Антимикробные пептиды, нацеленные на липид II мембран бактерий: ключевой принцип действия
The investigation of antibacterial activity of three-finger cobra cytotoxins towards Gram-negative and Gram-positive bacteria showed no activity against the former species, whereas M. luteus was found most susceptible to cytotoxins. A correlation was revealed between this activity and hydrophobicity of the toxins (HTL scores), total charge and its distribution over the toxin molecule: the absence of Glu-16 residue and the presence of positively charged residues (Lys30/His31) in the tip of the loop 2
Transmembrane (TM) helices are one of the most common structural elements in membrane proteins. Their interaction in lipid environment governs the formation of protein spatial structure formation and functioning in normal and pathology. Receptor tyrosine kinases are a wide class of protein molecules having single helix as their TM domain, so dimerization process is crucial for their functioning. But lipid environment may modulate these process, and molecular details are still unclear. In present work we use computer atomistic modeling to reveal the basis of protein-lipid interactions in a model system – human glycophorin A, its mutant forms and model polypeptides. It is shown that lipid environment makes a great contribution into free energy of TM domain association. For two known point mutations of glycophorin A we show different mechanisms of changing the dimer stability. Using long molecular dynamics simulations some protein-lipid interactions sites were detected in a hydrophobic core of the bilayer. Also we observe a correlation between lipid binding sites distribution and free energy estimations that propose entropic mechanism for lipid-induced dimerization of several TM domains. In the case of natural sequence of glycophorin A these mechanism is combined with optimal packing of protein residues.
Introduction: Being important representatives of various proteomes, membrane-active cationic peptides (CPs) are attractive objects as lead compounds in the design of new antibacterial, anticancer, antifungal, and antiviral molecules. Numerous CPs are found in insect and snake venoms, where many of them reveal cytolytic properties. Due to advances in omics technologies, the number of such peptides is growing dramatically.
Areas covered: To understand structure-function relationships for CPs in a living cell, detailed analysis of their hydrophobic/hydrophilic properties is indispensable. We consider two structural classes of membrane-active CPs - latarcins (Ltc) from spider and cardiotoxins (CTXs) from snake venoms. While the former are void off disulphide bonds and conformationally flexible, the latter are structurally rigid and cross-linked with disulphide bonds. In order to elucidate structure-activity relationships behind their antibacterial, anticancer, and hemolytic effects, the properties of these polypeptides are considered on a side-by-side basis.
Expert commentary: An ever increasing number of venom-derived membrane-active polypeptides requires new methods for identification of their functional propensities and sequence-based design of novel pharmacological substances. We address these issues considering a number of the designed peptides, based either on Ltc or CTX sequences. Experimental and computer modeling techniques required for these purposes are delineated.
A computational approach to the analysis of structural and dynamical properties of all components of model membranes - membrane proteins, lipids, water and ions - has been developed. It is established that local changes in the membrane environment play an important role in the binding of membrane-active peptides and peripherical membrane proteins, causing specific clustering of lipids and initiating the formation of defects in the membrane. It is shown for the first time that lipids make a significant contribution to the free energy of spontaneous dimerization of membrane proteins. The detailed balance of various energy contributions strongly depends on the composition of the membrane and the amino acid sequence of the protein. The assumption is made that the process of association of transmembrane alpha-helices in lipid bilayers has a predominantly entropic character.
Receptor tyrosine kinases (RTK) are vital players in cell signaling governing growth and proliferation. These integral membrane proteins work only in dimeric states, so the conformation of transmembrane dimer determines the signal transferred into cell. Here, we used modern molecular modeling techniques to study details of protein-protein and protein-lipid interactions in model systems containing monomers and dimers of several receptor tyrosine kinases with glycophorin-like dimerization motifs. Comparison of structural and dynamic aspects of ErbB family members and glycophorin A (GpA) revealed similarities in their properties, especially, for ErbB1, ErbB2 and ErbB4 receptors utilizing the same GpA-like motif for dimerization in their basal state. We demonstrated that they all have similar organization of TM domain’s molecular surface in terms of both relief, hydrophobic properties and lipid binding sites resembling GpA pattern studied before. All these RTKs strongly interact with lipid acyl chains, forming stable binding sites both in monomeric and dimeric states, and the most prominent binding areas are located in monomers on the future GpA-like dimerization interfaces. Then, lipids distribution changes upon dimer formation. This is not the case for alternative packing geometries observed for the second state of ErbB1 and, especially, ErbB3. We found higher numbers of immobilized lipids near C-terminus in ErbB1 and ErbB2 active dimers, thus assuming that the existing structure of ErbB3 is also active. However, there is non-functional GpA-like motif in ErbB3 with some bound lipids present near the N-terminus, suspecting another structure for inactive receptor. However, despite considerable similarities, these RTKs have different hydrophobicity distributions along helices, that can be important in terms of preferable lipid environment. The work was funded by the Russian Academic Excellence Project ‘5-100’ and Russian Foundation for Basic Research grant 18-54-15007.
Tris(1-alkylindol-3-yl)methanes were obtained and oxidized into tris(1-alkylindol-3-yl)methylium salts. The resulting salts are more toxic to cultured tumor cells than to non-tumor ones. The cytotoxicity of tris(1-alkylindol-3-yl)methylium salts depends on the length of the substituent at the N atom of the heterocycle, increasing from an N-unsubstituted derivative toward N-butyl- and N-pentyl derivatives. A further increase in the length of the N-alkyl substituent lowers the cytotoxicity. The cytotoxicity of tris(1-alkylindol-3-yl)methylium salts for tumor cells correlates with their antibacterial and antifungal activity. Tris(1-alkylindol-3-yl)methylium salts produced a cytocide effect on Gram-positive microorganisms and the most active compounds, on Gram-negative microorganisms as well. Similar patterns of the structure-activity relationship of N-alkylated tris(indol-3-yl)methylium derivatives, which was observed for various lines of tumor cells, bacteria, and fungi, suggest the general character of the mechanisms of the death of prokaryotic and eukaryotic cells induced by these compounds.