Search results for: PRAF proteins

Authors: Ewa Wywial, Shaneen M. Singh

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The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties.

Keywords: PRAF proteins, homology modeling, Arabidopsisthaliana

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Authors: Homa Torabizadeh

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This study proposes a basic molecular formula for all proteins. A total of 10,739 proteins belonging to 9 different protein groups classified on the basis of their functions were selected randomly. They included enzymes, storage proteins, hormones, signalling proteins, structural proteins, transport proteins, immunoglobulins or antibodies, motor proteins and receptor proteins. After obtaining the protein molecular formula using the ProtParam tool, the H/C, N/C, O/C, and S/C ratios were determined for each randomly selected sample. In this case, H, N, O, and S coefficients were specified per carbon atom. Surprisingly, the results demonstrated that H, N, O, and S coefficients for all 10,739 proteins are similar and highly correlated. This study demonstrates that despite differences in the structure and function, all known proteins have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30 ± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was found to be 0.9999.

Keywords: Protein molecular formula, Basic unit formula, Protparam tool.

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Authors: M. Michael Gromiha, Y. Yabuki, K. Imai, P. Horton, K. Fukui

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We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.

Keywords: Membrane proteins, database, transporters, discrimination, β-signal.

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Authors: F. Bamdad, Sh. Dokhani, J. Keramat, R. Zareie

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Biologically active peptides are of particular interest in food science and human nutrition because they have been shown to play several physiological roles. In vitro gastrointestinal digestion of lentil and whey proteins in this study produced high angiotensin-I converting enzyme inhibitory activity with 75.5±1.9 and 91.4±2.3% inhibition, respectively. High ACE inhibitory activity was observed in lentil after 5 days of germination (84.3±1.2%). Fractionation by reverse phase chromatography gave inhibitory activities as high as 86.3±2.0 for lentil, 94.8±1.8% for whey and 93.7±1.7% at 5th day of germination. Further purification by HPLC resulted in several inhibitory peptides with IC50 values ranging from 0.064 to 0.164 mg/ml. These results demonstrate that lentil proteins are a good source of peptides with ACE inhibitory activity that can be released by germination or gastrointestinal digestion. Despite the lower bioactivity in comparison with whey proteins, incorporation of lentil proteins in functional food formulations and natural drugs look promising.

Keywords: ACE inhibitory peptides, digestion, germination, lentil proteins, whey proteins

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Authors: E. Al Daoud

Abstract:

The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: Genome, species, blastp, conserved genes, cronobacter.

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Authors: Pawel Glibowski, Agnieszka Glibowska

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The rheological properties, structure and potential synergistic interactions of whey proteins (1-6%) and inulin (20%) in mixed gels in the presence of CaCl2 was the aim of this study. Whey proteins have a strong influence on inulin gel formation. At low concentrations (2%) whey proteins did not impair in inulin gel formation. At higher concentration (4%) whey proteins impaired inulin gelation and inulin impaired the formation of a Ca2+-induced whey protein network. The presence of whey proteins at a level allowing for protein gel network formation (6%) significantly increased the rheological parameters values of the gels. SEM micrographs showed that whey protein structure was coated by inulin moieties which could make the mixed gels firmer. The protein surface hydrophobicity measurements did not exclude synergistic interactions between inulin and whey proteins, however. The use of an electrophoretic technique did not show any stable inulin-whey protein complexes.

Keywords: gels, hydrophobicity, inulin, SEM, whey proteins.

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Authors: T. Mahalakshmi, Aswathi B. L., Achuthsankar S. Nair

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Transcription factors are a group of proteins that helps for interpreting the genetic information in DNA. Protein-protein interactions play a major role in the execution of key biological functions of a cell. These interactions are represented in the form of a graph with nodes and edges. Studies have showed that some nodes have high degree of connectivity and such nodes, known as hub nodes, are the inevitable parts of the network. In the present paper a method is proposed to identify hub transcription factor proteins using sequence information. On a complete data set of transcription factor proteins available from the APID database, the proposed method showed an accuracy of 77%, sensitivity of 79% and specificity of 76%.

Keywords: Transcription Factor Proteins, Hub Proteins, Shannon Index, Transfer Free Energy to Surface (TFES).

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Authors: Yu Bin, Zhang Yan

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The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a new method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. To access the effect of the method, 80 proteins with known 3D-structure from Mptopo database are chosen at random as the test objects (including 325 TMHs), 308 of which can be predicted accurately, the average predicted accuracy is 96.3%. In addition, the above 80 membrane proteins are divided into 13 groups according to their function and type. In particular, the results of the prediction of TMHs of the 13 groups are satisfying.

