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.

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.

Cloning and Characterization of Three Genes Encoding LMW-GSs from Triticum aestivum, Cultival Cheyenne

2012 ◽  
Vol 554-556 ◽  
pp. 1116-1120 ◽  
Author(s):  
Mei Rong Chen ◽  
Xing Shen ◽  
Lin Li ◽  
Song Qing Hu
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Amino Acid Residues ◽  
Repetitive Domain ◽  
Genebank Accession ◽  
Genes Encoding ◽  
Α Helix ◽  
Β Sheet

Three low molecular weight subunit genes, named LMW-CND1 (GeneBank accession JQ780048), LMW-CND2 (GeneBank accession JQ779840), LMW-CND3 (GeneBank accession JQ779841), with a ORF of 1053 bp, 903 bp, 969 bp, respectively, were isolated from cv. Cheyenne and characterized detailed in molecular level. The proteins encoded by the genes, with 350, 300, 322 amino acid residues respectively, differ only in repetitive domain of sequences due to insertion or deletion of repeats in this domain. Highly similarity in amino-acid sequence between these three subunits and other published LMW-GSs was also observed, showing that all three genes published here are typical LMW-GS genes and closely related to the genes on chromosome 1D. Besides, secondary structure prediction of proteins indicated that, in the three LMW-GSs, random loop accounts for no less than 70 %, α-helix amounts to 26 %, average, and only 1.4 %~1.7 % is β-sheet.

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.

scholarly journals Secondary-structure prediction revisited: Pβ and Pc represent structures of amyloids and aid elucidating phenomena in interspecies transmissions of prion

2016 ◽  
Author(s):  
Yuzuru Taguchi ◽  
Noriyuki Nishida
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Genetic Material ◽  
Structural Models ◽  
Infectious Agent ◽  
Random Coil ◽  
Primary Structures ◽  
Β Sheet

AbstractPrion is a unique infectious agent which consists solely of abnormally-folded prion protein (PrPSc) but possesses virus-like features, e.g. existence of strain diversity, adaptation to new hosts and evolutionary changes. These biological phenomena were attributed to the structural properties of PrPSc due to lack of genetic material of prion. Therefore, regardless of incompatibility with high-resolution structural analysis, many structural models of PrPSc have been hypothesized based on limited structural information and, recently, models consisting solely of β-sheets and intervening loops/kinks have been suggested, i.e. parallel in-register β-sheet models and β-solenoid model. Given the relatively simple structural models of PrPSc, we utilized values of theoretical β-sheet or random-coil propensity (Pβ or Pc, respectively) calculated by secondary structure prediction with a neural network to analyze interspecies transmissions of prion, because numerical conversion of the primary structures would enable quantitative comparison between PrP with distinct primary structures. Reviewing experiments in the literature, we ascertained biological relevance of Pβ and Pc and demonstrated how those parameters could aid interpretation and explain phenomena in interspecies transmissions. Our approach can lead to development of a versatile tool for investigation of not only prion but also other amyloids.

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.

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 Use of molecular mechanics for secondary structure prediction. Is it possible to reveal α-helix?

FEBS Letters ◽  
2001 ◽  
Vol 510 (1-2) ◽  
pp. 13-16 ◽  
Author(s):  
Gelena T Kilosanidze ◽  
Alexey S Kutsenko ◽  
Natalia G Esipova ◽  
Vladimir G Tumanyan
Keyword(s):  
Secondary Structure ◽  
Molecular Mechanics ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Α Helix

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.

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