Cloning of the Key Succinoglycan Biosynthesis Gene exoA and exoY from Agrobacterium sp. M-503 and the Sequence Analysis of Encoding Proteins

2013 ◽  
Vol 807-809 ◽  
pp. 2027-2030
Author(s):  
Ying Zi Liu ◽  
Qiang Li ◽  
Qing Hua Wang ◽  
Yu Mei Li ◽  
Yan Hong Qu ◽  
...  
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Random Coil ◽  
High Molecular Weight Polymer ◽  
Molecular Weight Polymer ◽  
Reading Frame ◽  
Molecular Weights ◽  
Biosynthesis Gene ◽  
Α Helix ◽  
Β Sheet

Succinoglycan is an acidic exopolysaccharide that is important for invasion of the nodules. It is a high-molecular-weight polymer consisting of repeating octasaccharide units. These units are synthesized by a complex pathway encoded by numbers of exo genes. In this study, two key genes,exoAandexoY, were cloned and sequenced, which controlled the first two glycosyltransferase reactions in the biosynthesis of succinoglycan. The sequences contained 999-base-pares (bp) and 681-bp Open reading Frame (ORF) encoding 332 and 236 amino-acid proteins with molecular weights of approximate 36.8 kDa and 25.5 kDa , respectively. The putative proteins, ExoA and ExoY, were analyzed by several online protein analysis softwares. The results showed ExoA and ExoY were the membrane proteins with three (ExoA) and one (ExoY) hydrophobic transmembrance domains. Their theoretical PI values were 9.49 and 9.34, respectively. The second structures analysis indicated that they were composed of 45.48% and 38.94% α-helix, 13.55% and 16.81% β-sheet, and 40.96% and 44.25% random coil structures respectively. These data will lay a foundation for the subsequent 3D structure prediction and gene mutation to improve succinoglycan production.

scholarly journals Homology modeling and insilico approach of cleome gynandra - an indigenous medicinal plant

2020 ◽  
Vol 7 (2) ◽  
pp. 1-6
Author(s):  
Nirubama K ◽  
Narendhirakannan R.T ◽  
Rubalakshmi G ◽  
Vijayakumar N ◽  
Vinodhini M
Keyword(s):  
Medicinal Plant ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Homology Modelling ◽  
3D Structure ◽  
Random Coil ◽  
Gastrointestinal Infections ◽  
Cleome Gynandra ◽  
Α Helix ◽  
Main Component

Cleome gynandra is a widespread medicinal plant belonging to the family Capparaceae. In Ayurvedic medicine C. gynandra is a main component in Narayana Churna. It has numerous properties like Anthelmintic, in ear diseases, pruritis and several other diseases like gastro intestinal disorders and gastrointestinal infections etc. This is an effort to gather and document evidence on different features of C. gynnadra and highlight the need for survey and development. In this current study, nine proteins of C. gynandra were identify by using of bioinformatics tools. The bioinformatic study of the characterization of proteins of C.gynandra were using Expasy Protparam server, 3D structure was done using SWISS MODEL. Plants ofdifferent family show uniqueness 98% and above were particular and its sequences retrieved, aligned using Clustal Omega. Secondary Structure prediction exhibited that α – helix, random coil, β – turn and long strand leads. Phylogenetic analysis of Glyceraldehyde 3 PO4 of C. gynandra exposes that the Capparaceae families are closely related. Insilco sequence analysis of C. gynandra showed that these proteins taken from different organisms linked organized evolutionarily as they possess conserved regions in their protein sequences.These results will be helpful to further study on C. gynandra protein functions at molecular or structural levels and also valuable in homology modelling and insilico approach.

Dominant β-thalassaemia with unusually high Hb A2 and Hb F caused by βCD121(−G) (HBB:c.364delG) in exon 3 of β-globin gene

2019 ◽  
Vol 73 (8) ◽  
pp. 511-513 ◽  
Author(s):  
Kritsada Singha ◽  
Rossarin Karnpean ◽  
Goonnapa Fucharoen ◽  
Supan Fucharoen
Keyword(s):  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Globin Gene ◽  
Random Coil ◽  
Nucleotide Position ◽  
Microcytic Anaemia ◽  
Blood Picture ◽  
Thai Patient ◽  
Α Helix ◽  
Β Sheet

We describe a dominant β-thalassaemia caused by a deletion of G at nucleotide position 364 in exon 3 of the β-globin gene. The heterozygosity of this mutation was found in a 36-year-old Thai patient who had moderate hypochromic microcytic anaemia with haemolytic blood picture. Haemoglobin (Hb) analysis revealed relatively higher Hbs A2 (6.8%) and F (4.7%) as compared with those of β0-thalassaemia (n=278) and β+-thalassaemia (n=55) carriers in our series. Secondary structure prediction of the elongated β-globin chain showed that the α-helix at the C-terminal is disrupted dramatically by the random coil and β-sheet, which should result in a highly unstable β-globin variant, undetectable in peripheral blood and a dominant clinical phenotypic feature.