Keywords: discrete wavelet transform, hydrophobicity, membrane protein, transmembrane helical segments

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: Santanu Ray, Alexander G. Shard

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The adsorption of bovine serum albumin (BSA), immunoglobulin G (IgG) and fibrinogen (Fgn) on fluorinated selfassembled monolayers have been studied using time of flight secondary ion mass spectrometry (ToF-SIMS) and Spectroscopic Ellipsometry (SE). The objective of the work has to establish the utility of ToF-SIMS for the determination of the amount of protein adsorbed on the surface. Quantification of surface adsorbed proteins was carried out using SE and a good correlation between ToF-SIMS results and SE was achieved. The surface distribution of proteins were also analysed using Atomic Force Microscopy (AFM). We show that the surface distribution of proteins strongly affect the ToFSIMS results.

Keywords: ToF-SIMS, Spectroscopic Ellipsometry, Protein, Atomic Force Microscopy.

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Authors: Yoshihiro Ochiai

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Globin superfamily proteins including myoglobin and hemoglobin, have welcome new members recently, namely, cytoglobin, neuroglobin and globin X, though their physiological functions are still to be addressed. Fish are the excellent models for the study of these globins, but their characteristics have not yet been discussed to date. In the present study, attempts have been made to characterize their structural uniqueness by making use of proteomics approach. This is the first comparative study on the characterization of globin superfamily proteins from fish.

Keywords: Globin, Superfamily, Protein, Fish, Structure

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Authors: Yu Bin, Zhang Yan

Abstract:

The prediction of transmembrane helical segments (TMHs) in membrane proteins is an important field in the bioinformatics research. In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1F88 was chosen as an example to describe the prediction of the number and location of TMHs in membrane proteins by using this method. One group of test data sets that contain total 19 protein sequences was utilized to access the effect of this method. Compared with the prediction results of DAS, PRED-TMR2, SOSUI, HMMTOP2.0 and TMHMM2.0, the obtained results indicate that the presented method has higher prediction accuracy.

Keywords: hydrophobicity, membrane protein, transmembranehelical segments, wavelet transform

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

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Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.

Keywords: Bioinformatics, Protein-protein interactions, One-Class Support Vector Machines

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Authors: Hanina M. N., Hairul Shahril M., Ismatul Nurul Asyikin I., Abdul Jalil A. K., Salina M. R., Maryam M. R., Rosfarizan M.

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The extracellular proteins secreted by bacteria may be increased in stressful surroundings, such as in the presence of antibiotics. It appears that many antibiotics, when used at low concentrations, have in common the ability to activate or repress gene transcription, which is distinct from their inhibitory effect. There have been comparatively few studies on the potential of antibiotics as a specific chemical signal that can trigger a variety of biological functions. Therefore, this study was carried out to determine the effect of Streptomycin Sulfate in regulating extracellular proteins secreted by Bacillus subtilis ATCC21332. Results of Microdilution assay showed that the Minimum Inhibition Concentration (MIC) of Streptomycin Sulfate on B. subtilis ATCC21332 was 2.5 mg/ml. The bacteria cells were then exposed to Streptomycin Sulfate at concentration of 0.01 MIC before being further incubated for 48h to 72 h. The extracellular proteins secreted were then isolated and analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins profile revealed that three additional bands with approximate sizes of 30 kDa, 22 kDa and 23 kDa were appeared for the treated bacteria with Streptomycin Sulfate. Thus, B. subtilis ATCC21332 in stressful condition with the presence of Streptomycin Sulfate at low concentration could induce the extracellular proteins secretion.

Keywords: Bacillus subtilis ATCC21332, Streptomycin Sulfate, extracellular proteins.

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Authors: Ratnakar Tripathi, Rajnikant Mishra

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The PAX6, a transcription factor, is essential for the morphogenesis of the eyes, brain, pituitary and pancreatic islets. In rodents, the loss of Pax6 function leads to central nervous system defects, anophthalmia, and nasal hypoplasia. The haplo-insufficiency of Pax6 causes microphthalmia, aggression and other behavioral abnormalities. It is also required in brain patterning and neuronal plasticity. In human, heterozygous mutation of Pax6 causes loss of iris [aniridia], mental retardation and glucose intolerance. The 3- deletion in Pax6 leads to autism and aniridia. The phenotypes are variable in peneterance and expressivity. However, mechanism of function and interaction of PAX6 with other proteins during development and associated disease are not clear. It is intended to explore interactors of PAX6 to elucidated biology of PAX6 function in the tissues where it is expressed and also in the central regulatory pathway. This report describes In-silico approaches to explore interacting proteins of PAX6. The models show several possible proteins interacting with PAX6 like MITF, SIX3, SOX2, SOX3, IPO13, TRIM, and OGT. Since the Pax6 is a critical transcriptional regulator and master control gene of eye and brain development it might be interacting with other protein involved in morphogenesis [TGIF, TGF, Ras etc]. It is also presumed that matricelluar proteins [SPARC, thrombospondin-1 and osteonectin etc] are likely to interact during transport and processing of PAX6 and are somewhere its cascade. The proteins involved in cell survival and cell proliferation can also not be ignored.

