Browsing by Subject "Proteins"

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Open Access
Algorithms for effective querying of compound graph-based pathway databases
(BioMed Central Ltd., 2009-11-16) Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün
Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood concepts of graph theory in order to predict their structural and dynamic properties. An extension of this graph representation, namely hierarchically structured or compound graphs, in which a member of a biological network may recursively contain a sub-network of a somehow logically similar group of biological objects, provides many additional benefits for analysis of biological pathways, including reduction of complexity by decomposition into distinct components or modules. In this regard, it is essential to effectively query such integrated large compound networks to extract the sub-networks of interest with the help of efficient algorithms and software tools. Results: Towards this goal, we developed a querying framework, along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, that is applicable to all sorts of graph-based pathway databases, from PPIs (protein-protein interactions) to metabolic and signaling pathways. The framework is unique in that it can account for compound or nested structures and ubiquitous entities present in the pathway data. In addition, the queries may be related to each other through "AND" and "OR" operators, and can be recursively organized into a tree, in which the result of one query might be a source and/or target for another, to form more complex queries. The algorithms were implemented within the querying component of a new version of the software tool PATIKAweb (Pathway Analysis Tool for Integration and Knowledge Acquisition) and have proven useful for answering a number of biologically significant questions for large graph-based pathway databases. Conclusion: The PATIKA Project Web site is http://www.patika.org. PATIKAweb version 2.1 is available at http://web.patika.org. © 2009 Dogrusoz et al; licensee BioMed Central Ltd.
Open Access
Atomic force microscopy for the investigation of molecular and cellular behavior
(Elsevier, 2016-10) Ozkan A.D.; Topal, A. E.; Dana, A.; Güler, Mustafa O.; Tekinay, A. B.
The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.
Open Access
Biocatalytic protein membranes fabricated by electrospinning
(Elsevier B.V., 2016) Kabay, G.; Kaleli, G.; Sultanova, Z.; Ölmez, T. T.; Şeker, U. Ö. Ş.; Mutlu, M.
In this study, a protein-based catalytic membrane was produced by electrospinning. Membrane activity was characterised in terms of response current for various glucose concentrations. We focused on the preparation of a scaffold by converting a globular protein to other structural forms using catastrophic solvents. A scaffolding protein, bovine serum albumin, and an enzyme, glucose oxidase (GOD), were selected as a model natural carrier matrix and a biologically active agent, respectively. Beta-mercaptoethanol (β-ME) was used to convert the globular protein to an amyloid-like form. A structural stabilising agent, 2,2,2-triflouroethanol (TFE), was used to maintain the final α-helical structure of the amyloid-like protein. The TFE:PBS (phosphate-buffered saline) ratio and various electrospinning parameters were analysed to minimise activity loss. Using this approach, we applied electrospinning to an active enzyme to obtain biocatalytic nanofibrous membranes. After optimising the protein electrospinning process, the activities of the protein nanofibrous membranes were monitored. GOD remained active in the new membrane structure. The highest enzyme activity was observed for the membranes prepared with a 1.5:1 (v:v) TFE:PBS solvent ratio. In that particular case, the immobilized enzyme created a current of 0.7 μA and the apparent activity was 2547 ± 132 U/m2.
Open Access
Controlled enzymatic stability and release characteristics of supramolecular chiral peptide amphiphile nanofiber gels
(Elsevier B.V., 2017) Zengin, A.; Cinar, G.; Güler, Mustafa O.
Supramolecular bioarchitectures formed by assembly of achiral or chiral building blocks play important roles in various biochemical processes. Stereochemistry of amino acids is important for structural organization of peptide and protein assemblies and structure-microenvironment interactions. In this study, oppositely charged peptide amphiphile (PA) molecules with L-, D- and mixture of L- and D-amino acid conformations are coassembled into supramolecular nanofibers and formed self-supporting gels at pH 7.4 in water. The enzymatic stability of the PA nanofiber gels was studied in the presence of proteinase K enzyme, which digest a broad spectrum of proteins and peptides. The structural changes on the chiral PA nanofibers were also analyzed at different time periods in the presence of enzymatic activity. Controlled release of a model cargo molecule through the chiral PA nanofiber gels was monitored. The diffusivity parameters were measured for all gel systems. Release characteristics and the enzymatic stability of the peptide nanofiber gels were modulated depending on organization of the chiral PA molecules within the supramolecular assemblies.
