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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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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 The synthesis, characterization, and theoretical hydrogen gas adsorption properties of copper(II)-3,3′-thiodipropionate complexes with imidazole derivatives(Taylor and Francis Ltd, 2013) Arici, Mursel; Yesilel, Okan Zafer; Sahin, Onur; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Three new coordination polymers, [Cu((3)-tdp)(im)(2)](n) (1), {[Cu((3)-tdp)(1-mim)(2)]0.5H(2)O}(n) (2) and {[Cu-2((3)-tdp)(2)(4-mim)(4)]H2O}(n) (3) [tdpH(2)=3,3-thiodipropionic acid, im=imidazole, 1-mim=1-methylimidazole and 4-mim=4-methylimidazole], have been prepared and characterized by spectroscopic techniques (IR and UV-Vis), elemental analyzes, magnetic measurements, thermal analyzes, and single-crystal X-ray diffraction. Complexes 1-3 crystallize in the monoclinic system with space groups of C2/c and P2(1)/c, respectively. In 1-3, tdp is a bridging ligand to form 1-D chains, which are extended into a 2-D layer by hydrogen bonding and interactions. The 3,3-thiodipropionate exhibits an unexpected coordination mode in 1-3. Simulations were used to assess the potential of the complexes in H-2 storage applications.Publication Metadata only The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides(Iop Publishing Ltd, 2009) N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Engin, Özge; Sayar, Mehmet; Erman, Burak; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering, College of Engineering; College of Engineering; N/A; 109820; 179997Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. the isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. the statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. these are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. a systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.Publication Metadata only Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers(Portland Press Ltd, 2016) Nussinov, Ruth; Jang, Hyunbum; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Muratçıoğlu, Serena; Keskin, Özlem; Gürsoy, Attila; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 26605; 8745Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the alpha 3 and alpha 4 interface; H-Ras-GTP favours alpha 4 and alpha 5. Both isoforms also populate a stable beta-sheet dimer interface formed by the effector lobe; a less stable beta-sandwich interface is sustained by salt bridges of the beta-sheet side chains. Raf's high-affinity beta-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms' dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.Publication Metadata only Identification and characterization of a new class of (6−4) photolyase from Vibrio cholerae(Amer Chemical Soc, 2019) Ozcelik, Gozde; Ozturk, Nuri; N/A; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Dikbaş, Uğur Meriç; Tardu, Mehmet; Gül, Şeref; Barış, İbrahim; Kavaklı, İbrahim Halil; Master Student; PhD Student; Researcher; Teaching Faculty; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 111629; 40319Light is crucial for many biological activities of most organisms, including vision, resetting of circadian rhythm, photosynthesis, and DNA repair. The cryptochrome/photolyase family (CPF) represents an ancient group of UV-A/blue light sensitive proteins that perform different functions such as DNA repair, circadian photoreception, and transcriptional regulation. The CPF is widely distributed throughout all organisms, including marine prokaryotes. The bacterium Vibrio cholerae was previously shown to have a CPD photolyase that repairs UV-induced thymine dimers and two CRY-DASHs that repair UV-induced single-stranded DNA damage. Here, we characterize a hypothetical gene Vca0809 encoding a new member of CPF in this organism. The spectroscopic analysis of the purified protein indicated that this enzyme possessed a catalytic cofactor, FAD, and photoantenna chromophore 6,7-dimethyl 8-ribityllumazin. With a slot blot-based DNA repair assay, we showed that it possessed (6-4) photolyase activity. Further phylogenetic and computational analyses enabled us to classify this gene as a member of the family of iron-sulfur bacterial cryptochromes and photolyases (FeS-BCP). Therefore, we named this gene Vc(6-4) FeS-BCP.Publication Metadata only Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behcet's disease pathogenesis(2020) Gür, Mert; Gölcük, Mert; Gül, Ahmet; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Behcet's disease is an inflammatory disorder of unknown etiology. Genetic tendency has an important role in its pathogenesis, and HLA-B51, a class I MHC antigen, has been recognized as the strongest susceptibility factor for Behcet's disease. Despite the confirmation of the association of HLA-B51 with Behcet's disease in different populations, its pathogenic mechanisms remain elusive. HLA-B51 differs in only two amino acids from HLA-B52, other split antigen of HLA-B5, which is not associated with Behcet's disease. These two amino acids are located in the B pocket of the antigen-binding groove, which occupies the second amino acids of the bound peptides. To understand the nature of the HLA-peptide interactions, differences in structure and dynamics of two HLA alleles were investigated by molecular dynamics simulations using YAYDGKDYI, LPRSTVINI, and IPYQDLPHL peptides. For HLA-B51, all bound peptides fluctuated to larger extent than HLA-B52. Free energy profiles of unbinding process for YAYDGKDYI by steered molecular dynamics simulations showed that unbinding from HLA-B52 results in greater free energy differences than HLA-B51. These results suggest the possibility of an instability of HLA-B51 associated with the repertoire of peptides, and this finding may provide significant insight to its pathogenic role in Behcet's disease.Publication Metadata only Quantification of interactions among circadian clock proteins via surface plasmon resonance(Wiley, 2014) N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kepsütlü, Burcu; Kızılel, Rıza; Kızılel, Seda; Master Student; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 114475; 28376Circadian clock is an internal