Characterization of Putative a (1,3)-β-D-glucan (curdlan) Synthase for a Low Molecular Weight Curdlan Biosynthesis from Agrobacterium sp. M503

2013 ◽  
Vol 807-809 ◽  
pp. 2031-2034
Author(s):  
Yu Mei Li ◽  
Qiang Li ◽  
Sheng Han ◽  
Dong Xue Song ◽  
Yan Hong Qu ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Random Coil ◽  
Low Molecular Weight ◽  
Base Pairs ◽  
Reading Frame ◽  
Coil Structure ◽  
Α Helix ◽  
Encoding Protein ◽  
Β Sheet

A β-(1,3)-D-glucan (curdlan) synthase gene for a low molecular weight curdlan biosynthesis, crdSAg, from Agrobacterium sp. M503 was cloned and its encoding protein was characterized by several online protein analysis softwares. The crdSAg consists of 1965-base-pairs Open Reading Frame (ORF) encoding a protein with molecular weight approximate 73.5 kDa, which contains the conserved domain of CESA-CelA_like belonging to glycosyltransferase family 2 (GT2). Moreover, CrdSAg was a membrane protein with seven hydrophobic transmembrance domains. The second structure analysis indicated it was composed of 43.12% α-helix, 17.89% β-sheet, and 38.99% random coil structure. These data will lay a foundation to clarify the biosynthesis mechanism of the low molecular weight curdlan.

Influence of Post-Treatment with Methanol Vapor on the Properties of SF/P(LLA-CL) Nanofibrous Scaffolds

2011 ◽  
Vol 236-238 ◽  
pp. 2221-2224
Author(s):  
Kui Hua Zhang ◽  
Xiu Mei Mo
Keyword(s):  
Electrospun Nanofibers ◽  
Random Coil ◽  
Methanol Vapor ◽  
Nanofibrous Scaffolds ◽  
Nanofibrous Structure ◽  
Α Helix ◽  
Β Sheet ◽  
Ideal Method ◽  
C Nmr

In order to improve water-resistant ability silk fibroin (SF) and SF/P(LLA-CL) blended nanofibrous scaffolds for tissue engineering applications, methanol vapor were used to treat electrospun nanofibers. SEM indicated SF and SF/ P(LLA-CL) scaffolds maintained nanofibrous structure after treated with methanol vapor and possessed good water-resistant ability. Characterization of 13C NMR clarified methanol vapor induced SF conformation from random coil or α- helix to β-sheet. Moreover, treated SF/ P (LLA-CL) nanofibrous scaffolds still kept good mechanical properties. Methanol vapor could be ideal method to treat SF and SF/ P(LLA-CL) nanofibrous scaffolds for biomedical applications.

scholarly journals Structural and Physical Properties of a Necrosis-Inducing Toxin from Pyrenophora tritici-repentis

1997 ◽  
Vol 87 (2) ◽  
pp. 154-160 ◽  
Author(s):  
Hui-Fen Zhang ◽  
Leonard J. Francl ◽  
James G. Jordahl ◽  
Steven W. Meinhardt
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Cd Spectroscopy ◽  
Tan Spot ◽  
Pyrenophora Tritici Repentis ◽  
Membrane Adhesion ◽  
Α Helix ◽  
Β Sheet

Cultivar-specific toxic metabolites of Pyrenophora tritici-repentis are involved in the appearance of necrotic and chlorotic foliar lesions characteristic of tan spot. A P. tritici-repentis necrosis-inducing toxin, Ptr necrosis toxin, was purified from isolate 86-124, sequenced by gas-phase amino acid microsequencing, and characterized by circular dichroism (CD) spectroscopy and isoelectric focusing. The purified protein had a similar amino acid composition and molecular weight as previously reported. Analysis of the CD spectrum from 178 to 250 nm indicated a protein consisting of 13% α-helix, 36% antiparallel β-sheet, 25% turns, and 25% other structures. The Ptr necrosis toxin from isolate 86-124 has an isoelectric point near pH 10. Using overlapping proteolytic fragments obtained from the toxin, a sequence of 101 continuous amino acids was obtained, but the amino terminus was blocked and 9 to 16 amino acids could not be sequenced. Secondary structure prediction based on the amino acid sequence indicated a β-sheet protein with little α-helix, which is in agreement with the structure determined by CD spectroscopy. Sequence analysis indicated the presence of a possible membrane adhesion site and several possible phosphorylation sites that may be involved in phytotoxicity.

