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Publication Metadata only A molecular dynamics study of allosteric transitions in Leishmania mexicana pyruvate kinase(Cell Press, 2015) Naithani, Ankita; Taylor, Paul; Walkinshaw, Malcolm D.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997A comparative molecular dynamics analysis of the pyruvate kinase from Leishmania mexicana is presented in the absence and presence of the allosteric effector fructose 2,6-bisphosphate. Comparisons of the simulations of the large 240 kDa apo and holo tetramers show that binding of fructose 2,6-bisphosphate cools the enzyme and reduces dynamic movement, particularly of the B-domain. The reduced dynamic movement of the holo form traps the pyruvate kinase tetramer in its enzymatically active state with the B-domain acting as a lid to cover the active site. The simulations are also consistent with a transition of the mobile active-site alpha 6' helix, which would adopt a helical conformation in the active R-state and a less structured coil conformation in the inactive T-state. Analysis of the rigid body motions over the trajectory highlights the concerted anticorrelated rigid body rocking motion of the four protomers, which drives the T to R transition. The transitions predicted by these simulations are largely consistent with the Monod-Wyman-Changeux model for allosteric activation but also suggest that rigidification or cooling of the overall structure upon effector binding plays an additional role in enzyme activation.Publication Metadata only A new dataset of non-redundant protein/protein interfaces(Biophysical Society, 2003) Tsai, CJ; Wolfson, H; Nussinov, R; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605Publication Metadata only An all-aqueous approach for physical immobilization of PEG-lipid microgels on organoid surfaces(Elsevier, 2020) N/A; N/A; Department of Chemical and Biological Engineering; Akolpoğlu, Mükrime Birgül; İnceoğlu, Yasemin; Kızılel, Seda; Master Student; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 28376Emulsion-based generation of hydrogel particles has been widely explored for numerous applications in fields such as biomedical, food, and drug delivery. Water-in-water emulsion (w/w) is an organic solvent-free approach and exploits solely aqueous media to generate nano- or micropartides. This strategy is environment-friendly and favorable for biomedical applications where biocompatibility is the ultimate criterion. Hence, PEG-based microgels can be synthesized with desired size and functionality using w/w emulsion technique. To estimate the influence of emulsification parameters on size and stability of PEG-lipid microgels, optimizations using three independent input variables were carried out: (i) ultrasonication power, (ii) ultrasonication duration, and (iii) duration of light exposure. Physical immobilization of microgels on islet-organoids was achieved through hydrophobic interactions. Cell function and viability were assessed thoroughly after microgel immobilization. Microgel size is dependent on ultrasonication parameters and microgel stability is vastly determined by the duration of light exposure. Immobilization of microgels with 5 mM lipid moiety promoted coating of islet-organoids. Coated organoids retained their function and viability without significant adverse effects. This is important for understanding fundamental aspects of PEG-lipid microgels using w/w emulsion, useful for possible drug/gene delivery applications to increase treatment efficiency and ultimately lead to clinical translation of PEG microgels for biomedical applications.Publication Metadata only Conformation and aggregation of peptides at interfaces(Cell Press, 2014) Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; Department of Mechanical Engineering; College of Engineering; 109820Publication Metadata only Cyto/hemocompatible magnetic hybrid nanoparticles (ag2s-fe3o4) with luminescence in the near-infrared region as promising theranostic materials(Elsevier, 2015) Grandfils, Christian; Ojea-Jimenez, Isaac; Rossi, Francois; Dogan, Nurcan; Department of Physics; N/A; Department of Chemistry; Department of Chemistry; N/A; Kiraz, Alper; Hocaoğlu, İbrahim; Aşık, Didar; Acar, Havva Funda Yağcı; Ulusoy, Gülen; Faculty Member; PhD Student; Master Student; Faculty Member; N/A; Department of Physics; Department of Chemistry; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 22542; N/A; N/A; 178902; N/ASmall hybrid nanoparticles composed of highly biocompatible Ag2S quantum dots (QD) emitting in the near-infrared region and superparamagnetic iron oxide (SPION) are produced in a simple extraction method utilizing ligand exchange mechanism. Hybrid nanoparticles luminesce at the same wavelength as the parent QD, therefore an array of hybrid nanoparticles with emission between 840 and 912 nm were easily produced. Such hybrid structures have (1) strong luminescence in the medical imaging window eliminating the autofluoresence of cells as effective optical probes, (2) strong magnetic response for magnetic targeting and (3) good cyto/hemocompatibility. An interesting size dependent cytotoxicity behavior was observed in HeLa and NIH/3T3 cell lines: smallest particles are internalized significantly more by both of the cell lines, yet showed almost no significant cytotoxicity in HeLa between 10 and 25 mu g/mL Ag concentration but were most toxic in NIH/3T3 cells. Cell internalization and hence the cytotoxicity enhanced when cells were incubated with the hybrid nanoparticles under magnetic field, especially with the hybrid nanoparticles containing larger amounts of SPION in the hybrid composition. These results prove them as effective optical imaging agents and magnetic delivery vehicles. Combined with the known advantages of SPIONs as a contrast agent in MRI, these particles are a step forward for new theranostics for multimode imaging and magnetic targeting.Publication Metadata only