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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 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.Publication Metadata only Gas adsorption and diffusion in a highly CO2 selective metal-organic framework: molecular simulations(Taylor and Francis Ltd, 2013) N/A; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Grand canonical Monte Carlo and equilibrium molecular dynamics simulations were used to assess the performance of an rht-type metal–organic framework (MOF), Cu-TDPAT, in adsorption-based and membrane-based separation of CH4/H2, CO2/CH4 and CO2/H2 mixtures. Adsorption isotherms and self-diffusivities of pure gases and binary gas mixtures in Cu-TDPAT were computed using detailed molecular simulations. Several properties of Cu-TDPAT such as adsorption selectivity, working capacity, diffusion selectivity, gas permeability and permeation selectivity were computed and compared with well-known zeolites and MOFs. Results showed that Cu-TDPAT is a very promising adsorbent and membrane material especially for separation of CO2 and it can outperform traditional zeolites and MOFs such as DDR, MFI, CuBTC, IRMOF-1 in adsorption-based CO2/CH4 and CO2/H2 separations.Publication Metadata only KLE-(V)AR: A new identification technique for reduced order disturbance models with application to sheet forming processes(Elsevier Sci Ltd, 2001) Rigopoulos; Apostolos; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526A new identification technique that combines the Karhunen-Loeve expansion (KLE) with the use of Vector AutoRegressive processes (VAR) is presented in this paper. Given measurements, collected over a period of time, of a set of correlated random variables the method generates a reduced order state-space dynamic model describing the spatial and temporal relationship among the variables. Some of the advantages of the new method are the fewer number of parameters needed to be estimated compared with traditional subspace methods, and its ability to efficiently track nonstationary random processes. Simulation examples from high dimensional sheet forming processes are included for illustration. (C) 2001 Elsevier Science Ltd. All rights reserved.Publication Metadata only Transcriptional regulation of the starch synthases isoforms in the leaf and the stem under long and short photoperiod in lentil(Wiley-Blackwell, 2014) Gercek, Y. C.; Oz, G. Cevahir; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Barış, İbrahim; Kavaklı, İbrahim Halil; Teaching Faculty; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; 111629; 40319N/A