CONFORMATION AND PHASE TRANSITION OF POLY-GLUTAMINE

2006 ◽  
Vol 17 (02) ◽  
pp. 235-246 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
TARIK ÇELİK
Keyword(s):  
Low Temperatures ◽  
Low Energy ◽  
Random Coil ◽  
Polyglutamine Diseases ◽  
Aggregate Formation ◽  
Two Phase ◽  
Coil Transition ◽  
Energy Stable ◽  
Α Helix ◽  
Β Sheet

In order to provide insights into the misfolding mechanism and the subsequent aggregate formation which cause what are known as the neurodegenerative polyglutamine diseases, we have simulated a 10-residue polyglutamine (poly-Q) chain in vacuum and in solvent by multicanonical method, which enabled us to study the system in a wide temperature range and discuss thermodynamic properties. It is understood that the system in vacuum shows two phase transitions, first of them occur at high temperature that is the well-known helix-coil transition and the second one is a solid-solid transition. However, the poly-Q chain in solvent is in a random coil state at higher temperatures, goes through a conformational change at T = 200 K and assumes predominantly a mixture of anti-parallel β-sheet and α-helix structures at low temperatures. One-residue glutamine dipeptide is also simulated and low-energy stable conformations are identified.

Breakdown and reassociation of bacterial spinae

1982 ◽  
Vol 28 (7) ◽  
pp. 795-808
Author(s):  
K. B. Easterbrook ◽  
R. W. Coombs
Keyword(s):  
Ionic Strength ◽  
Protein Conformation ◽  
High Ionic Strength ◽  
Random Coil ◽  
Temperature Dependent ◽  
Calcium Effect ◽  
Α Helix ◽  
Low Ionic Strength ◽  
Β Sheet ◽  
Polymeric Structures

The tubular appendage, spina (Easterbrook and Coombs. 1976. Can. J. Microbiol. 22: 438–440), dissociates most efficiently under conditions of low ionic strength (0.01 M), high pH (10), and high temperature (95 °C). The protomer, spinin, thus produced is stable under these conditions and reassociates on cooling to give two distinct filamentous polymeric structures that differ in their stability, protein conformation, and reassociation characteristics. Under conditions of low ionic strength (0.01 M), reassociation is relatively slow and leads to a product that has significant amounts of α-helix in addition to the high β-sheet component; under conditions of high ionic strength (1 M), reassociation is rapid and the non-β-sheet component is in the random coil configuration. Since polymerization of the latter structure is "seeded" by either endogenous or exogenously supplied spina fragments, the protomers comprising it are assumed to be in the same conformation as in the spinae. High ionic strength induces folding of the protomer, multimeric association, and finally, elongation by a temperature-dependent process. Reassociation appears to be pH (6–10) independent and, apart from a possible minor calcium effect, cation nonspecific.

scholarly journals Raman Evidence of p53-DBD Disorder Decrease upon Interaction with the Anticancer Protein Azurin

2019 ◽  
Vol 20 (12) ◽  
pp. 3078 ◽  
Author(s):  
Sara Signorelli ◽  
Salvatore Cannistraro ◽  
Anna Rita Bizzarri
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Principal Component ◽  
Intrinsically Disordered Protein ◽  
Random Coil ◽  
Disordered Proteins ◽  
Conformational Heterogeneity ◽  
Intrinsically Disordered ◽  
Tryptophan Residues ◽  
Α Helix ◽  
Β Sheet

Raman spectroscopy, which is a suitable tool to elucidate the structural properties of intrinsically disordered proteins, was applied to investigate the changes in both the structure and the conformational heterogeneity of the DNA-binding domain (DBD) belonging to the intrinsically disordered protein p53 upon its binding to Azurin, an electron-transfer anticancer protein from Pseudomonas aeruginosa. The Raman spectra of the DBD and Azurin, isolated in solution or forming a complex, were analyzed by a combined analysis based on peak inspection, band convolution, and principal component analysis (PCA). In particular, our attention was focused on the Raman peaks of Tyrosine and Tryptophan residues, which are diagnostic markers of protein side chain environment, and on the Amide I band, of which the deconvolution allows us to extract information about α-helix, β-sheet, and random coil contents. The results show an increase of the secondary structure content of DBD concomitantly with a decrease of its conformational heterogeneity upon its binding to Azurin. These findings suggest an Azurin-induced conformational change of DBD structure with possible implications for p53 functionality.