Designing covalent organic framework-based light-driven microswimmers towards therapeutic applications(Wiley, 2023) Sridhar, Varun; Yıldız, Erdost; Rodríguez-Camargo, Andrés; Lyu, Xianglong; Yao, Liang; Wrede, Paul; Aghakhani, Amirreza; Akolpoglu, Birgul M.; Podjaski, Filip; Lotsch, Bettina V.; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 297104While micromachines with tailored functionalities enable therapeutic applications in biological environments, their controlled motion and targeted drug delivery in biological media require sophisticated designs for practical applications. Covalent organic frameworks (COFs), a new generation of crystalline and nanoporous polymers, offer new perspectives for light-driven microswimmers in heterogeneous biological environments including intraocular fluids, thus setting the stage for biomedical applications such as retinal drug delivery. Two different types of COFs, uniformly spherical TABP-PDA-COF sub-micrometer particles and texturally nanoporous, micrometer-sized TpAzo-COF particles are described and compared as light-driven microrobots. They can be used as highly efficient visible-light-driven drug carriers in aqueous ionic and cellular media. Their absorption ranging down to red light enables phototaxis even in deeper and viscous biological media, while the organic nature of COFs ensures their biocompatibility. Their inherently porous structures with ≈2.6 and ≈3.4 nm pores, and large surface areas allow for targeted and efficient drug loading even for insoluble drugs, which can be released on demand. Additionally, indocyanine green (ICG) dye loading in the pores enables photoacoustic imaging, optical coherence tomography, and hyperthermia in operando conditions. This real-time visualization of the drug-loaded COF microswimmers enables unique insights into the action of photoactive porous drug carriers for therapeutic applications.Publication Metadata only Detection of human kappa-opioid antibody using microresonators with integrated optical readout(Elsevier advanced Technology, 2010) N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Timurdoğan, Erman; Özber, Natali; Nargül, Sezin; Yavuz, Serhat; Kılıç, M. Salih; Kavaklı, İbrahim Halil; Ürey, Hakan; Alaca, Burhanettin Erdem; PhD Student; Master Student; PhD Student; Master Student; Resercher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; 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; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40319; 8579; 115108Label-free detection of the interaction between hexahistidine-tagged human kappa-opioid receptor membrane protein and anti-His antibody is demonstrated in liquid by an optical microelectromechanical system utilizing electromagnetically actuated microresonators Shift in resonance frequency due to accretion of mass on the sensitive surface of microresonators is monitored via an integrated optical readout a frequency resolution of 2 Hz is obtained Together with a sensitivity of 7 ppm/(ng/ml)) this leads to a minimum detectable antibody concentration of 57 ng/ml for a 50-kHz device the measurement principle is shown to impart immunity to environmental noise, facilitate operation in liquid media and bring about the prospect for further miniaturization of actuator and readout leading to a portable biochemical sensor.Publication Metadata only Digital monitoring of the microchannel filling flow dynamics using a non-contactless smartphone-based nano-liter precision flow velocity meter(Elsevier Advanced Technology, 2024) Xu, Weiming; Köydemir, Hatice Ceylan; Department of Mechanical Engineering; Atik, Abdulkadir Yasin; Beker, Levent; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of EngineeringMicrofluidic systems find widespread applications in diagnostics, biological research, chemistry, and engineering studies. Among their many critical parameters, flow rate plays a pivotal role in maintaining the functionality of microfluidic systems, including droplet-based microfluidic devices and those used in cell culture. It also significantly influences microfluidic mixing processes. Although various flow rate measurement devices have been developed, the challenge remains in accurately measuring flow rates within customized channels. This paper presents the development of a 3D-printed smartphone-based flow velocity meter. The 3D-printed platform is angled at 30 degrees to achieve transparent flow visualization, and it doesn't require any external optical components such as external lenses and filters. Two LED modules integrated into the platform create a uniform illumination environment for video capture, powered directly by the smartphone. The performance of our platform, combined with a customized video processing algorithm, was assessed in three different channel types: uniform straight channels, straight channels with varying widths, and vessel-like channel patterns to demonstrate its versatility. Our device effectively measured flow velocities from 5.43 mm/s to 24.47 mm/s, with video quality at 1080p resolution and 60 frames per second, for which the measurement range can be extended by adjusting the frame rate. This flow velocity meter can be a useful analytical tool to evaluate and enhance microfluidic channel designs of various lab-on-a-chip applications.Publication Metadata only Dynamic estimation of FRET correction factors to study redox protein interactions(Cell Press, 2017) Department of Chemistry; N/A; Bayraktar, Halil; Manioğlu, Selen; Faculty Member; Master Student; Department of Chemistry; College of Sciences; Graduate School of Sciences and Engineering; 201764; N/AN/APublication Metadata only Effect of polymeric viscoelastic environment on multiscale structural dynamics of lipid bilayers(Cell Press, 2022) N/A; N/A; Department of Chemical and Biological Engineering; Karaz, Selcan; Şenses, Erkan; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 280298N/A
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