time keeping system recurring 24h daily rhythm in physiology and behavior of organisms. Circadian clock contains transcription and translation feedback loop involving CLOCK/NPaS2, BMaL1, Cry1/2, and Per1/2. in common, heterodimer of CLOCK/NPaS2 and BMaL1 binds to EBOX element in the promoter of Per and Cry genes in order to activate their transcription. CRY and PER making heterodimeric complexes enter the nucleus in order to inhibit their own BMaL1-CLOCK-activated transcription. the aim of this study was to investigate and quantify real-time binding affinities of clock proteins among each other on and off DNa modes using surface plasmon resonance. the pairwise interaction coefficients among clock proteins, As well as interaction of PER2, CRY2, and PER2:CRY2 proteins with BMaL1:CLOCK complex in the presence and absence of EBOX motif have been investigated via analysis of surface plasmon resonance data with pseudo first-order reaction kinetics approximation and via nonlinear regression curve fitting. the results indicated that CRY2 and PER2, BMaL1, and CLOCK proteins form complexes in vitro and that PER2, CRY2 and PER2:CRY2 complex have similar affinities toward BMaL1:CLOCK complex. CRY2 protein had the highest affinity toward EBOX complex, whereas PER2 and CRY2:PER2 complexes displayed low affinity toward EBOX complex. the quantification of the interaction between clock proteins is critical to understand the operation mechanism of the biological clock and to address the behavioral and physiological disorders, and it will be useful for the design of new drugs toward clock-related diseases.Publication Metadata only Characterization and prediction of protein interfaces to infer protein-protein interaction networks(Bentham Science Publ Ltd, 2008) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Tunçbağ, Nurcan; Gürsoy, Attila; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; College of Engineering; College of Engineering; College of Engineering; 26605; 245513; 8745Complex protein-protein interaction networks govern biological processes in cells. Protein interfaces are the sites where proteins physically interact. Identification and characterization of protein interfaces will lead to understanding how proteins interact with each other and how they are involved in protein-protein interaction networks. What makes a given interface bind to different proteins; how similar/different the interactions in proteins are some key questions to be answered. Enormous amount of protein structures and experimental protein-protein interactions data necessitate advanced computational methods for analyzing and inferring new knowledge. Interface prediction methods use a wide range of sequence, structural and physico-chemical characteristics that distinguish interface residues from non-interface surface residues. Here, we present a review focusing on the characteristics of interfaces and the current status of interface prediction methods.Publication Metadata only Ca3[BN2]I3: the first halide-rich alkaline earth nitridoborate with isolated [BN2]3 - units(Wiley, 2015) Aydemir, Umut; Drathen, Christina; Akselrud, Lev; Prots, Yurii; Hoehn, Peter; Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Toros, Turna Ezgi; Yahyaoğlu, Müjde; Somer, Mehmet Suat; Undergraduate Student; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 178882The title compound Ca-3[BN2]I-3 was obtained from reactions of mixtures of the starting materials Ca-3[BN2](2) and CaI2 in a 1:4 ratio in sealed Nb tubes at 1223 K. The crystal structure was solved from powder synchrotron diffraction data. Ca-3[BN2]I-3 is the first example of a halide-rich nitridoborate crystallizing in the rhombohedral space group R32 [no. 155, Pearson code: hR96; Z = 12; a = 16.70491(2) angstrom, c = 12.41024(2) angstrom]. The crystal structure is built up by two interpenetrating networks of condensed edge-sharing [BN2]@Ca-6 and [square]@I-6 trigonal antiprisms (square = void). In Ca-3[BN2]I-3 two crystallograhically distinct [BN2](3-) anions are present with d(B1-N) = 1.393(2) angstrom and d(B2-N) = 1.369(9) angstrom. Their bond angles are practically linear, varying only slightly: N-B1-N = 179(1)degrees and N-B2-N = 180 degrees. Vibrational spectra were interpreted based on the D-infinity h symmetry of the discrete linear [N-B-N](3-) moieties, considering the site symmetry reduction and the presence of two distinct [BN2](3-) groups.Publication Metadata only Transcriptomic and fatty acid analyses of neochloris aquatica grown under different nitrogen concentration(Springer Heidelberg, 2022) Akgül, Rıza; Morgil, Hande; Kızılkaya, İnci Tüney; Cevahir, Gül; Akgül, Füsun; N/A; Department of Chemical and Biological Engineering; Sarayloo, Ehsan; Kavaklı, İbrahim Halil; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 40319In this study, we characterized the fatty acid production in Neochloris aquatica at transcriptomics and biochemical levels under limiting, normal, and excess nitrate concentrations in different growth phases. At the stationary phase, N. aquatica mainly produced saturated fatty acids such as stearic acid under the limiting nitrate concentration, which is suitable for biodiesel production. However, it produced polyunsaturated fatty acids such as alpha-linolenic acid under the excess nitrate concentration, which has nutritional values as food supplements. In addition, RNA-seq was employed to identify genes and pathways that were being affected in N. aquatica for three growth phases in the presence of the different nitrate amounts. Genes that are responsible for the production of saturated fatty acids were upregulated in the cells grown under a limiting nitrogen amount while genes that are responsible for the production of polyunsaturated fatty acid were upregulated in the cells grown under excess nitrogen amount. Further analysis showed more genes differentially expressed (DEGs) at the logarithmic phase in all conditions while a relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase under limiting and excess nitrogen. Our results provide a foundation for identifying developmentally important genes and understanding the biological processes in the different growth phases of the N. aquatica in terms of biomass and lipid production.