Browsing by Author "Iliev S."
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Item Characteristics of a Folate Receptor-α Anchored into a Multilipid Bilayer Obtained from Atomistic Molecular Dynamics Simulations(2020-01-14) Gocheva G.; Ivanova N.; Iliev S.; Petrova J.; Madjarova G.; Ivanova A.Thorough computational description of the properties of membrane-anchored protein receptors, which are important for example in the context of active targeting drug delivery, may be achieved by models representing as close as possible the immediate environment of these macromolecules. An all-atom bilayer, including 35 different lipid types asymmetrically distributed among the two monolayers, is suggested as a model neoplastic cell membrane. One molecule of folate receptor-α (FRα) is anchored into its outer leaflet, and the behavior of the system is explored by atomistic molecular dynamics simulations. The total number of atoms in the model is â¼185â»000. Three 1-μs-long simulations are carried out, where physiological conditions (310 K and 1 bar) are maintained with three different pressure scaling schemes. To evaluate the structure and the phase state of the membrane, the density profiles of the system, the average area per lipid, and the deuterium order parameter of the lipid tails are calculated. The bilayer is in liquid ordered state, and the specific arrangement varies between the three trajectories. The changes in the structure of FRα are investigated and are found time- A nd ensemble-dependent. The volume of the ligand binding pocket fluctuates with time, but this variation remains independent of the more global structural alterations. The latter are mostly ``waving`` motions of the protein, which periodically approaches and retreats from the membrane. The semi-isotropic pressure scaling perturbs the receptor most significantly, while the isotropic algorithm induces rather slow changes. Maintaining constant nonzero surface tension leads to behavior closest to the experimentally observed one.Item The genomic history of southeastern Europe(2018-03-08) Mathieson I.; Alpaslan-Roodenberg S.; Posth C.; Szécsényi-Nagy A.; Rohland N.; Mallick S.; Olalde I.; Broomandkhoshbacht N.; Candilio F.; Cheronet O.; Fernandes D.; Ferry M.; Gamarra B.; Fortes G.G.; Haak W.; Harney E.; Jones E.; Keating D.; Krause-Kyora B.; Kucukkalipci I.; Michel M.; Mittnik A.; Nägele K.; Novak M.; Oppenheimer J.; Patterson N.; Pfrengle S.; Sirak K.; Stewardson K.; Vai S.; Alexandrov S.; Alt K.W.; Andreescu R.; Antonović D.; Ash A.; Atanassova N.; Bacvarov K.; Gusztáv M.B.; Bocherens H.; Bolus M.; Boroneanţ A.; Boyadzhiev Y.; Budnik A.; Burmaz J.; Chohadzhiev S.; Conard N.J.; Cottiaux R.; Čuka M.; Cupillard C.; Drucker D.G.; Elenski N.; Francken M.; Galabova B.; Ganetsovski G.; Gély B.; Hajdu T.; Handzhyiska V.; Harvati K.; Higham T.; Iliev S.; Janković I.; Karavanić I.; Kennett D.J.; Komšo D.; Kozak A.; Labuda D.; Lari M.; Lazar C.; Leppek M.; Leshtakov K.; Vetro D.L.; Los D.; Lozanov I.; Malina M.; Martini F.; McSweeney K.; Meller H.; Mentušić M.; Mirea P.; Moiseyev V.; Petrova V.; Douglas Price T.; Simalcsik A.; Sineo L.; Šlaus M.; Slavchev V.; Stanev P.; Starović A.; Szeniczey T.; Talamo S.; Teschler-Nicola M.; Thevenet C.; Valchev I.; Valentin F.; Vasilyev S.; Veljanovska F.; Venelinova S.; Veselovskaya E.; Viola B.; Virag C.; Zaninović J.; Zaüner S.; Stockhammer P.W.; Catalano G.; Krauß R.; Caramelli D.; Zariną G.; Gaydarska B.; Lillie M.; Nikitin A.G.; Potekhina I.; Papathanasiou A.; Borić D.; Bonsall C.; Krause J.; Pinhasi R.; Reich D.Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.