scholarly journals Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

2020 ◽  
Author(s):  
CHITTARANJAN BARUAH ◽  
PAPARI DEVI ◽  
DHIRENDRA K SHARMA
Keyword(s):  
Functional Analysis ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Structure Prediction ◽  
Functional Characterization ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Bat Coronavirus ◽  
Close Relatedness

<p>This paper has attempted into the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and <i>ab-initio</i> modeling. The evolutionary analysis of both the proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus.</p> <p> </p>

scholarly journals Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

2020 ◽  
Author(s):  
CHITTARANJAN BARUAH ◽  
PAPARI DEVI ◽  
DHIRENDRA K SHARMA
Keyword(s):  
Functional Analysis ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Structure Prediction ◽  
Functional Characterization ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Bat Coronavirus ◽  
Close Relatedness

<p>This paper has attempted into the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and <i>ab-initio</i> modeling. The evolutionary analysis of both the proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus.</p> <p> </p>

scholarly journals Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Chittaranjan Baruah ◽  
Papari Devi ◽  
Dhirendra K. Sharma
Keyword(s):  
Sequence Analysis ◽  
Drug Design ◽  
Structure Prediction ◽  
Nonstructural Protein ◽  
Evolutionary Relationship ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Structure Based Drug Design ◽  
Bat Coronavirus ◽  
Close Relatedness

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.

scholarly journals Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins

2021 ◽  
Vol 12 (3) ◽  
pp. 3259-3304
Keyword(s):  
Structure Prediction ◽  
Active Sites ◽  
Homo Sapiens ◽  
Functional Characterization ◽  
Protein Structures ◽  
Three Dimensional ◽  
Experimental Models ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that transmitted from animal to human became a life-threatening pandemic in 2020. Scientists are currently testing several drugs to eradicate the COVID-19 outbreak. However, there is no 100 % effective drug or vaccine against SARS-CoV-2 has been discovered so far. In this study, we explored the structure prediction and functional analysis of 75 Malaysia SARS-CoV-2 strain’s structural and accessory proteins without the presence of experimental models. Physiochemical analysis, secondary structure analysis, structure prediction, functional characterization, active site identification, and evolutionary analysis based on the amino acid sequences retrieved from National Centre for Biotechnology Information (NCBI). Three-dimensional (3-D) protein structures were built using the Swiss model. The quality of protein models was verified by ERRAT, PROCHECK, and Verify 3D tools. Active prediction analysis revealed the high potential active sites of proteins where the anti-viral drug or vaccine may bind and inhibit the viral activities. Molecular phylogenetic analysis of ORF10, ORF8, and ORF6 proteins from five different species was analyzed. The results from this analysis proved that Homo sapiens SARS-CoV-2 had high genetic similarity with the bat coronavirus. These analyses may help in designing structure-based anti-viral drugs or to develop potential vaccines for SARS-CoV-2.

scholarly journals Factor D̄ of the alternative pathway of human complement. Purification, alignment and N-terminal amino acid sequences of the major cyanogen bromide fragments, and localization of the serine residue at the active site

1980 ◽  
Vol 187 (3) ◽  
pp. 863-874 ◽  
Author(s):  
D M Johnson ◽  
J Gagnon ◽  
K B Reid
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Alternative Pathway ◽  
Amino Acid Sequences ◽  
Serine Residue ◽  
Amino Acid Sequence Analysis ◽  
Terminal Amino Acid ◽  
Terminal Amino ◽  
Terminal Amino Acid Sequence

The serine esterase factor D of the complement system was purified from outdated human plasma with a yield of 20% of the initial haemolytic activity found in serum. This represented an approx. 60 000-fold purification. The final product was homogeneous as judged by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis (with an apparent mol.wt. of 24 000), its migration as a single component in a variety of fractionation procedures based on size and charge, and its N-terminal amino-acid-sequence analysis. The N-terminal amino acid sequence of the first 36 residues of the intact molecule was found to be homologous with the N-terminal amino acid sequences of the catalytic chains of other serine esterases. Factor D showed an especially strong homology (greater than 60% identity) with rat ‘group-specific protease’ [Woodbury, Katunuma, Kobayashi, Titani, & Neurath (1978) Biochemistry 17, 811-819] over the first 16 amino acid residues. This similarity is of interest since it is considered that both enzymes may be synthesized in their active, rather than zymogen, forms. The three major CNBr fragments of factor D, which had apparent mol.wts. of 15 800, 6600 and 1700, were purified and then aligned by N-terminal amino acid sequence analysis and amino acid analysis. By using factor D labelled with di-[1,3-14C]isopropylphosphofluoridate it was shown that the CNBr fragment of apparent mol.wt. 6600, which is located in the C-terminal region of factor D, contained the active serine residue. The amino acid sequence around this residue was determined.

scholarly journals In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3160 ◽  
Author(s):  
Kumar Manochitra ◽  
Subhash Chandra Parija
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Treatment Modalities ◽  
Bioinformatic Tools ◽  
Complex Protein ◽  
A Cell ◽  
Quaternary Structures

BackgroundAmoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-richEntamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal inE. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential. However, studies in this aspect are scant. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using appropriatein-silicomethods.MethodsThe amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.ResultsThe protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be an extracellular protein, peroxiredoxin a peripheral membrane protein while Gal/GalNAc lectin was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc lectin, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All the three proteins exhibited similarity in their structures and were mostly composed of loops.DiscussionThe structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures of SREHP and peroxiredoxin predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

scholarly journals Molecular Analysis of Resistance to Streptogramin A Compounds Conferred by the Vga Proteins of Staphylococci

