Bioinformatics Analysis and Characteristics of Ser/Thr Protein Kinase Encoded by UL13 Gene of Duck Plague Virus

2011 ◽  
Vol 393-395 ◽  
pp. 617-627
Author(s):  
Xi Xia Hu ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Protein Kinase ◽  
Secondary Structure ◽  
Physicochemical Properties ◽  
Evolutionary Relationship ◽  
Alpha Helix ◽  
Structural Features ◽  
Functional Study ◽  
Online Tools ◽  
Multiple Sequences ◽  
Sequences Alignment

This report showed some physicochemical properties and structural features about DPV-UL13 protein predicted by some software and online tools. The online analysis of the physicochemical properties demonstrates that the protein has thirty-four potential phosphorylation sites when the threshold of prediction score is above 0.5 and both the signal peptide and the transmembrance region are not found. In addition, the protein has hydrophilic amine acid districts more than hydrophobic districts and subcellular localization largely locates at mitochondrial with 43.5%. The secondary structure results revealed that random coils dominated among secondary structure elements followed by alpha helix and extended strand. The phylogenetic tree shows that DPV-UL13 protein has close evolutionary relationship with the genus Mardivirus. And the multiple sequences alignment of UL13 protein in 156-436 sequence among DPV, HSV-1 and Mardivirus genus suggests highly conserved characteristic. These analysis surpports the guess that DPV-UL13 product may be a Ser/Thr protein kinase. All the data will be a basis for the further functional study of the DPV-UL13 protein.

Bioinformatic Analysis and Characteristics of Glycoprotein L(gL) Encoded by UL1 Gene of Duck Plague Virus

2013 ◽  
Vol 647 ◽  
pp. 250-257
Author(s):  
Ling Jie Zuo ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Secondary Structure ◽  
Physicochemical Properties ◽  
Evolutionary Relationship ◽  
Alpha Helix ◽  
Bioinformatic Analysis ◽  
Random Coil ◽  
Phosphorylation Sites ◽  
Duck Plague Virus ◽  
Online Tools ◽  
Glycosylation Sites

Glycoprotein L(gL) is encoded by UL1 gene of duck plague virus (DPV). Through predicting and analyzing the structure and physicochemical properties of DPV gL protein by using some software and online tools to gain more information of DPV gL protein. The phylogenetic tree shows that DPV gL protein has close evolutionary relationship with the genus Simplexvirus. The online analysis of the physicochemical properties demonstrates that the protein has ten potential phosphorylation sites and five potential O-linked glycosylation sites, and without both the signal peptide and the transmembrance region. In addition, the subcellular localization of gL protein largely locates at mitochondrial with 47.8%. The secondary structure results reveal that random coil dominate among secondary structure elements followed by alpha helix, extended strand and β-turn for all sequences. All the data will help a basis for further functional and physiological features study of the DPV gL protein.

scholarly journals A bioinformatics study concerning structural and functional properties of human caveolin proteins

2014 ◽  
Vol 79 (2) ◽  
pp. 133-150
Author(s):  
Adriana Isvoran ◽  
Dana Craciun ◽  
Alecu Ciorsac ◽  
Nahuel Perrot ◽  
Veronica Beswick ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Physicochemical Properties ◽  
Functional Properties ◽  
Chemical Properties ◽  
Caveolin 1 ◽  
Physico Chemical ◽  
Structural And Functional Properties ◽  
Bioinformatics Study ◽  
Sequences Alignment ◽  
Good Agreement

We performed a bioinformatics study to predict and compare the structural and functional properties of human caveolins: caveolin-1, -2 and -3. The computed local physico-chemical properties, predictions of their secondary structure elements and interacting partners of caveolin-2 and -3 are compared to experimentally proved structural and functional properties of caveolin-1. These data combined with the sequences alignment of the three caveolins, allowed predicting and characterizing the functional domains of caveolin-2 and -3. The hydrophobic regions of these proteins are highly similar in sequences and physicochemical properties and it is in good agreement with their known membrane locations and functions. The most divergent in sequences and properties are the C-terminal regions of caveolins suggesting that they might be responsible for their distinct predicted interactions, with direct consequences on signalling processes.

scholarly journals In Silico prediction and Comparative Modeling of proteins in Creeping Fig (Ficus pumila) plant

2021 ◽  
Vol 23 (08) ◽  
pp. 898-905
Author(s):  
P. Revathi ◽  
◽  
K. Nirubama ◽  
G. Thamotharan ◽  
M. Beutline Malgija ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Transmembrane Helix ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Comparative Modeling ◽  
Structural Features ◽  
Vital Role ◽  
Random Coil ◽  
Dimensional Structure ◽  
Grand Average

In the present study, the Ficus pumila have taken to analyze the proteins by their preliminary characters from the database and predicted vital role of different sequences. The F. pumila (Creeping fig) is a prostrate/climbing shrub, experiments proved various active phytochemicals and antioxidant, antimicrobial, antimutagenic, analgesic, anti-inflammatory, antiproliferative, hypoglycemic, hypolipidemic, antihyperprolactinemic, anticholinesterase, nephroprotective properties. In addition to all metabolites, it also constitutes specific proteins that were evaluated through insilico homology modeling. Though it is considered as a poisonous weed, the protein present in this plant is evaluated by physicochemical, phylogeny and amino acid proportions by protparam, Swiss model, SOPMA, Clustal omega tools to describe its structural features and to understand molecular function. The computed theoretical isoelectric point (pI) found to be more than 7 indicates basic nature of proteins. The aliphatic index ranges 67-113 indicates thermal stability of proteins. The predicted Grand average hydropathy(GRAVY) shows possibilities of enhanced interaction of these proteins with water by lowest value. Functional analysis of these proteins was performed by SOSUI server which predicted transmembrane helix and solubility. Secondary structure analysis was carried out by SOPMA revealed that Alpha helix and random coil dominated followed by extended strand, and beta turns among secondary structure elements. The modelling of three-dimensional structure of proteins was performed by Swiss model. The model was validated using protein structure checking tool- VADAR. Particularly, NAD(P)H –quinoneoxidoreductase and Glyceraldehyde-3-phosphate dehydrogenase structures were analysed by phylogenetic analysis to trace relationship and reported. The results suggesting its possible role in cellular and metabolic functions.

scholarly journals Characterization of intron 7 to exon 8 of heat shock protein 90-aa1 (hsp90aa1) gene in dominant brown layer chicken using some bioinformatic tools

2021 ◽  
Vol 78 (2) ◽  
pp. 55
Author(s):  
Young IRIVBOJE ◽  
Adeboye FAFIOLU ◽  
Oluwabusayo IRIVBOJE ◽  
Christian IKEOBI
Keyword(s):  
Heat Stress ◽  
Secondary Structure ◽  
Homology Modelling ◽  
Phosphorylation Site ◽  
Evolutionary Relationship ◽  
Structural Features ◽  
Avian Species ◽  
Phosphorylation Sites ◽  
Post Translational Modification ◽  
Relationship Study

HSP90AA1, an isoform of HSP90 has been characterized to indicate it plays important roles in basic cellular events. It is activated in chicken in response to heat stress. This study was aimed at the computational analysis of the biochemical cum structural features and an evolutionary relationship study on the HSP90AA1 gene in Dominant brown layers (DBL) and some selected avian species using bioinformatics tools. ProtParam for physicochemical properties. Scanprosite for post-translational modification sites, Netphos-3.1 for phosphorylation sites, BDM-PUB program for Ubiquitination sites, PDBSUM for Secondary structure and homology modelling with SWISS-model. The findings revealed that intron 7 and exon 8 of HSP90AA1 protein in DBL had a molecular weight of 24681.19Da and an instability index of 27.60, contains N-myristoylation, Protein-kinase-C-phosphorylation and Tyrosine-kinase-phosphorylation site-2 post-translational modification sites, 4-serine and 2-threonine phosphorylation sites and 12-ubiquitination sites. The evolutionary relationship study found Japanese quail to be in a sister branch close to DBL and chicken. Motifs detected in the avian species revealed the gene to be highly conserved. The secondary structure consisted of 16-helices, 3-sheets and 14-strands. The homology modelling was 87.25% sequence identity with human MC-HSP90-alpha. The study elucidates the components and characteristics of HSP90AA1 in DBL in response to heat stress.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

scholarly journals Physicochemical characterisation of kafirins extracted from sorghum grain and dried distillers grain with solubles related to their biomaterial functionality

