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Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
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Publication Open Access Bosonic helium droplets with cationic impurities: onset of electrostriction and snowball effects from quantum calculations(American Institute of Physics (AIP) Publishing, 2007) Coccia, E.; Bodo, E.; Marinetti, F.; Gianturco, F. A.; Yıldırım, E.; Yurtsever, M.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Variational Monte Carlo and diffusion Monte Carlo calculations have been carried out for cations such as Li(+), Na(+), and K(+) as dopants of small helium clusters over a range of cluster sizes up to about 12 solvent atoms. The interaction has been modeled through a sum-of-potential picture that disregards higher order effects beyond atom-atom and atom-ion contributions. The latter were obtained from highly correlated ab initio calculations over a broad range of interatomic distances. This study focuses on two of the most striking features of the microsolvation in a quantum solvent of a cationic dopant: electrostriction and snowball effects. They are discussed here in detail and in relation with the nanoscopic properties of the interaction forces at play within a fully quantum picture of the cluster features.Publication Open Access ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium content regulation(Wiley, 2022) Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Tiryaki, Fatmanur; Deretic, Jovana; Karalar, Elif Nur Fırat; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 206349Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their dysfunction causes cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of stable microtubules that maintain their length at a steady-state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified the Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that regulates microtubule organization and stability. Consistently, we observed an increase in tubulin polymerization and microtubule stability, as well as disrupted microtubule organization in ENKD1 overexpression. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results advance our understanding of the functional and regulatory relationship between MAPs and the primary cilium.
Publication Metadata only Multiscale dynamics of lipid vesicles in polymeric microenvironment(Mdpi, 2022) N/A; N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Karaz, Selcan; Han, Mertcan; Akay, Gizem; Önal, Asım; Nizamoğlu, Sedat; Kızılel, Seda; Şenses, Erkan; Master Student; Master Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 130295; 28376; 280298Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation. Tremendous interest in tissue engineering has made it possible to design polymeric scaffolds mimicking the topology and mechanical properties of the native extracellular microenvironment; however, A fundamental question remains unanswered: that is, how the viscoelastic extracellular environment modifies the hierarchical dynamics of lipid membranes. in this work, we used aqueous solutions of poly(ethylene glycol) (PEG) with different molecular weights to mimic the viscous medium of cells and nearly monodisperse unilamellar DMPC/DMPG liposomes as a membrane model. Using small-angle X-ray scattering (SaXS), dynamic light scattering, temperature-modulated differential scanning calorimetry, bulk rheology, and fluorescence lifetime spectroscopy, we investigated the structural phase map and multiscale dynamics of the liposome-polymer mixtures. the results suggest an unprecedented dynamic coupling between polymer chains and phospholipid bilayers at different length/time scales. the microviscosity of the lipid bilayers is directly influenced by the relaxation of the whole chain, resulting in accelerated dynamics of lipids within the bilayers in the case of short chains compared to the polymer-free liposome case. at the macroscopic level, the gel-to-fluid transition of the bilayers results in a remarkable thermal-stiffening behavior of polymer-liposome solutions that can be modified by the concentration of the liposomes and the polymer chain length.