Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
119 results
Search Results
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 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 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 Classification of cytochrome P450 inhibitors with respect to binding free energy and pIC50 using common molecular descriptors(Amer Chemical Soc, 2009) N/A; Department of Chemical and Biological Engineering; Department of Industrial Engineering; Dağlıyan, Onur; Kavaklı, İbrahim Halil; Türkay, Metin; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 40319; 24956Virtual screening of chemical libraries following experimental assays of drug candidates is a common procedure in structure based drug discovery. However, the relationship between binding free energies and biological activities (pIC(50)) of drug candidates is sfill an unsolved issue that limits the efficiency and speed of drug development processes. In this study, the relationship between them is investigated based on a common molecular descriptor set for human cytochrome P450 enzymes (CYPs). CYPs play an important role in drug-drug interactions, drug metabolism, and toxicity. Therefore, in silico prediction of CYP inhibition by drug candidates is one of the major considerations in drug discovery. The combination of partial leastsquares regression (PLSR) and a variety of classification algorithms were employed by considering this relationship as a classification problem. Our results indicate that PLSR with classification is a powerful tool to predict more than one output such as binding free energy and pIC(50) simultaneously. PLSR with mixedinteger linear programming based hyperboxes predicts the binding free energy and pIC(50) with a mean accuracy of 87.18% (min: 81.67% max: 97.05%) and 88.09% (min: 79.83% max: 92.90%), respectively, for the cytochrome p450 superfamily using the common 6 molecular descriptors with a 10-fold cross- val idati on.Publication Metadata only Control of optical anisotropy at large deformations in PMMA/chlorinated-PHB (PHB-Cl) blends: mechano-optical behavior(Elsevier Sci Ltd, 2006) Yalçın, Barış; Çakmak, Mükerrem; Arkın, Ali Hakan; Hazer, Baki; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997There is a continuing need to produce polymer films with high optical clarity with ability to dial in the optical properties including refractive indices and optical anisotropies. In this research, we investigated the mechano-optical behavior of PMMA/PHB-Cl blend films during uniaxial deformation and mapped out the composition-birefringence-processing relationships. The results indicate the presence of a broad glass transition for the composition range investigated that indicates the development of micro-heterogeneities particularly at the higher concentration of PHB-Cl. However, this did not detrimentally influence the optical transparency of the solvent cast films as the size of these micro-heterogeneities remains well below the size range to affect the transparency. Optical retardation behavior of the films can be altered from negative to positive by increasing the PHB-Cl concentration from 0 to 20 wt%. The films with 18 wt% PHB-Cl are predicted to exhibit zero birefringence even when they are stretched to large deformations. This dialability of optical properties makes these materials suitable for optical device applications such as CD and DVDs as well as optical retarder films for liquid-crystal display applications. (c) 2006 Elsevier Ltd. All rights reserved.Publication Metadata only Gap metric concept and implications for multilinear model-based controller design(Amer Chemical Soc, 2003) Galan, O.; Romagnoli, J.A.; Palazoglu, A.; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526The gap metric concept is used within the context of multilinear model-based control. The concept of distance between dynamic systems is used as a criterion for selecting a set of models that can explain the nonlinear plant behavior in a given operating range. The case studies presented include a CSTR and a pH neutralization reactor. The gap metric is used to analyze the relationships among candidate models, resulting in a reduced model set that provides enough information to design multilinear controllers. The simulation and experimental results indicate good performance and stability features.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 Palladium nanoparticles by electrospinning from Poly(acrylonitrile- co -acrylic acid)-PdCl 2 solutions. relations between preparation conditions, particle size, and catalytic activity(American Chemical Society (ACS), 2004) Demir, MM; Gülgün, MA; Menceloğlu, YZ; Abramchuk, SS; Makhaeva, EE; Khokhlov, AR; Matveeva, VG; Sulman, MG; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Catalytic palladium (Pd) nanoparticles on electrospun copolymers of acrylonitrile and acrylic acid (PAN-AA) mats were produced via reduction of PdCl2 with hydrazine. Fiber mats were electrospun from homogeneous solutions of PAN-AA and PdCl2 in dimethylformamide (DMF). Pd cations were reduced to Pd metals when fiber mats were treated in an aqueous hydrazine solution at room temperature. Pd atoms nucleate and form small crystallites whose sizes were estimated from the peak broadening of X-ray diffraction peaks. Two to four crystallites adhere together and form agglomerates. Agglomerate sizes and fiber diameters were determined by scanning and transmission electron microscopy. Spherical Pd nanoparticles were dispersed homogeneously on the electrospun nanofibers. The effects of copolymer composition and amount of PdCl2 on particle size were investigated. Pd particle size mainly depends on the amount of acrylic acid functional groups and PdCl2 concentration in the spinning solution. Increasing acrylic acid concentration on polymer chains leads to larger Pd nanoparticles. In addition, Pd particle size becomes larger with increasing PdCl2 concentration in the spinning solution. Hence, it is possible to tune the number density and the size of metal nanoparticles. The catalytic activity of the Pd nanoparticles in electrospun mats was determined by selective hydrogenation of dehydrolinalool (3,7-dimethyloct-6-ene-1-yne-3-ol, DHL) in toluene at 90 degreesC. Electrospun fibers with Pd particles have 4.5 times higher catalytic activity than the current Pd/Al2O3 catalyst.Publication Metadata only Use of gap metric for model selection in multi-model based control design: an experimental case study of PH control(Elsevier, 2000) Palazoglu, Ahmet; Romagnoli, J.A.; Galan, O.; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526The gap metric concept is extended to multi-linear model-based control framework. The concept of distance between systems is used as a criterion to select a set of models that can explain the nonlinear plant behavior. Gap metric is used to analyze the relationships among candidate models, resulting in a reduced model set which provides enough information to design a H∞-robust controller.Publication Metadata only Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior(Wiley, 2009) Gerek, Z. Nevin; Ozkan, S. Banu; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605PDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse-grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific-Gaussian Network Model (s-GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class 11 type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s-GNM is further tested on a dual-specific PDZ which showed only Class I specificity when a point mutation exists on the beta A-beta B loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. in addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s-GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs.