Organizational Unit: Department of Chemical and Biological Engineering
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Publication Metadata only Targeting cancer cells via tumor-homing peptide CREKA functional PEG nanoparticles(Elsevier, 2016) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Okur, Aysu Ceren; Erkoç, Pelin; Kızılel, Seda; Master Student; PhD 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; 28376Targeting cell microenvironment via nano-particle based therapies holds great promise for treatment of various diseases. One of the main challenges in targeted delivery of nanoparticles for cancer therapy includes reduced localization of delivery vehicles at tumor site. The therapeutic efficacy of drugs can be improved by recruiting delivery vehicles towards specific region of tumorigenesis in the body. Here, we demonstrate an effective approach in creating PEG particles via water-in-water emulsion technique where tumor-homing peptide CREKA was used for functionalization. Simultaneous conjugation of laminin peptide IKVAV into hydrogel network and influence of altered combinations of ligands on intracellular uptake of anticancer drugs by HeLa cells were investigated. CREKA conjugated hydrogel nanoparticles were more effective to improve apoptotic effects of the model drug Doxorubicin (DOX) compared to that of particles conjugated with other peptides. Fluorescence intensity analysis on confocal micrographs suggested significantly higher cellular uptake of CREKA conjugated PEG particles than internalization of nanoparticles in other groups. We observed that fibrin binding ability of PEG particles could be increased up to 94% through CREKA conjugation. Our results suggest the possibility of cancer cell targeting via CREKA-functional PEG nanoparticles.Publication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.Publication Metadata only [BMIM][OAc] coating layer makes activated carbon almost completely selective for CO2(Elsevier Science Sa, 2022) N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Durak, Özce; Zeeshan, Muhammad; Keskin, Seda; Uzun, Alper; Master Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); 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; College of Engineering; College of Engineering; N/A; N/A; 40548; 59917Tuning the molecular affinity of porous materials towards desired gases is important to achieve superior selectivity for a target separation. Herein, we report a novel composite, prepared by coating an ordinary activated carbon (AC) with an ionic liquid (IL) (1-butyl-3-methylimidazolium acetate, [BMIM][OAc]) offering an almost complete CO2 selectivity over N-2 and CH4. Data indicated that pore blockage by the IL accompanied with the enhancement in polarity and reduction in the hydrophobic character of the surface hindered the sorption of N-2 and CH4. For CO2, on the other hand, new chemisorption and physisorption sites became available associated with the IL layer on the surface, making the composite material significantly selective. Newly formed chemisorption sites attributed to the cation's acidic C2H sites, which become available with bi-layer formation. Presence of multiple competitive sorption sites with different energies was further proven with thermal analysis and detailed spectroscopic analysis. Data showed that CO2/CH4 and CO2/N-2 ideal selectivities boosted from 3.3 to 688.3 (2.3 to 54.7) and from 15.6 to 903.7 (7.1 to 74.3) at 0.1 (1) bar and 25 degrees C, respectively, upon the deposition of IL layer. Especially at lower pressures, the IL/AC material became almost fully selective for CO2 offering ideal selectivities in the order of several tens of thousands. To the best of our knowledge, the remarkable enhancement in the ideal CO2 selectivity by a straightforward post-synthesis modification of an ordinary AC, as reported here, sets a new benchmark in high-performance and efficient gas separation for similar porous materials.Publication Metadata only Performance of high capacity Li-ion pouch cells over wide range of operating temperatures and discharge rates(Elsevier Science Sa, 2020) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Alipour, Mohammad; Esen, Ekin; Varzeghani, Amir Rahimi; Kızılel, Rıza; PhD Student; PhD Student; PhD Student; Researcher; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 114475Operating temperature of Lithium-ion batteries (LIBs) significantly affects their electrochemical-thermal performance, cycle life, and cost. This study presents the thermal and electrochemical performance of 20 Ah LiFePO4 cells for 8 current rates (0.2C-5C) at 8 operating temperatures (-20 degrees C to 50 degrees C). Results show that the effects of operating temperature and current rate on cell performance differ above 10 degrees C, between 10 degrees C and 0 degrees C, and at subzero temperatures. Based on the electrochemical impedance spectroscopy (EIS) measurements, significantly higher bulk and charge-transfer resistances in conjunction with the lower diffusion coefficients results in poor battery efficiency at subzero temperatures. Optimum operating condition is 50 degrees C at a rate of 0.2C, in terms of utilized power and capacity, while a considerable power loss and capacity decrease occur below 20 degrees C. Furthermore, increasing the current rate is detrimental above 0 degrees C, whereas it improves cell performance at -10 degrees C, in terms of cell capacity. Moreover, cell temperature reaches an undesirable value at 50 degrees C and 5C rate, thus a thermal management system is necessary for high capacity LiFePO4 cells at higher temperatures and/or at higher C-rates. Additionally, temperature differences on the surface of high capacity cells reach 10 degrees C below room temperature at high current rates which can lead to nonuniform material utilization, and consequently cell failures. Finally, the cycle life of 20 Ah LiFePO4 cells decreases dramatically as discharge current rate increases. (C) 2020 Elsevier B.V. All rights reserved.Publication Metadata only Proteome analysis of