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Umar Shah ◽  
Deepak Dwivedi ◽  
Mark Hackett ◽  
Hani Al-Salami ◽  
Ranjeet P. Utikar ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Physicochemical Properties ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Chemical Properties ◽  
X Ray ◽  
Distillers Grain ◽  
Sorghum Grain ◽  
Dried Distillers Grain ◽  
Polypeptide Profile

AbstractKafirin, the hydrophobic prolamin storage protein in sorghum grain is enriched when the grain is used for bioethanol production to give dried distillers grain with solubles (DGGS) as a by-product. There is great interest in DDGS kafirin as a new source for biomaterials. There is however a lack of fundamental understanding of how the physicochemical properties of DDGS kafirin having been exposed to the high temperature conditions during ethanol production, compare to kafirin made directly from the grain. An understanding of these properties is required to catalyse the utilisation of DDGS kafirin for biomaterial applications. The aim of this study was to extract kafirin directly from sorghum grain and from DDGS derived from the same grain and, then perform a comparative investigation of the physicochemical properties of these kafirins in terms of: polypeptide profile by sodium-dodecyl sulphate polyacrylamide gel electrophoresis; secondary structure by Fourier transform infra-red spectroscopy and x-ray diffraction, self-assembly behaviour by small-angle x-ray scattering, surface morphology by scanning electron microscopy and surface chemical properties by energy dispersive x-ray spectroscopy. DDGS kafirin was found to have very similar polypeptide profile as grain kafirin but contained altered secondary structure with increased levels of β-sheets. The structure morphology showed surface fractals and surface elemental composition suggesting enhanced reactivity with possibility to endow interfacial wettability. These properties of DDGS kafirin may provide it with unique functionality and thus open up opportunities for it to be used as a novel food grade biomaterial.

scholarly journals Characterization of porcine osteonectin extracted from foetal calvariae

1988 ◽  
Vol 253 (1) ◽  
pp. 139-151 ◽  
Author(s):  
C Domenicucci ◽  
H A Goldberg ◽  
T Hofmann ◽  
D Isenman ◽  
S Wasi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Type I Collagen ◽  
Culture Shock ◽  
Gel Filtration ◽  
Alpha Helix ◽  
Type I ◽  
Homologous Proteins ◽  
Compact Structure ◽  
Significant Difference

Osteonectin, extracted from foetal porcine calvariae with 0.5 M-EDTA, was purified to homogeneity by using gel filtration and polyanion anion-exchange fast protein liquid chromatography under dissociative conditions without the need of reducing agents. The purified protein migrated with an Mr of 40,300 on SDS/polyacrylamide gels and was similar to bovine osteonectin in both amino acid composition and in its ability to bind to hydroxyapatite in the presence of 4 M-guanidinium hydrochloride (GdmCl). However, unlike the bovine protein, porcine osteonectin did not bind selectively to hydroxyapatite when EDTA tissue extracts were used. In addition, purified porcine osteonectin did not show any apparent affinity for either native or denatured type I collagen, but did bind to serum albumin. Primary sequence analysis revealed an N-terminal alanine residue, with approximately one-half of the subsequent 35 residues identified as small hydrophobic amino acids and one-quarter as acidic amino acids. The only significant difference between the N-terminal sequences of the bovine and porcine proteins was the deletion of the tripeptide Val-Ala-Glu in porcine osteonectin. In contrast with bovine osteonectin, far-u.v.c.d. of porcine osteonectin revealed considerable secondary structure, of which 27% was alpha-helix and 39% was beta-sheet. Cleavage of the molecule with CNBr under non-reducing conditions generated five fragments, of which two major fragments (Mr 27,900 and 12,400) stained blue with Stains All, a reagent that stains sialic-acid-rich proteins/phosphate-containing proteins and/or Ca2+-binding proteins blue while staining other proteins pink. The 12,400-Mr fragment bound 45Ca2+ selectively, indicating a Ca2+-binding site in this part of the molecule. The 27,900-Mr fragment did not bind Ca2+, and since biosynthetic studies with 32PO4(3-) did not show phosphorylation of porcine osteonectin, this fragment is likely to be highly acidic. The incomplete cleavage of the molecule with CNBr and the ability of the molecule to regain its secondary structure after exposure to 7 M-urea are features consistent with the molecule having a compact structure that is stabilized by numerous disulphide bridges. The chemical and binding properties of porcine osteonectin are closely similar to the recently described ‘culture shock’, SPARC and BM-40 proteins, indicating that these are homologous proteins.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

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