Papers by Keyword: Protein

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Authors: R. Kannadasan, M.S. Saleembasha, I. Arnold Emerson
Abstract: Applications of computer and information technology are indispensable in various fields especially in the field of biology. The use of computer aided tools plays a key role in solving biological problems. The spontaneous process of molecular docking is important for finding potentially strong candidate of drug for various viruses. The binding of protein receptors with ligand molecules is essential in drug discovery process. The aim of molecular docking tools is to predict the interaction between protein and ligand. This review outlines the major tools for protein - ligand docking which in turn emphasize the importance of molecular docking in modern drug discovery process.
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Authors: Jun Feng Gu, Xi Cheng Wang
Abstract: A threading program based on genetic algorithm, is proposed for the protein fold recognition problem. Proper algorithm is designed in which genetic operators can be effectively implemented, and a more realistic energy model is adopted in this work. The performance of the genetic threading method is tested on a standard fold recognition benchmark, and the results show that the genetic threading method has good alignment accuracy and fold recognition ability. The analysis of the results demonstrates the rationality of our energy model.
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Authors: Yu Jun Wang, Kazumi Sanai, Masao Nakagaki
Abstract: Aquatic Larvae of Stenopsychid caddisfly (Stenopsychie marmorata) survive by attaching its catching nets at the bottom of the rocks in the flowing water. It was hypothesized that S. marmorata larva connects small pebbles by producing both silk-like protein and strong adhesive protein simultaneously. A 98 kDa protein(Smap-98k)was identified as an adhesive component by constructing a silk gland –specific cDNA library of S. marmorata. The cDNA sequence of Smap-98k was 2,679 bp long and encoding a 893 amino acids–long open reading frame (ORF) in which the first 19 residues are predict to be the signal peptide. The alignment of the Cys residues indicated the primary structure of this protein to consist of 15 degenerated repeats, each about 50 residues long and contains 6 conserved Cys residues. The Smap-98k was characterized by an abundance of Cys residues and charged amino acids with epidermal growth factor-like (EGF-like) structure. The most common amino acid of this protein was Cys (11.98%), with Pro (9.91%) and Glu (9.26%) following order of magnitude. Cys was assumed to play a role in maintaining the topology of charged amino acids on the molecular surface by intramolecular disulphide-bond formation. The gene was expressed specially in the silk gland similarity to the major silk proteins such like heavy fibroin (H-fibroin) and Light fibroin (L-fibroin) of S. marmorata larvae. The sequence of the protein showed certain homology to the silk-185 kDa of Chironomus pallidivittatus (Midge) which also spin silk underwater. The characterizations of abundance of Cys residues and charged amino acids also shared by Megabalanus rosa cement protein (Mrcp-20k ) and Mytilus galloprovincialis foot protein 2 (Mgfp 2) which both were produced in the marine environment. Although the similarity among Smap-98k, Mrcp-20k and Mgfp 2 sequences were very low, the functional relationship in underwater adhesion of these proteins should be noted.
1631
Authors: Guang Jie Duan, Rui Jing Su, Deng Xin Li
Abstract: Activated sludge process has been applied worldwide in municipal and industrial wastewater treatment practices. Excess sewage sludge, produced in sedimentation after wastewater bio-treatment, is an inevitable by-product of wastewater treatment processes. In any case sludge treatment and disposal should always be considered as an integral part of treatment of wastewater. Currently, the most widely available options in the world are the agriculture utilization, the waste disposal sites, the land reclamation and restoration, the incineration and other novel uses. Extracellular polymeric substances (EPS), as high-molecular weight compounds are secreted by activated sludge microorganisms, which can significantly influence the physicochemical properties and function of activated sludge flocs. Because of the crucial roles of EPS, many researchers have been made to explore their chemical compositions and physicochemical properties. Polysaccharides, humic substances and proteins are usually found to be the major components of EPS. The present paper sought to review past and future trends in sludge handling, focusing mainly at the organic matters.