High-Pressure FTIR Studies of the Secondary Structure of Proteins

1996 ◽  
Author(s):  
Yoshihiro Taniguchi ◽  
Naohiro Takeda
Keyword(s):  
High Pressure ◽  
Secondary Structure ◽  
Cytochrome C ◽  
Ribonuclease A ◽  
Random Coil ◽  
Absorbance Spectroscopy ◽  
Α Helix ◽  
Bovine Pancreas ◽  
Β Sheet ◽  
Denaturation Of Proteins

Infrared spectra of five globular proteins (bovine pancreas ribonuclease A, horse skeletal muscle myoglobin, bovine pancreas insulin, horse heart cytochrome c, egg white lysozyme) in 5% D2O solutions (pD 7.0) were measured as a function of pressure up to 1470 MPa at 30 °C. According to the second-derivative spectral changes in the observed amide I band of the proteins, which indicate that the α-helix and β-sheet substructures of the secondary structures break dramatically into the random coil conformation, ribonuclease A and myoglobin are denatured reversibly at 850 MPa and 350 MPa, respectively. Lysozyme denatures partially and reversibly at 670 MPa, as shown by decrease in the α-helix and β-turn substructures, but no change occurs in the random coil and β-sheet substructures. The secondary structure of cytochrome c is not disrupted at pressures up to 1470 MPa, and partial transformation of the α-helix of insulin to random coil starts at 960 MPa. Hydrogen-deuterium exchange of protons on the amide groups in the protein interior is increased by external pressure and is associated with the pressure-induced protein conformational changes. A number of studies on the effects of pressure on protein denaturation have been carried out using various high-pressure detection methods: ultraviolet absorbance spectroscopy (Brandts et al., 1970; Hawley, 1971), visible absorbance spectroscopy (Zipp & Kauzmann, 1973), fluorescence intensity spectroscopy (Li et al., 1976), polarization fluorescence spectroscopy (Chryssomallis et al., 1981), and enzyme activity assays (Taniguchi & Suzuki, 1983; Makimoto et al., 1989). These techniques have the great advantage of being applicable to pressure-induced reversible denaturation of proteins to identify the thermodynamic parameters, especially the volume change and compressibility of a protein in solution, because the experiments can be run under dilute conditions at a protein concentration of less than 0.05% w/v. Therefore, these data reflect the intramolecular phenomena of reversible pressure changes and provide the volume changes accompanying the denaturation of proteins, which are due to the difference in partial molal (specific) volume between the native and denatured proteins in solution.

Experimental Study on Flow-Front Fingering Instabilities in Injection Molding of Polymer Solutions and Melts

2004 ◽  
Author(s):  
Kalonji K. Kabanemi ◽  
Jean-Franc¸ois He´tu ◽  
Samira H. Sammoun
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Polymer Solutions ◽  
Low Molecular Weight ◽  
Flow Front ◽  
High Molecular Weight Polymer ◽  
Molecular Weight Polymer ◽  
Polymer Molecules ◽  
Molecular Weights ◽  
Solvent Molecules

An experimental investigation of the flow behavior of dilute, semi-dilute and concentrated polymer solutions has been carried out to gain a better understanding of the underlying mechanisms leading to the occurrence of instabilities at the advancing flow front during the filling of a mold cavity. Experiments were performed using various mass concentrations of low and high molecular weight polyacrylamide polymers in corn syrup and water. This paper reports a new type of elastic fingering instabilities at the advancing flow front that has been observed only in semi-dilute polymer solutions of high molecular weight polymers. These flow front elastic instabilities seem to arise as a result of a mixture of widely separated high molecular weight polymer molecules and low molecular weight solvent molecules, which gives rise to a largely non-uniform polydisperse solution, with respect to all the kinds of molecules in the resulting mixture (solvent molecules and polymer molecules). The occurrence of these instabilities appears to be independent of the injection flow rate and the cavity thickness. Moreover, these instabilities do not manifest themselves in dilute or concentrated regimes, where respectively, polymer molecules and solvent molecules are minor perturbation of the resulting solution. In those regimes, smooth flow fronts are confirmed from our experiments. Based on these findings, the experimental investigations have been extended to polymer melts. Different mixtures of polycarbonate melts of widely separated molecular weights (low and high molecular weights) were first prepared. The effect of the large polydispersity of the resulting mixtures on the flow front behavior was subsequently studied. The same instabilities at the flow front were observed only in the experiments where a very small amount of high molecular weight polycarbonate polymer has been mixed to a low molecular weight polycarbonate melt (oligomers).

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