Open Access
Detection of insect damaged wheat kernels by impact acoustics
(IEEE, 2005-03) Pearson, T. C.; Çetin, A. Enis; Tewfik, A. H.
Insect damaged wheat kernels (IDK) are characterized by a small hole bored into the kernel by insect larvae. This damage decreases flour quality as insect proteins interfere with the bread-making biochemistry and insect fragments are very unsightly. A prototype system was set up to detect IDK by dropping them onto a steel plate and processing the acoustic signal generated when kernels impact the plate. The acoustic signal was processed by three different methods: 1) modeling of the signal in the time domain, 2) computing time domain signal variances in short time windows, and 3), analysis of the frequency spectra magnitudes. Linear discriminant analysis was used to select a subset of features and perform classification. 98% of un-damaged kernels and 84.4% of IDK were correctly classified.
Open Access
Diabetic wound regeneration using heparin-mimetic peptide amphiphile gel in db/db mice
(Royal Society of Chemistry, 2017) Senturk, Berna; Demircan, Burak M.; Ozkan, Alper D.; Tohumeken, Sehmus; Delibasi, T.; Güler, Mustafa O.; Tekinay, Ayse B.
There is an urgent need for more efficient treatment of chronic wounds in diabetic patients especially with a high risk of leg amputation. Biomaterials capable of presenting extracellular matrix-mimetic signals may assist in the recovery of diabetic wounds by creating a more conducive environment for blood vessel formation and modulating the immune system. In a previous study, we showed that glycosaminoglycan-mimetic peptide nanofibers are able to increase the rate of closure in STZ-induced diabetic rats by induction of angiogenesis. The present study investigates the effect of a heparin-mimetic peptide amphiphile (PA) nanofiber gel on full-thickness excisional wounds in a db/db diabetic mouse model, with emphasis on the ability of the PA nanofiber network to regulate angiogenesis and the expression of pro-inflammatory cytokines. Here, we showed that the heparin-mimetic PA gel can support tissue neovascularization, enhance the deposition of collagen and expression of alpha-smooth muscle actin (α-SMA), and eliminate the sustained presence of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) in the diabetic wound site. As the absence of neovascularization and overexpression of pro-inflammatory markers are a hallmark of diabetes and interfere with wound recovery by preventing the healing process, the heparin-mimetic PA treatment is a promising candidate for acceleration of diabetic wound healing by modulating angiogenesis and local immune response. © 2017 The Royal Society of Chemistry.
Open Access
Effect of oxygen supply on metabolism of immobilized and suspended Escherichia coli
(John Wiley & Sons Inc, New York, NY, United States, 1996) Inanç, E.; Miller J. E.; DiBiasio, D.
The effect of reduced oxygen supply on the production of a recombinant protein (plasmid-encoded β-galactosidase) was investigated in Escherichia coli. A novel modified bubble tank reactor was used to provide a direct comparison between immobilized and suspended cells in identical environments except for the immobilization matrix. Decreased oxygen supply led to increased β-galactosidase synthesis by both immobilized and suspended cells. Immobilized cells produced similar amounts of β-galactosidase as the suspended cells. Lactose consumption and acetate production, on a per cell basis, were significantly higher in immobilized cells, suggesting that immobilized cells utilized fermentative metabolism. However, a transport analysis of the immobilized cell system showed that immobilized cells were not subject to either external or internal mass transfer gradients.The effect of reduced oxygen supply on the production of a recombinant protein (plasmid-encoded β-galactosidase) was investigated in Escherichia coli. A novel modified bubble tank reactor was used to provide a direct comparison between immobilized and suspended cells in identical environments except for the immobilization matrix. Decreased oxygen supply led to increased β-galactosidase synthesis by both immobilized and suspended cells. Immobilized cells produced similar amounts of β-galactosidase as the suspended cells. Lactose consumption and acetate production, on a per cell basis, were significantly higher in immobilized cells, suggesting that immobilized cells utilized fermentative metabolism. However, a transport analysis of the immobilized cell system showed that immobilized cells were not subject to either external or internal mass transfer gradients.
Open Access
Encapsulation of two different TLR ligands into liposomes confer protective immunity and prevent tumor development
(Elsevier B.V., 2017) Bayyurt, B.; Tincer, G.; Almacioglu, K.; Alpdundar, E.; Gursel, M.; Gursel, I.