the circadian clock protein PERIOD2(Wiley, 2022) Gül, Hüseyin; Selvi, Saba; Yılmaz, Fatma; Özçelik, Gözde; Olfaz-Aslan, Senanur; Yazan, Şeyma; Tiryaki, Büşra; Gül, Şeref; Öztürk, Nuri; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Yurtseven, Ali; Kavaklı, İbrahim Halil; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; 40319; 105301Circadian rhythms are a series of endogenous autonomous 24-h oscillations generated by the circadian clock. At the molecular level, the circadian clock is based on a transcription-translation feedback loop, in which BMAL1 and CLOCK transcription factors of the positive arm activate the expression of CRYPTOCHROME (CRY) and PERIOD (PER) genes of the negative arm as well as the circadian clock-regulated genes. There are three PER proteins, of which PER2 shows the strongest oscillation at both stability and cellular localization level. Protein-protein interactions (PPIs) or interactome of the circadian clock proteins have been investigated using classical methods such as two-dimensional gel electrophoresis, immunoprecipitation-coupled mass spectrometry, and yeast-two hybrid assay where the dynamic and weak interactions are difficult to catch. To identify the interactome of PER2 we have adopted proximity-dependent labeling with biotin and mass spectrometry-based identification of labeled proteins (BioID). In addition to known interactions with such as CRY1 and CRY2, we have identified several new PPIs for PER2 and confirmed some of them using co-immunoprecipitation technique. This study characterizes the PER2 protein interactions in depth, and it also implies that using a fast BioID method with miniTurbo or TurboID coupled to other major circadian clock proteins might uncover other interactors in the clock that have yet to be discovered.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 Quasi-harmonic fluctuations of two bound peptides(Wiley-Blackwell, 2012) N/A; Department of Chemical and Biological Engineering; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 216930; 179997Binding of two short peptides of sequences ASN-ASP-MET-PHE-ARG-LEU and LEU-LEU-PHE-MET-GLN-HIS and their bound complex structures is studied. Molecular dynamic simulations of the three structures around their respective minimum energy conformations are performed and a quasi-harmonic analysis is performed over the trajectories generated. The fluctuation correlation matrix is constructed for all C-alpha-atoms of the peptides for the full trajectory. The spring constant matrix between peptide C-alpha-atoms is obtained from the correlation matrix. Statistical thermodynamics of fluctuations, the energies, entropies, and the free energies of binding are discussed in terms of the quasi-harmonic model. Sites contributing to the stability of the system and presenting high affinity for binding are determined. Contribution of hydrophobic forces to binding is discussed. Quasi-harmonic approximation identifies the essential subspace of motions, the important interactions, and binding sites, gives the energetic contribution of each individual interaction, and filters out noise observed in molecular dynamics owing to uncorrelated motions. Comparison of the molecular dynamics results with those of the quasi-harmonic model shows the importance of entropy change, resulting from water molecules being liberated from the surfaces of the two peptides upon binding.Publication Metadata only How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues(Cell Press, 2005) Haliloğlu, Türkan; Ma, Buyong; Nussinov, Ruth; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high-frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.Publication Metadata only Determination of the correspondence between mobility (rigidity) and conservation of the interface residues(IEEE, 2010) N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; N/A; Keskin, Özlem; Gürsoy, Attila; Makinacı, Gözde Kar; Faculty Member; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Department of Computer Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26605; 8745; N/AHot spots at protein interfaces may play specific functional roles and contribute to the stability of the protein complex. These residues are not homogeneously distributed along the protein interfaces; rather they are clustered within locally tightly packed regions forming a network of interactions among themselves. Here, we investigate the organization of computational hot spots at protein interfaces. A list of proteins whose free and bound forms exist is examined. Inter-residue distances of the interface residues are compared for both forms. Results reveal that there exist rigid block regions at protein interfaces. More interestingly, these regions correspond to computational hot regions. Hot spots can be determined with an average positive predictive value (PPV) of 0.73 and average sensitivity value of 0.70 for seven protein complexes.Publication Metadata only Opportunities and challenges of MOF-based membranes in gas separations(Elsevier, 2015) Avci, Ahmet K.; N/A; Department of Chemical and Biological Engineering; Adatoz, Elda Beruhil; Keskin, Seda; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 40548Gas separation using metal organic framework (MOF) membranes has become an increasingly important research field over the last years. Several recent studies have shown that thin-film MOF membranes and MOF/polymer composite membranes can outperform well known polymer and zeolite membranes in various gas separation applications. The continuously increasing number of experimental and computational studies emphasizes the superior membrane properties of MOFs. In this review, we present a summary of experimental and computational studies both for thin-film MOF membranes and MOF/polymer composite membranes. We aim to address opportunities and challenges related with use of MOF membranes for gas separations as well as give directions on the requirements for employing these membranes in practical applications. (C) 2015 Elsevier B.V. All rights reserved.