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{ 1 H}-15 N-NOEs (A), longitudinal (B) and transverse (C) relaxation data for partially N-15 labelled maximin H6 in DPC (black) and SDS (grey) micelles given as a function of residue number.
Source publication
In order to investigate the functional and structural properties of cationic alpha-helical peptides in two different membranes, we studied the 20-residue peptide maximin H6 in two membrane-mimetic systems by NMR spectroscopy using partially (15)N-labeled peptide and paramagnetic relaxation enhancements. Maximin H6, which is found in skin secretions...
Contexts in source publication
Context 1
... order to investigate the dynamic behaviour of maximin H6 in SDS and DPC micelles, we determined their longitudinal (T 1 ) and transverse (T 2 ) relaxation times as well as { 1 H} 15 N-NOEs of par- tially 15 N-labeled maximin H6 (Fig. 4). The peptide shows a quite rigid structure between residues 5 and 18 in both micelle systems (high T 1 , low T 2 and high hetero NOEs) with more flexibility at the N-and C-termini. However, even at the termini, the peptide cannot be described as freely flexible, as such a situation would be charac- terized by negative { 1 H} 15 N-NOEs. The relaxation data also show that maximin H6 is more mobile in SDS. This enhanced flexibility in SDS micelles is probably the reason for the a-helix being better defined for a longer stretch in DPC micelles. The rmsd for the back- bone between the two mean structures of maximin H6 in DPC and in SDS micelles is 1.14 (for residues ...
Context 2
... order to investigate the dynamic behaviour of maximin H6 in SDS and DPC micelles, we determined their longitudinal (T 1 ) and transverse (T 2 ) relaxation times as well as { 1 H} 15 N-NOEs of par- tially 15 N-labeled maximin H6 (Fig. 4). The peptide shows a quite rigid structure between residues 5 and 18 in both micelle systems (high T 1 , low T 2 and high hetero NOEs) with more flexibility at the N-and C-termini. However, even at the termini, the peptide cannot be described as freely flexible, as such a situation would be charac- terized by negative { 1 H} 15 N-NOEs. ...
Citations
... Orientations parallel to the surface were also found for the antimicrobial peptide maximin H6 in both SDS and DPC micelles [37]. This amphipathic α-helical peptide showed generally higher solvent PREs in SDS compared to DPC micelles and 15 N relaxation times indicated that this peptide is relatively rigid in SDS and even more in DPC micelles. ...
... One striking difference to the anionic outer membrane of bacteria is that eukaryotic ones mainly consist of neutral and zwitterionic lipids and as a result do not have a net charge, which diminishes the interaction with the cationic AMPs [63]. Nevertheless, side effects on eukaryotic cells cannot be ruled out as, for example, hemolytic activity was shown for a number of AMPs like melittin [64] and maximin H6 [37]. For a better understanding of AMPs not only the 3D atomic resolution structure but also the dynamics, immersion depth and the orientation of the peptides relative to the membrane are of interest. ...
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
... This leads to solvent PREs (paramagnetic relaxation enhancements) which depend on the distance to the surface of the micelle and allow the positioning of individual nuclei within the micelle. [18][19][20]23 Gd(DTPA-BMA) has been shown to be inert against proteins and micelle forming lipids. 20,24 Experimental solvent PREs for the investigated macrolides are indicated on the prototypic structure of azithromycin in Figure 2. ...
Interactions of macrolide antibiotics with biological membranes contribute to their bioavailability but are also involved in the formation of phospholipidosis, which is caused by the inhibition of phospholipase A(1) activity. We determined the interaction strength and localization of macrolide antibiotics with membrane-mimetics. Macrolides bind to membrane-mimetics with the positively charged amino groups being close to the micelle surface and thereby protect the lipids from being degraded by phospholipase A(1) rather than inhibiting the enzyme.
... In cases where the number of PREs does not enable a stable least-square fitting the proportionality constant obtained on a larger system can be used. This method was so far used to obtain the complete positioning of the antimicrobial peptides CM15 and maximin H6 in DPC and SDS micelles [18, 47] as well as the transmembrane helix 7 of yeast V-ATPase [47]. The use of Gd(DTPA-BMA) to make the environment paramagnetic has the considerable advantage that it does not require isotopic labeling or any chemical modification of the system under study. ...
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
... Consequently, a number of structural studies of antimicrobial peptides have used DPC as a model for mammalian membranes. Examples include indolicidin (Rozek et al., 2000), maximin H6 (Kosol and Zangger, 2010), fallaxidin 4.1a (Sherman et al., 2009), and a number of other peptides (Porcelli et al., 2008; for a recent review, see Haney et al., 2009). CD spectra were recorded for 1018, 1019, Bac2A, and W3 in DPC micelles to determine the structure these peptides adopt in the presence of uncharged lipids. ...
The structure and function of the synthetic innate defense regulator peptide 1018 was investigated. This 12 residue synthetic peptide derived by substantial modification of the bovine cathelicidin bactenecin has enhanced innate immune regulatory and moderate direct antibacterial activities. The solution state NMR structure of 1018 in zwitterionic dodecyl phosphocholine (DPC) micelles indicated an α-helical conformation, while secondary structures, based on circular dichroism measurements, in anionic sodium dodecyl sulfate (SDS) and phospholipid vesicles (POPC/PG in a 1:1 molar ratio) and simulations revealed that 1018 can adopt a variety of folds, tailored to its different functions. The structural data are discussed in light of the ability of 1018 to potently induce chemokine responses, suppress the LPS-induced TNF-α response, and directly kill both Gram-positive and Gram-negative bacteria.