Nucleic acid-based Toll-like receptor (TLR) ligands are promising adjuvants and immunotherapeutic agents. Combination of TLR ligands potentiates immune response by providing synergistic immune activity via triggering different signaling pathways and may impact antigen dependent T-cell immune memory. However, their short circulation time due to nuclease attack hampers their clinical performance. Liposomes offer inclusion of protein and nucleic acid-based drugs with high encapsulation efficiency and drug loading. Furthermore, they protect cargo from enzymatic cleavage while providing stability, and enhancing biological activity. Herein, we aimed to develop a liposomal carrier system co-encapsulating TLR3 (polyinosinic-polycytidylic acid; poly(I:C)) and TLR9 (oligodeoxynucleotides (ODN) expressing unmethylated CpG motifs; CpG ODN) ligands as immunoadjuvants together with protein antigen. To demonstrate that this depot system not only induce synergistic innate immune activation but also boost antigen-dependent immune response, we analyzed the potency of dual ligand encapsulated liposomes in long-term cancer protection assay. Data revealed that CpG ODN and poly(I:C) co-encapsulation significantly enhanced cytokine production from spleen cells. Activation and maturation of dendritic cells as well as bactericidal potency of macrophages along with internalization capacity of ligands were elevated upon incubation with liposomes co-encapsulating CpG ODN and poly(I:C). Immunization with co-encapsulated liposomes induced OVA-specific Th1-biased immunity which persisted for eight months post-booster injection. Subsequent challenge with OVA-expressing tumor cell line, E.G7, demonstrated that mice immunized with liposomes co-encapsulating dual ligands had significantly slower tumor progression. Tumor clearance was dependent on OVA-specific cytotoxic memory T-cells. These results suggest that liposomes co-encapsulating TLR3 and TLR9 ligands and a specific cancer antigen could be developed as a preventive cancer vaccine. ï¿½ 2017 Elsevier B.V.
Open Access
Finite size effects in cooperative molecular motors
(Elsevier B.V., 2003) Taneri, S.; Yalabik, M. C.
We have studied the ballistic and damped dynamics of finite size cooperative molecular motors. We study the effect of finite size on average quantities such as sliding velocity, as well as the statistics of fluctuations in these quantities. We observed stalling for the over damped case.
Open Access
Genetically encoded conductive protein nanofibers secreted by engineered cells
(Royal Society of Chemistry, 2017-06) Kalyoncu, E.; Ahan, R. E.; Olmez, T. T.; Safak Seker, U. O.
Bacterial biofilms are promising tools for functional applications as bionanomaterials. They are synthesized by well-defined machinery, readily form fiber networks covering large areas, and can be engineered for different functionalities. In this work, bacterial biofilms have been engineered for use as conductive biopolymers to interface with electrodes and connect bacterial populations to electronic gadgets. Bacterial biofilms are designed with different conductive peptide motifs, as the aromatic amino acid content of fused peptide motifs has been suggested to contribute to electronic conductivity by influencing monomer stacking behavior. To select the best candidates for constructing conductive peptide motifs, conductivity properties of aromatic amino acids are measured using two different fiber scaffolds, an amyloid-like fiber (ALF) forming peptide, and the amyloidogenic R5T peptide of CsgA protein. Three repeats of aromatic amino acids are added to fiber-forming peptide sequences to produce delocalized π clouds similar to those observed in conductive polymers. Based on the measurements, tyrosine and tryptophan residues provide the highest conductivity. Therefore, the non-conductive E. coli biofilm is switched into a conductive form by genetically inserted conductive peptide motifs containing different combinations of tyrosine and tryptophan. Finally, synthetic biofilm biogenesis is achieved with conductive peptide motifs using controlled biofilm production. Conductive biofilms on living cells are formed for bioelectronics and biosensing applications.
Open Access
Genetically-tunable mechanical properties of bacterial functional amyloid nanofibers
(American Chemical Society, 2017) Abdelwahab, M. T.; Kalyoncu, E.; Onur, T.; Baykara, M. Z.; Seker U.O.S.