2005 ◽  
Vol 49 (3) ◽  
pp. 973-980 ◽  
Author(s):  
Olivier Chesneau ◽  
Heidi Ligeret ◽  
Negin Hosan-Aghaie ◽  
Anne Morvan ◽  
Elie Dassa
Keyword(s):  
Antibiotic Resistance ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Polyclonal Antibodies ◽  
Amino Acid Sequences ◽  
Gene Products ◽  
Β Subunit ◽  
Abc Proteins ◽  
Gram Positive Bacteria ◽  
Resistance Determinants

ABSTRACT The Vga and Msr resistance determinants, encoded by mobile genetic elements in various staphylococcal strains, belong to a family of ATP-binding cassette (ABC) proteins whose functions and structures are ill defined. Their amino acid sequences are similar to those of proteins involved in the immunity of streptomycetes to the macrolide-lincosamide-streptogramin antibiotics that they produce. Sequence analysis of the genomes of the gram-positive bacteria with low G+C contents revealed that Lmo0919 from Listeria monocytogenes is more closely related to Vga variants than to Msr variants. In the present study we compared the antibiotic resistance profiles conferred by the Vga-like proteins in two staphylococcal hosts. It was shown that Vga(A), the Vga(A) variant [Vga(A)v], and Lmo0919 can confer resistance to lincosamides and streptogramin A compounds, while only Vga(B) is able to increase the level of resistance to pristinamycin, a mixture of streptogramin A and streptogramin B compounds. By using polyclonal antibodies, we found that the Vga(A) protein colocalized with the β subunit of the F1-F0 ATPase in the membrane fractions of staphylococcal cells. In order to identify functional units in these atypical ABC proteins, such as regions that might be involved in substrate specificity and/or membrane targeting, we analyzed the resistance phenotypes conferred by various plasmids carrying parts or modified versions of the vga(A) gene and we determined the subcellular localization of the gene products. Only polypeptides composed of two ABC domains were detected in the cell membranes. No region of drug specificity was identified. Resistance properties were dependent on the integrities of both Walker B motifs.

scholarly journals Proteins sequence analysis of Contagious Caprine Pleuropneumonia

2017 ◽  
Vol 33 (3) ◽  
pp. 309-319
Author(s):  
Ayuba Dauda ◽  
Abdulmojeed Yakubu ◽  
Ihe Dim ◽  
Deeve Gwaza
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Alpha Helix ◽  
Amino Acid Sequences ◽  
Contagious Bovine Pleuropneumonia ◽  
Isoleucine Leucine ◽  
Grand Average

A total of twenty (20) contagious bovine pleuropneumonia (CCPP) proteins were retrieved from the GenBank (www.ncbi.nlm.nih.gov). The proteins sequences were used to investigate the molecular identity of various CCPP proteins. The physico-chemical properties of CCPP proteins were performed using protparam tool. Isoelectric point (pI), molecular weight (MW), extinction coefficient (EC); instability index (II), aliphatic index (AI) and grand average of hydropathicity (GRAVY) were computed. The study revealed that the pI of CCPP proteins were acidic and basic in nature. The EC and II of CCPP proteins indicate better stability which is an indication of resistant to mutation and thermally stable. The GRAVY of CCPP proteins revealed some are positive while some are negative. The positive value indicates solubility (hydrophilic) in water while negative is not soluble (hydrophobic) in water. The amino acid composition of CCPP proteins indicates that they are rich in isoleucine, leucine and lysine. The three dimensional structures (3D) of the CCPP proteins were determine using Phyre2 server. The amino acid sequences of CCPP proteins were subjected to secondary structure prediction using ExPASy?s SOPMA tool. The proteins are more of alpha helix structure. The genetic information eminating from this study may bring insight into mutagenesis and pharmacogenetic. <br><br><font color="red"><b> This article has been retracted. Link to the retraction <u><a href="http://dx.doi.org/10.2298/BAH1803369E">10.2298/BAH1803369E</a><u></b></font>

scholarly journals Cloning and Sequence Analysis of Genes Encoding Staphylococcus hyicus Exfoliative Toxin Types A, B, C, and D

2004 ◽  
Vol 186 (6) ◽  
pp. 1833-1837 ◽  
Author(s):  
Peter Ahrens ◽  
Lars Ole Andresen
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Serine Proteases ◽  
Amino Acid Sequences ◽  
Coding Sequence ◽  
Exfoliative Toxin ◽  
Genes Encoding

ABSTRACT Exfoliative toxins produced by certain strains of Staphylococcus hyicus mediate exudative epidermitis in pigs. In this study the genes coding for four different exfoliative toxin from S. hyicus (ExhA, ExhB, ExhC, and ExhD) were cloned and sequenced. The coding sequence of the four toxin genes ranged from 816 to 834 bp. The amino acid sequences of these four toxins were homologous to the earlier described exfoliative toxins SHETB from S. hyicus and ETA, ETB, and ETD from Staphylococcus aureus. The homology between the S. hyicus toxins was at the same level as the homology to the exfoliative toxins from S. aureus. The toxins showed similarity to serine proteases, including preservation of the catalytic tract in ExhA, ExhB, and ExhC. However, in ExhD, Asp in the putative catalytic tract was replaced with Glu. The recombinant toxins could be expressed in Escherichia coli, and three of the four toxins were recognized by monoclonal antibodies raised against native exfoliative toxins.

Sign in / Sign up

Export Citation Format

Share Document