Keywords: Interacting Proteins, Pax6, PIP, STRING

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

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Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: N. Tuncbag, T. Haliloglu, O. Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: D. Leskauskaite, I. Jasutiene, M. Kersiene, E. Malinauskyte, P. Matusevicius

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In vitro gastro-duodenal digestion model was used to investigate the changes of emulsions under digestion conditions. Oil in water emulsions stabilized by whey proteins (2%) and stabilized by whey proteins (2%) with addition of carboxymethyl cellulose (0.75%) as gelling agent of continuous phase were prepared at pH7. Both emulsions were destabilized under gastric conditions; however the protective role of carboxymethyl cellulose was indicated by recording delay of fat digestibility of this emulsion. In the presence of carboxymethyl cellulose whey proteins on the interfacial surface of droplets were more resistant to gastric degradation causing limited hydrolysis of fat due to the poor acceptability of lipids for the enzymes. Studies of emulsions using in vivo model supported results from in vitro studies. Lower content of triglycerides in blood serum and higher amount of fecal fat of rats were determined when rats were fed by diet containing emulsion made with whey proteins and carboxymethyl cellulose. 

Keywords: Digestibility, emulsions, lipids, rats.

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Authors: Jelena Zagorska, Inga Ciprovica

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the obligatory step during immunoglobulin and lysozyme concentration process is thermal treatment. The combination of temperature and time used in processing can affect the structure of the proteins and involve unfolding and aggregation. The aim of the present study was to evaluate the heat stability of total Igs, the particular immunoglobulin classes and lysozyme in milk. Milk samples were obtained from conventional dairy herd in Latvia. Raw milk samples were pasteurized in different regimes: 63 °C 30 min, 72 °C 15-20 s, 78 °C 15-20 s, 85 °C 15-20 s, 95 °C 15-20 s. The concentrations of Igs (IgA, IgG, IgM) and lysozyme were determined by turbodimetric method. During research was established, that activity of antimicrobial proteins decreases differently. Less concentration reduce was established in a case of lysozyme.

Keywords: immunoglobulins, lysozyme, milk, pasteurization

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Authors: Maria Toader, Gheorghe Valentin Roman, Alina Maria IonescuMaria Toader, Gheorghe Valentin Roman, Alina Maria Ionescu

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Crops diversity and maintaining and enhancing the fertility of agricultural lands are basic principles of organic farming. With a wider range of crops in agroecosystem can improve the ability to control weeds, pests and diseases, and the performance of crops rotation and food safety. In this sense, the main objective of the research was to study the productivity and chemical composition of some alternative crops and their adaptability to soil and climatic conditions of the agricultural area in Southern Romania and to cultivation in the organic farming system. The alternative crops were: lentil (7 genotypes); five species of grain legumes (5 genotypes); four species of oil crops (5 genotypes). The seed production was, on average: 1343 kg/ha of lentil; 2500 kg/ha of field beans; 2400 kg/ha of chick peas and blackeyed peas; more than 2000 kg/ha of atzuki beans, over 1250 kg/ha of fenugreek; 2200 kg/ha of safflower; 570 kg/ha of oil pumpkin; 2150 kg/ha of oil flax; 1518 kg/ha of camelina. Regarding chemical composition, lentil seeds contained: 22.18% proteins, 3.03% lipids, 33.29% glucides, 4.00% minerals, and 259.97 kcal energy values. For field beans: 21.50% proteins, 4.40% lipids, 63.90% glucides, 5.85% minerals, 395.36 kcal energetic value. For chick peas: 21.23% proteins, 4.55% lipids, 53.00% glucides, 3.67% minerals, 348.22 kcal energetic value. For blackeyed peas: 23.30% proteins, 2.10% lipids, 68.10% glucides, 3.93% minerals, 350.14 kcal energetic value. For adzuki beans: 21.90% proteins, 2.60% lipids, 69.30% glucides, 4.10% minerals, 402.48 kcal energetic value. For fenugreek: 21.30% proteins, 4.65% lipids, 63.83% glucides, 5.69% minerals, 396.54 kcal energetic value. For safflower: 12.60% proteins, 28.37% lipids, 46.41% glucides, 3.60% minerals, 505.78 kcal energetic value. For camelina: 20.29% proteins, 31.68% lipids, 36.28% glucides, 4.29% minerals, 526.63 kcal energetic value. For oil pumpkin: 29.50% proteins, 36.92% lipids, 18.50% glucides, 5.41% minerals, 540.15 kcal energetic value. For oil flax: 22.56% proteins, 34.10% lipids, 27.73% glucides, 5.25% minerals, 558.45 kcal energetic value.