Bacterial biofilms are highly ordered, complex, dynamic material systems including cells, carbohydrates, and proteins. They are known to be resistant against chemical, physical, and biological disturbances. These superior properties make them promising candidates for next generation biomaterials. Here we investigated the morphological and mechanical properties (in terms of Young’s modulus) of genetically-engineered bacterial amyloid nanofibers of Escherichia coli (E. coli) by imaging and force spectroscopy conducted via atomic force microscopy (AFM). In particular, we tuned the expression and biochemical properties of the major and minor biofilm proteins of E. coli (CsgA and CsgB, respectively). Using appropriate mutants, amyloid nanofibers constituting biofilm backbones are formed with different combinations of CsgA and CsgB, as well as the optional addition of tagging sequences. AFM imaging and force spectroscopy are used to probe the morphology and measure the Young’s moduli of biofilm protein nanofibers as a function of protein composition. The obtained results reveal that genetically-controlled secretion of biofilm protein components may lead to the rational tuning of Young’s moduli of biofilms as promising candidates at the bionano interface.
Open Access
GOPred: GO molecular function prediction by combined classifiers
(2010) Saraç Ö.S.; Atalay V.; Cetin-Atalay, R.
Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred). © 2010 Saraç et al.
Open Access
Hybridization of fano and vibrational resonances in surface-enhanced infrared absorption spectroscopy of streptavidin monolayers on metamaterial substrates
(2014) Alici, K. B.
We present spectral hybridization of organic and inorganic resonant materials and related bio-sensing mechanism. We utilized a bound protein (streptavidin) and a Fano-resonant metasurface to illustrate the concept. The technique allows us to investigate the vibrational modes of the streptavidin and how they couple to the underlying metasurface. This optical, label-free, nonperturbative technique is supported by a coupled mode-theory analysis that provides information on the structure and orientation of bound proteins. We can also simultaneously monitor the binding of analytes to the surface through monitoring the shift of the metasurface resonance. All of this data opens up interesting opportunities for applications in biosensing, molecular electronics and proteomics. © 2014 IEEE.
Open Access
Identification of relative protein bands in Polyacrylamide Gel Electrophoresis (PAGE) using multiresolution snake algorithm
(IEEE, 1998-10) Gürcan, Metin Nafi; Koyutürk, Mehmet; Yıldız, H. Serkan; Çetin Atalay, Rengül; Çetin, A. Enis
Polyacrylamide Gel Electrophoresis (PAGE) is one of the most widely used techniques in protein research. In the protein purification process, it is important to determine the efficiency of each purification step in terms of percentage of protein of interest found in the protein mixture. This study provides a rapid and reliable way to determine this percentage. The region of interest containing the protein is detected using the snake algorithm. The iterative snake algorithm is implemented in a multiresolutional framework. The snake is initialized on a low resolution image. Then, the final position of the snake at low resolution is used as the initial position in the higher resolution image. Finally, tile area of the protein is estimated as the area enclosed by the final position of the snake.
Open Access
A novel model-based method for feature extraction from protein sequences for classification
(IEEE, 2006) Saraç, Ö. S.; Atalay, V.; Çetin-Atalay, Rengül
Representation of amino-acid sequences constitutes the key point in classification of proteins into functional or structural classes. The representation should contain the biologically meaningful information hidden in the primary sequence of the protein. Conserved or similar subsequences are strong indicators of functional and structural similarity. In this study we present a feature mapping that takes into account the models of the subsequences of protein sequences. An expectation-maximization algorithm along with an HMM mixture model is used to cluster and learn the models of subsequences of a given set of proteins.
Open Access
pH-dependent ionic-current-rectification in nanopipettes modified with glutaraldehyde cross-linked protein membranes
(Royal Society of Chemistry, 2016) Şen, M.; Demirci, A.
In this study, we investigated for the first time the influence of an artificial membrane on the ionic current rectification of nanopipettes at various pH levels. The nanopipettes were fabricated and then modified with bovine serum albumin-glutaraldehyde (BSA-GA) artificial membranes. We determined the degree of ionic current rectification of these nanopipettes and compared them with those of bare nanopipettes. In contrast to the bare nanopipettes, the BSA-GA-modified nanopipettes demonstrated pH-dependent ionic current rectification. We also examined the tunability of the degree of rectification using streptavidin (STV) whose isoelectric point differs from that of BSA. The results showed that the ionic current rectification of nanopipettes can be tuned as the addition of STV into the BSA-GA artificial membrane increases the degree of rectification. Using the proposed approach, nanoscale spearhead pH sensors could be fabricated for highly localized extracellular or intracellular pH measurement. Moreover, it is possible to realize the applications of nano-sized channels in relatively larger channels using the present method.
