Lipid-II forms potential “landing terrain” for lantibiotics in simulated bacterial membrane
Bacterial cell wall is targeted by many antibiotics. Among them are lantibiotics, which realize their function via interaction with transmembrane lipid-II molecule — a chemically conserved part of the cell wall synthesis pathway. To investigate structural and dynamic properties of this molecule, we have performed a series of nearly microsecond-long molecular dynamics simulations (MD) of lipid-II and some of its analogs in zwitterionic single component and charged mixed model phospholipid bilayers (the reference and mimic of the bacterial plasmatic membrane, respectively). Extensive analysis revealed that lipid-II forms a unique “amphiphilic pattern” exclusively on the surface of the model bacterial membrane (and not in the reference bilayer). We hypothesize that conserved features of lipid-II along with characteristic modulation of the bacterial membrane provide a recognition spot for many lantibiotics. This putative recognition mechanism opens new opportunities for studies on lantibiotics action and design of novel armament against resistant bacterial strains.
The proceedings is a compilation of the reports of XI International science-technical conference "Modern Trends in Biological Physics and Chemistry. BPPC-2016", organized by Sevastopol State University 25-29 of April, 2016. The proceedings contains materials of research papers, devoted to modern trends in general and molecular biophysics, nanobiophysics, and problems of modern biological, biophysical and medicinal chemistry. The publication is intended for scientists, postgraduate, students.
Alkaliphilic fungi are fundamentally different from alkalitolerant ones in terms of mechanisms of adaptation. They accumulate trehalose in cytosol and phosphatidic acids (PA) in the membrane lipids, whereas alkalitolerants contain these compounds in low amounts. But it is unclear how the composition of osmolytes and lipids changes during cytodifferentiation. In this article the composition of lipids and soluble cytosol carbohydrates in the mycelium and fruit bodies of the alkaliphilic fungus Sodiomyces alkalinus was studied. In the mycelium, mannitol and trehalose dominated, while in fruit bodies only trehalose was predominant. Phosphatidylcholines (PC), PA and sterols were major membrane lipids of the mycelium, while PC and sterols were predominant in fruit bodies. The degree of fatty acids unsaturation of the main mycelium phospholipids (PC and PA) increased with age, while that of PC did not change regardless of the developmental stage. In young mycelium, storage lipids were represented mainly by free fatty acids, and in mature mycelium and fruit bodies—by triacylglycerols. Fruit bodies contained three times less membrane lipids and twice as many storage lipids as mycelium. Trehalose was the main cytosol carbohydrate in the mycelium and fruit bodies, which confirms its key value for alkaliphily.
The proceedings is a compilation of the reports of XI International science-technical conference "Modern Trends in Biological Physics and Chemistry. BPPC-2017", organized by Sevastopol State University 2-6 of October, 2017. The proceedings contains materials of research papers, devoted to modern trends in general and molecular biophysics, nanobiophysics, problems of modern biological, biophysical and medicinal chemistry, and biophysical education. The publication is intended for scientists, postgraduate, students.
It is common to use the first-order language as a formal tool for describing properties of various (computational) structures. On the one hand, this language is well understood and easy to use; on the other, many questions that are im-portant from the applications point of view related to this language are algorithmically undecidable, i.e., cannot be answered using a computer program. These days, there exist various alternative languages that can be used for describing computational processes and their properties, for which the corresponding questions are, in contrast to the first-order language, algorithmically decidable. In this paper, we consider one of such languages, – the language of the Computational Tree Logic (CTL). It is commonly used for program verification as it is capable of describing properties of computational processes, – in particular, properties of the binary relation used in the Kripke semantics. The authors investigate the possibility of finding algorithmically first-order formulas defining the same classes of Kripke frames as the formulas of the language of CTL. It is well known the problem of finding first-order correspondents of propositional intuitionistic formulas is algorithmically undecidable. The authors reduce – using the Gödel translation of intuitionistic formulas into modal ones, and subsequently a translation of resultant modal formulas into CTL-formulas – the first-order correspondence problem for propositional intuitionistic formulas to the first-order correspondence problem for CTL-formulas on Kripke frames. As a result of this reduction, they prove that the first-order correspondence problem for CTL-formulas is algorithmically undecidable. In the conclusion, the authors discuss some possible modifications of their construction for fragments of the language of CTL as well as algorithmic decidability of the CTL correspondence problem for first-order formulas.
Neural oscillations are ubiquitously observed in the mammalian brain, but it has proven difficult to tie oscillatory patterns to specific cognitive operations. Notably, the coupling between neural oscillations at different timescales has recently received much attention, both from experimentalists and theoreticians. We review the mechanisms underlying various forms of this cross-frequency coupling. We show that different types of neural oscillators and cross-frequency interactions yield distinct signatures in neural dynamics. Finally, we associate these mechanisms with several putative functions of cross-frequency coupling, including neural representations of multiple environmental items, communication over distant areas, internal clocking of neural processes, and modulation of neural processing based on temporal predictions.
Information systems have been developed in parallel with computer science, although information systems have roots in different disciplines including mathematics, engineering, and cybernetics. Research in information systems is by nature very interdisciplinary. As it is evidenced by the chapters in this book, dynamics of information systems has several diverse applications. The book presents the state-of-the-art work on theory and practice relevant to the dynamics of information systems. First, the book covers algorithmic approaches to numerical computations with infinite and infinitesimal numbers. Also the book presents important problems arising in service-oriented systems, such as dynamic composition, analysis of modern service-oriented information systems, and estimation of customer service times on a rail network from GPS data. After that, the book addresses the complexity of the problems arising in stochastic and distributed systems. In addition, the book discusses modulating communication for improving multi-agent learning convergence. Network issues, in particular minimum risk maximum clique problems, vulnerability of sensor networks, influence diffusion, community detection, and link prediction in social network analysis, as well as a comparative analysis of algorithms for transmission network expansion planning are described in subsequent chapters. We thank all the authors and anonymous referees for their advice and expertise in providing valuable contributions, which improved the quality of this book. Furthermore, we want to thank Springer for helping us to produce this book.
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.