Keywords: Adaptability, alternative crops, chemical composition, organic farming productivity.

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Authors: Xin Kai, Juan Li, Sexin Huang, Zengliang Bai

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Ethanol is generally used as a therapeutic reagent against Hepatocellular carcinoma (HCC or hepatoma) worldwide, as it can induce Hepatocellular carcinoma cell apoptosis at low concentration through a multifactorial process regulated by several unknown proteins. This paper provides a simple and available proteomic strategy for exploring differentially expressed proteins in the apoptotic pathway. The appropriate concentrations of ethanol required to induce HepG2 cell apoptosis were first assessed by MTT assay, Gisma and fluorescence staining. Next, the central proteins involved in the apoptosis pathway processs were determined using 2D-PAGE, SDS-PAGE, and bio-software analysis. Finally the downregulation of two proteins, AFP and survivin, were determined by immunocytochemistry and reverse transcriptase PCR (RT-PCR) technology. The simple, useful method demonstrated here provides a new approach to proteomic analysis in key bio-regulating process including proliferation, differentiation, apoptosis, immunity and metastasis.

Keywords: Hepatocellular carcinoma, Ethanol, Proteomics, survivin and AFP

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Authors: Jafar Ahmadi, Nafiseh Noormohammadi, Sedigheh Fabriki Ourang

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GRF, Growth regulating factor, genes encode a novel class of plant-specific transcription factors. The GRF proteins play a role in the regulation of cell numbers in young and growing tissues and may act as transcription activations in growth and development of plants. Identification of GRF genes and their expression are important in plants to performance of the growth and development of various organs. In this study, to better understanding the structural and functional differences of GRFs family, 45 GRF proteins sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H. vulgare and S. bicolor, have been collected and analyzed through bioinformatics data mining. As a result, in secondary structure of GRFs, the number of alpha helices was more than beta sheets and in all of them QLQ domains were completely in the biggest alpha helix. In all GRFs, QLQ and WRC domains were completely protected except in AtGRF9. These proteins have no trans-membrane domain and due to have nuclear localization signals act in nuclear and they are component of unstable proteins in the test tube.

Keywords: Domain, Gene Family, GRF, Motif.

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Authors: N. Ngadi, J. Abrahamson, C. Fee, K. Morison

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Adsorption of proteins onto a solid surface is believed to be the initial and controlling step in biofouling. A better knowledge of the fouling process can be obtained by controlling the formation of the first protein layer at a solid surface. A number of methods have been investigated to inhibit adsorption of proteins. In this study, the adsorption kinetics of

Keywords: E-casein, QCM-D, stainless steel, bimodal brush, PEG

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Authors: Omer Nebil Yaveroglu, Tolga Can

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In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

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The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: Aggregation prone regions, amyloids, thermophilic proteins, amino acid residues, machine learning.

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

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In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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Authors: Zelmina Lubovac, Björn Olsson, Jonas Gamalielsson

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This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

Keywords: Modules, systems biology, protein interactionnetworks, yeast.

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Authors: Yanhua Jin, Won Suk Lee

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The two-dimensional gel electrophoresis method (2-DE) is widely used in Proteomics to separate thousands of proteins in a sample. By comparing the protein expression levels of proteins in a normal sample with those in a diseased one, it is possible to identify a meaningful set of marker proteins for the targeted disease. The major shortcomings of this approach involve inherent noises and irregular geometric distortions of spots observed in 2-DE images. Various experimental conditions can be the major causes of these problems. In the protein analysis of samples, these problems eventually lead to incorrect conclusions. In order to minimize the influence of these problems, this paper proposes a partition based pair extension method that performs spot-matching on a set of gel images multiple times and segregates more reliable mapping results which can improve the accuracy of gel image analysis. The improved accuracy of the proposed method is analyzed through various experiments on real 2-DE images of human liver tissues.

Keywords: Proteomics, spot-matching, two-dimensionalelectrophoresis.

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Authors: S. Banerjee, A. Apte Deshpande, N. Mandi, S. Padmanabhan

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We report a novel fusion tag for expressing recombinant proteins in E. coli. The fusion tag is the C-terminus part of the human GMCSF gene comprising 45 amino acids, which aid in over expression of otherwise non expressible genes. Expression of hIFN a2b with this fusion tag also escapes the requirement of rare codons for expression. This is also a first report of a small fusion tag of human origin having affinity to heparin sepharose column facilitating the purification of fusion protein.

Keywords: fusion tag, bacterial expression, rare codons, human GMCSF

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Authors: M. Azizur Rahman, Tamotsu Oomori

Abstract:

Calcite aCalcite and aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cellfree proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps.nd aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cell-free proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps. KeywordsBiomineralization, Calcite, Cell-free protein, Soft coral

Keywords: Biomineralization, Calcite, Cell-free protein, Soft coral

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