Background
COVID-19 is a worldwide threat because of the incessant spread of SARS-CoV-2 which urges the development of suitable antiviral drug to secure our society. Already, a group of peptides have been recommended for SARS-CoV-2, but not yet established. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins.
Methods
Here, we have summarized several reported amphiphilic peptides and their in-silico docking analysis with spike glycoprotein of SARS-CoV-2.
Result
The result revealed the complex formation of spike protein and amphiphilic peptides with higher binding affinity. It was also observed that PalL1 (ARLPRTMVHPKPAQP), 10AN1 (FWFTLIKTQAKQPARYRRFC), THETA defensin (RCICGRGICRLL) and mucroporin M1 (LFRLIKSLIKRLVSAFK) showed the binding free energy more than -1000 kcal/mol. Molecular pI and hydrophobicity are also important factors of peptides to enhance the binding affinity with spike protein of SARS-CoV-2
Conclusion
In the light of these findings, it is necessary to check the real efficacy of amphiphilic peptides in-vitro to in-vivo experimental set up to develop an effective anti-SARS-CoV-2 peptide drug, which might help to control the current pandemic situation.
A synthetic route to a trifluoromethyl and thiol containing glucose derivative (2,2,2-trifluoroethyl 6-thio-β-d-glucopyranoside) is presented, which is based on microwave-assisted Fischer glycosylation under increased pressure. This water-soluble, neutral thiol-compound can be used to selectively introduce a fluorine probe for 19F NMR spectroscopy on cysteines in proteins. It can be attached under mild conditions in an aqueous environment without the risk of denaturing the protein. This tag has been applied to determine the redox-state of two cysteine residues in a bacterial transcription activator. Qualitative information about the solvent accessibility can be obtained from F-19 solvent PREs.
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
Many important processes in life take place in or around the cell membranes. Lipids have different properties regarding their membrane-forming capacities, their mobility, shape, size and surface charge, and all of these factors influence the way that proteins and peptides interact with the membrane. In order for us to correctly understand these interactions, we need to be able to study all aspects of the interplay between lipids and peptides and proteins. Solution-state NMR offers a somewhat unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating peptide-lipid interaction, and special attention is given to the various membrane mimetics that are used to model the membrane. Examples from the field of cell-penetrating peptides and their lipid interactions will be given. The importance of studying lipid and peptide dynamics, which reflect on the effect that peptides have on bilayers, is highlighted, and in this respect, also the need for realistic membrane models.
To understand how membrane-active peptides (MAPs) function in vivo, it is essential to obtain structural information about them in their membrane-bound state. Most biophysical approaches rely on the use of bilayers prepared from synthetic phospholipids, i.e. artificial model membranes. A particularly successful structural method is solid-state NMR, which makes use of macroscopically oriented lipid bilayers to study selectively isotope-labelled peptides. Native biomembranes, however, have a far more complex lipid composition and a significant non-lipidic content (protein and carbohydrate). Model membranes, therefore, are not really adequate to address questions concerning for example the selectivity of these membranolytic peptides against prokaryotic vs eukaryotic cells, their varying activities against different bacterial strains, or other related biological issues.
Here, we discuss a solid-state 19F-NMR approach that has been developed for structural studies of MAPs in lipid bilayers, and how this can be translated to measurements in native biomembranes. We review the essentials of the methodology and discuss key objectives in the practice of 19F-labelling of peptides. Furthermore, the preparation of macroscopically oriented biomembranes on solid supports is discussed in the context of other membrane models. Two native biomembrane systems are presented as examples: human erythrocyte ghosts as representatives of eukaryotic cell membranes, and protoplasts from Micrococcus luteus as membranes from Gram-positive bacteria. Based on our latest experimental experience with the antimicrobial peptide gramicidin S, the benefits and some implicit drawbacks of using such supported native membranes in solid-state 19F-NMR analysis are discussed.
We investigated the molecular mechanisms of short peptides interacting with membrane-mimetic systems. Three short peptides were selected for this study: penetratin as a cell-penetrating peptide (CPP), and temporin A and KSL as antimicrobial peptides (AMP). We investigated the detailed interactions of the peptides with dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles, and the subsequent peptide insertion based on free energy calculations by using all-atomistic molecular dynamics simulations with the united atom force field and explicit solvent models. First, we found that the free energy barrier to insertion for the three peptides is dependent on the chemical composition of the micelles. Because of the favorable electrostatic interactions between the peptides and the headgroups of lipids, the insertion barrier into an SDS micelle is less than a DPC micelle. Second, the peptides' secondary structures may play a key role in their binding and insertion ability, particularly for amphiphilic peptides such as penetratin and KSL. The secondary structures with a stronger ability to bind with and insert into micelles are the ones that account for a smaller surface area of hydrophobic core, thus offering a possible criterion for peptide design with specific functionalities.