Open Access
Prediction of protein subcellular localization based on primary sequence data
(IEEE, 2004) Özarar, M.; Atalay, V.; Çetin-Atalay, Rengül
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to find the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features for classification by the help of multi layer perceptrons. This approach allows a classification independent of the length of the sequence. In addition to these, the use of a new encoding scheme is described for the amino acids that conserves biological function based on point of accepted mutations (PAM) substitution matrix. The statistical test results of the system is presented on a four class problem. P2SL achieves slightly higher prediction accuracy than the similar studies.
Open Access
Presentation of functional groups on self-assembled supramolecular peptide nanofibers mimicking glycosaminoglycans for directed mesenchymal stem cell differentiation
(Royal Society of Chemistry, 2017) Yasa, Oncay; Uysal, Ozge; Ekiz, Melis Sardan; Güler, Mustafa O.; Tekinay, Ayse B.
Organizational complexity and functional diversity of the extracellular matrix regulate cellular behaviors. The extracellular matrix is composed of various proteins in the form of proteoglycans, glycoproteins, and nanofibers whose types and combinations change depending on the tissue type. Proteoglycans, which are proteins that are covalently attached to glycosaminoglycans, contribute to the complexity of the microenvironment of the cells. The sulfation degree of the glycosaminoglycans is an important and distinct feature at specific developmental stages and tissue types. Peptide amphiphile nanofibers can mimic natural glycosaminoglycans and/or proteoglycans, and they form a synthetic nanofibrous microenvironment where cells can proliferate and differentiate towards different lineages. In this study, peptide nanofibers were used to provide varying degrees of sulfonation mimicking the natural glycosaminoglycans by forming a microenvironment for the survival and differentiation of stem cells. The effects of glucose, carboxylate, and sulfonate groups on the peptide nanofibers were investigated by considering the changes in the differentiation profiles of rat mesenchymal stem cells in the absence of any specific differentiation inducers in the culture medium. The results showed that a higher sulfonate-to-glucose ratio is associated with adipogenic differentiation and a higher carboxylate-to-glucose ratio is associated with osteochondrogenic differentiation of the rat mesenchymal stem cells. Overall, these results demonstrate that supramolecular peptide nanosystems can be used to understand the fine-tunings of the extracellular matrix such as sulfation profile on specific cell types. © 2017 The Royal Society of Chemistry.
Open Access
Protein folding rates correlate with heterogeneity of folding mechanism
(American Physical Society, 2004) Öztop, B.; Ejtehadi, M. R.; Plotkin, S. S.
The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics.
Open Access
Self-assembled proteins and peptides as scaffolds for tissue regeneration
(Wiley-VCH Verlag, 2015) Loo, Y.; Goktas, M.; Tekinay, A. B.; Güler, Mustafa O.; Hauser, C. A. E.; Mitraki, A.
Self-assembling proteins and peptides are increasingly gaining interest for potential use as scaffolds in tissue engineering applications. They self-organize from basic building blocks under mild conditions into supramolecular structures, mimicking the native extracellular matrix. Their properties can be easily tuned through changes at the sequence level. Moreover, they can be produced in sufficient quantities with chemical synthesis or recombinant technologies to allow them to address homogeneity and standardization issues required for applications. Here. recent advances in self-assembling proteins, peptides, and peptide amphiphiles that form scaffolds suitable for tissue engineering are reviewed. The focus is on a variety of motifs, ranging from minimalistic dipeptides, simplistic ultrashort aliphatic peptides, and peptide amphiphiles to large "recombinamer" proteins. Special emphasis is placed on the rational design of self-assembling motifs and biofunctionalization strategies to influence cell behavior and modulate scaffold stability. Perspectives for combination of these "bottom-up" designer strategies with traditional "top-down" biofabrication techniques for new generations of tissue engineering scaffolds are highlighted. Recent advances in self-assembling proteins, peptides, and peptide amphiphiles that form scaffolds suitable for tissue engineering are discussed. Rational design and biofunctionalization strategies for a variety of motifs ranging from minimalistic dipeptides, ultrashort aliphatic peptides, and peptide amphiphiles to large "recombinamer" proteins are reviewed and challenges and perspectives for their widespread adoption in applications are highlighted.