

A fourth scale sensitive to the magnetic field; intermolecular frequency symmetry in a specific interaction between protein and low-molecular compound

We found a new method that a specific interaction between prion, i.e., high-molecular compound, and Cp-60, i.e., low-molecular one, could be successfully elucidated with intermolecular frequency symmetry (IFS). To accomplish this, the former sequence is analyzed with a sequence Fourier analysis used average nuclear (N) resonant frequency scale as a fourth one, and the latter structure with a ¹³C-NMR software. Further, such the symmetry could be observed in a specific interaction between a segment of human immunodeficiency virus (HIV)gag and PA-457 or between 1918 neuraminidase and peramivir. Therefore, the IFS rule seems to be evolutionarily conserved as a necessary condition even in a specific protein-organic compound interaction.

Analysis of the peptides (Prp106-126, MSI-78A, and Oxaldie 1) with the same biological activity by discrete Fourier transform: toward a selection rule in ligand-receptor interaction

Here, we first report a novel method in which the "desired cross-spectrum" of the peptides Prp106-126, MSI-78A, and oxaldie 1 with the same biological activities is obtained by the multiplication of two cross-spectra derived from the RNA sequence and from the cognate amino acid sequence by discrete Fourier transform (DFT), respectively. Based on a well-known method reported previously, we investigated the cross-spectrum by the multiplication of two of three desired cross-spectra. As a result, we found that one prominent peak occurring in the three cross-spectra showed the same frequency when a binary scale was used as a parameter of nucleotide or amino acid in the analysis. Moreover, we examined the relationship between a binary scale and other physicochemical ones. Almost the same results could be reproduced when the absolute electronegativity scale (or the absolute hardness one) was used, but not in the case of the hydrophobic or electron-ion interacting potential scale reported previously. This indicates that either the absolute electronegativity scale (or the absolute hardness one) or a binary scale, or both is very useful in extracting the information desired for various proteins by the present method from the amino acid and the RNA sequence.

Novel biological activity of the region (106-126) on human prion sequence

We report that the synthetic peptide Prp106-126 (KTNMKHMAGAAAAGAVVGGLG-COOH) and the reversed peptide Prp126-106 (GLGGVVAGAAAAGAMHKMNTK-COOH) of human prion (hPrp) can express the decarboxylase activity for oxaloacetate in the presence of trifluoroethanol, similar to that of Oxaldie 1 (LAKLLKALAKLLKK-CONH2) reported previously. The degree of the relative activity of Prp106-126 and Prp126-106 to Oxaldie 1 is 0.47 and 0.21, respectively. Based on this experimental result, we applied the informational system method (ISM) developed by Veljkovic et al. to the amino acid sequence of Prp106-126 and Prp126-106 to extract a common factor. The same spectra were obtained, indicating that the same periodicity may be conserved on their sequences, as a necessary factor for expressing the same biological activity, irrespective of the orientation of the primary sequence.

The structure, dynamics and orientation of antimicrobial peptides in membranes by multidimensional solid-state NMR spectroscopy

Linear peptide antibiotics have been isolated from amphibians, insects and humans and used as templates to design cheaper and more potent analogues for medical applications. Peptides such as cecropins or magainins are < or = 40 amino acids in length. Many of them have been prepared by solid-phase peptide synthesis with isotopic labels incorporated at selected sites. Structural analysis by solid-state NMR spectroscopy and other biophysical techniques indicates that these peptide antibiotics strongly interact with lipid membranes. In bilayer environments they exhibit amphipathic alpha-helical conformations and alignments of the helix axis parallel to the membrane surface. This contrasts the transmembrane orientations observed for alamethicin or gramicidin A. Models that have been proposed to explain the antibiotic and pore-forming activities of membrane-associated peptides, as well as other experimental results, include transmembrane helical bundles, wormholes, carpets, detergent-like effects or the in-plane diffusion of peptide-induced bilayer instabilities.