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Authors: M. Morikawa, Y. Kuboki, Tsukasa Akasaka, Shigeaki Abe, H. Takita, Fumio Watari
Abstract: For application of carbon nanotubes (CNTs) as biomaterials, it is important to clarify the interaction between CNTs and proteins, which may affect on cell proliferation and differentiation. In this study, the adsorption behavior was investigated for representative proteins, bovine serum albumin, lysozyme and fetal bovine serum by using chromatography system. It was also aimed whether the different treatment conditions of CNTs affected the adsorption of proteins. CNTs used for this study had a straight shape and about 70nm in a diameter from SEM observation. There was not much difference between untreated and treated CNTs from SEM images. In chromatography experiments, all the proteins of albumin, lysozyme and serum were eluted immediately after injected to the column of untreated CNTs. Second elution appeared after buffer was changed from phosphate saline buffer to 25mM sodium hydroxide (NaOH). The same tendency was confirmed for CNTs with only acid treatment. However the eluted peaks became remarkably smaller after the column was changed to CNTs with thermal and twice acid treatments. These results indicated that treatment conditions for CNTs affected the adsorption behavior of proteins.
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Authors: Xiao Chun Li, Ji Liang Cao
Abstract: The soybean/casein/polyvinyl alcohol blend fiber was treated in sodium carbonate solutions to evaluate its alkali resistance which was very important for wet processing. The weight loss and whiteness of the treated fibers were examined. UV spectra of the alkaline treatment solutions were analyzed. The study showed that the fiber exhibited poor alkali resistance. Treating temperature, time and alkali concentration affected the weight loss of the treated fibers. A high weight loss was found even at low alkali concentration. The weight loss was primarily due to the hydrolysis of casein.
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Authors: Bram Neirinck, Ferdinand Singer, Annabel Braem, Sannakaisa Virtanen, Jef Vleugels
Abstract: Magnesium and magnesium alloys are gaining considerable attention for use in biomedical applications due to their capability to completely resorb in the human body without noticeable side effects. For structural biomedical applications however, the resorption rate is too large. In order to decrease this rate researchers are investigating magnesium alloys with an increased corrosion resistance and/or biodegradable coatings, such as dense protein layers, which retard the resorption.In this work, we demonstrate the electrophoretic deposition of Bovine Serum Albumin (BSA) directly onto pure magnesium substrates using unbalanced alternating fields (AC-EPD). The effect of the obtained coatings on the corrosion behavior of the substrates was evaluated by potentiodynamic polarization. The results show that an albumin layer deposited by AC-EPD from a 50/50 ethanol/H2O medium significantly reduces the corrosion rate.
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Authors: Mohd Nazrin Md Isa, Sohiful Anuar Zainol Murad, Mohamad Imran Ahmad, Muhammad M. Ramli, Rizalafande Che Ismail
Abstract: Computing alignment matrix score to search for regions of homology between biological sequences is time consuming task. This is due to the recursive nature of the dynamic programming-based algorithms such as the Smith-Waterman and the Needleman-Wunsch algorithmns. Typical FPGA-based protein sequencer comprises of two main logic blocks. One for computing alignment scores i.e. the processing element (PE), while another logic block for configuring the PE with coefficients. During alignment matrix computation, the logic block for configuring the PE are left unused until the time consuming alignment matrix computation finished. Therefore, a new technique, known as overlap computation and configuration (OCC) is proposed to minimize the time overhead for performing biological sequence alignment. The OCC technique simultaneously updating substitution matrix in a processing element (PE) systolic array, while computing alignment matrix scores. Results showed that, the sequencer achieves more than two order of magnitude speed-up higher compared to the state of the art, at negligible area overhead, if any.
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Authors: Niang Hui Li, Ping Ping Wu, Ru Qiang Huang
Abstract: The nutrition composition of Longan seeds was analysed in this paper.The results showed that starch,reducing sugar and protein are abundant in Longan seeds,as well as mineral elements which mainly contain K,Ca,Mg,P.The content of VA(<0.56µg/100g) and VE(0.55mg/kg) were determined.It suggests that Logan seeds are favorable nutrient resource of health food.
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Authors: Zdzisław Wiśniowski, Mateusz Banach, Irena Roterman
Abstract: The possible mechanism protecting the organisms against the freezing is shown. The presence of highly soluble proteins with no specific interaction allows the organism surviving the temperature below zero Celsius degree. The role of hydrophobic core and its structure (recognized as accordant with the idealized one) appears to be critical for antifreeze function of protein. The possible application of the model for biotechnological preparation of compounds protecting the solutions against freezing is discussed.
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