Lipid II as a Target for Novel Antibiotics:Structural and Molecular Dynamics Studies.
The growing problem of antibiotic resistance in medicine raises the attention to antimicrobial substances that act on non-protein molecules, which have more conservative structure comparing to proteins or peptides. One of the most promising and studied targets is lipid II — the participant of the bacterial cell wall biosynthetic pathway. Lipid II is present in the bacterial membrane only and has a conservative chemical structure. There are several classes of natural antibiotics acting on lipid II, some of which block the peptidoglycan synthesis by formation of a strong complex with lipid II, and others have an additional bactericidal mechanism involved a violation of the membrane integrity. This review examines the prospects for using such antibacterial substances as new drugs to combat antibiotic-resistant pathogens. The main emphasis is made on the studies of membrane-embedded lipid II structure and molecular mechanisms of its recognition by water-soluble antibiotics, and also on computer modelling of their interaction.
Insulin receptor (IR) family is represented by three membrane proteins participating in organism development, growth, and vital activity. Modulation of the functioning of these receptors by external agents looks very perspective from a pharmaceutical point of view. Although IR is well studied, little is known about the role of its transmembrane (TM) domain in receptor activity. Nowadays, the major model of signal transfer by these receptors describes ligand-triggered conformational changes in the extracellular domain, bringing together TM domains that dimerize. This allows trans-autophosphorylation of intracellular domains followed by activation of secondary messengers. However, the conformation of the TM dimeric state is still unknown. Here, we studied in silico dimerization of TM segments of two closest members of the family: IR and IGF-1R. As a result, TM dimeric structures were predicted. This was done taking into account available structural data on extra- and intracellular parts of the receptors. Inspection of the extracellular segment mobility in the basal state revealed several modes of protein motion, although none of them allow TM domain dimerization. The calculated molecular dynamics of TM helices linked to intracellular domain led to a conclusion about autonomic behavior of the TM domain. Based on this data, the dimerization of TM domains was further simulated without extramembrane parts. The most probable models of TM dimeric structures were predicted and the free energy of helix-helix association in explicit lipid bilayers was evaluated. Two most energetically favorable models for IR and one for IGF-1R were delineated. Despite the lack of sequence homology, TM segments in both receptors pack in similar parallel dimers, thus suggesting a close activation mechanism.
Tk-hefu is an artificial peptide designed based on the ɑ-hairpinin scaffold, which selectively blocks voltage-gated potassium channels Kv1.3. Here we present its spatial structure resolved by NMR spectroscopy and analyze its interaction with channels using computer modeling. We apply Protein Surface Topography to suggest mutations and increase Tk-hefu affinity to Kv1.3 channel isoform. We redesign the functional surface of Tk-hefu to better match the respective surface of the channel pore vestibule. The resulting peptide Tk-hefu-2 retains Kv1.3 selectivity and displays ~20 times greater activity compared to Tk-hefu. We verify the mode of Tk-hefu-2 binding to the channel outer vestibule experimentally by site-directed mutagenesis. We argue that scaffold engineering aided by Protein Surface Topography represents a reliable tool for design and optimization of specific ion channel ligands.
Atomistic aspects of the structural organization, dynamics, and functioning of hydrated lipid bilayers - model cell membranes - are primarily governed by the fine balance of intermolecular interactions between all constituents of these systems. Besides the hydrophobic effect, which shapes the overall skeleton of lipid membranes, very important contribution to their behavior is made by hydrogen bonds (H-bonds) between lipid head groups. The latter determine such crucial phenomena in cell membranes, like dynamic ultra-nanodomain organization, hydration, fine-tuning of microscopic physico-chemical properties that allow the membrane to adapt quickly when binding/insertion external agents (proteins, etc.) The characteristics of such H-bonds (strength, spatial localization, etc.) dramatically depend on the local polarity properties of the lipid-water environment. In this work, we calculated free energies of H-bonded complexes between typical donor (NH3+, NH, OH) and acceptor (C=O, OH, COO-, COOH) groups of lipids in vacuo and in a set of explicit solvents with dielectric constants (ε) from 1 to 78.3, which mimic membrane environment at different depth. This was done using Monte Carlo simulations and an assessment of the corresponding Potential of Mean Force profiles. The strongest H-bonded complexes were observed in the nonpolar environment and their strength increased sharply with decreasing ε below 17. When ε changed, the largest free energy gain (> 10.8 kcal/mol) was observed for pairs of acceptors C=O and O(H) with donor NH3+. The complexation of the same acceptors with NH-donor in this range of ε was rather less sensitive to the environmental polarity: by ~1.5 kcal/mol. Dielectric-dependent interactions of polar lipid groups with water were evaluated as well. The results explain the delicate balance that determines the unique pattern of H-bonds for a particular lipid bilayer. Understanding the factors that regulate the propensity to H-bonding in lipid bilayers provides a fundamental basis for the rational design of new membrane nano-objects with predefined properties.
Acid-sensing ion channels (ASICs), members of the family of amiloride-sensitive degenerin/epithelial Na + -channels, are expressed in neurons of both the peripheral and central nervous system. Among six currently known isoforms of mammalian ASICs, two, namely ASIC1a and ASIC3 are widespread and have the largest physiological contribution such as synaptic plas- ticity, learning and memory as well as pain perception and inflammation development. We have previously shown that seva- nol, a new lignan isolated from Thymus armeniacus, inhibits ASIC1a and ASIC3 currents and exerts analgesic and anti- inflammatory effects when administered intravenously. Here we present a scheme for the synthesis of sevanol, which was devel- oped for the first time. In addition, sevanol analogues were syn- thesized, in which the basic core of the molecule of epiphyllic acid remained unchanged, while substituents for carboxyl groups in positions 9,10 were modified. These analogues demonstrate a clear correlation between the activity of the molecule and the number of free carboxyl groups in it. Using molecular modeling and analysis of the activity of sevanol in the presence of ASIC1a potentiator, an RF-amide peptide, we established a possible bind- ing site for sevanol on the channel. We also showed that with intranasal administration, sevanol can have the same effective analgesic effect as with intravenous administration. Such struc- tural and functional analysis demonstrates a correlation between the inhibitory effect value and the number of functional groups of the molecule, which may be important for the rational design of biologically active sevanol-based compounds.
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.
The dynamics of a two-component Davydov-Scott (DS) soliton with a small mismatch of the initial location or velocity of the high-frequency (HF) component was investigated within the framework of the Zakharov-type system of two coupled equations for the HF and low-frequency (LF) fields. In this system, the HF field is described by the linear Schrödinger equation with the potential generated by the LF component varying in time and space. The LF component in this system is described by the Korteweg-de Vries equation with a term of quadratic influence of the HF field on the LF field. The frequency of the DS soliton`s component oscillation was found analytically using the balance equation. The perturbed DS soliton was shown to be stable. The analytical results were confirmed by numerical simulations.
Radiation conditions are described for various space regions, radiation-induced effects in spacecraft materials and equipment components are considered and information on theoretical, computational, and experimental methods for studying radiation effects are presented. The peculiarities of radiation effects on nanostructures and some problems related to modeling and radiation testing of such structures are considered.