scholarly journals Analysis of Conserved, Computationally Predicted Epitope Regions for VP5 and VP7 Across three Orbiviruses

2018 ◽  
Vol 12 ◽  
pp. 117793221875534 ◽  
Author(s):  
Bonnie L Russell ◽  
Nishal Parbhoo ◽  
Samantha Gildenhuys
Keyword(s):  
Amino Acid ◽  
Viral Protein ◽  
Consensus Sequence ◽  
Amino Acid Sequences ◽  
Hemorrhagic Disease ◽  
African Horse Sickness Virus ◽  
Consensus Sequences ◽  
Preventative Measures ◽  
Amino Acid Sequence Conservation ◽  
Homology Models

Orbiviruses are double-stranded RNA viruses that have profound economic and veterinary significance, 3 of the most important being African horse sickness virus (AHSV), bluetongue virus (BTV), and epizootic hemorrhagic disease virus (EHDV). Currently, vaccination and vector control are used as preventative measures; however, there are several problems with the current vaccines. Comparing viral amino acid sequences, we obtained an AHSV-BTV-EHDV consensus sequence for VP5 (viral protein 5) and for VP7 (viral protein 7) and generated homology models for these proteins. The structures and sequences were analyzed for amino acid sequence conservation, entropy, surface accessibility, and epitope propensity, to computationally determine whether consensus sequences still possess potential epitope regions. In total, 5 potential linear epitope regions on VP5 and 11 on VP7, as well as potential discontinuous B-cell epitopes, were identified and mapped onto the homology models created. Regions identified for VP5 and VP7 could be important in vaccine design against orbiviruses.

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

2011 ◽  
Vol 6 (4) ◽  
pp. 545-557 ◽  
Author(s):  
Malay Choudhury ◽  
Takahiro Oku ◽  
Shoji Yamada ◽  
Masaharu Komatsu ◽  
Keita Kudoh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Structural Features ◽  
Lipid Binding ◽  
Japanese Eel ◽  
Amino Acid Sequences ◽  
Novel Genes ◽  
Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

scholarly journals Single Passage of Human Metapneumovirus in LLC-MK2 Cells Does Not Affect Viral Protein-Coding Capacity

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Simon Loevenich ◽  
Aleksandr Ianevski ◽  
Eneli Oitmaa ◽  
Denis E. Kainov ◽  
Marit W. Anthonsen
Keyword(s):  
Amino Acid ◽  
Viral Protein ◽  
Complete Genome ◽  
Human Metapneumovirus ◽  
Amino Acid Sequences ◽  
Paired Comparisons ◽  
Genome Sequences ◽  
Protein Coding ◽  
Single Passage ◽  
Coding Capacity

ABSTRACT Here, we report the complete genome sequences of human metapneumovirus (HMPV) prior to and after passaging in LLC-MK2 cells. Paired comparisons of the 13,335-nucleotide genomes revealed that the virus acquired the T10736C transition in its genome, which did not affect the amino acid sequences of HMPV proteins.

scholarly journals The variable subunit associated with protein phosphatase 2A0 defines a novel multimember family of regulatory subunits

1996 ◽  
Vol 317 (1) ◽  
pp. 187-194 ◽  
Author(s):  
Stanislaw ZOLNIEROWICZ ◽  
Christine VAN HOOF ◽  
Nataša ANDJELKOVIĆ ◽  
Peter CRON ◽  
Ilse STEVENS ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Phosphatase ◽  
Amino Acid Sequences ◽  
Regulatory Subunits ◽  
Consensus Sequences ◽  
Reverse Transcription Pcr ◽  
Genes Encoding ◽  
Phosphatase 2A ◽  
Molecular Masses ◽  
Specific Mrnas

Two protein phosphatase 2A (PP2A) holoenzymes were isolated from rabbit skeletal muscle containing, in addition to the catalytic and PR65 regulatory subunits, proteins of apparent molecular masses of 61 and 56 kDa respectively. Both holoenzymes displayed low basal phosphorylase phosphatase activity, which could be stimulated by protamine to an extent similar to that of previously characterized PP2A holoenzymes. Protein microsequencing of tryptic peptides derived from the 61 kDa protein, termed PR61, yielded 117 residues of amino acid sequence. Molecular cloning by enrichment of specific mRNAs, followed by reverse transcription–PCR and cDNA library screening, revealed that this protein exists in multiple isoforms encoded by at least three genes, one of which gives rise to several splicing variants. Comparisons of these sequences with the available databases identified one more human gene and predicted another based on a rabbit cDNA-derived sequence, thus bringing the number of genes encoding PR61 family members to five. Peptide sequences derived from PR61 corresponded to the deduced amino acid sequences of either α or β isoforms, indicating that the purified PP2A preparation was a mixture of at least two trimers. In contrast, the 56 kDa subunit (termed PR56) seems to correspond to the ϵ isoform of PR61. Several regulatory subunits of PP2A belonging to the PR61 family contain consensus sequences for nuclear localization and might therefore target PP2A to nuclear substrates.

scholarly journals Homologues of insulinase, a new superfamily of metalloendopeptidases

1991 ◽  
Vol 275 (2) ◽  
pp. 389-391 ◽  
Author(s):  
N D Rawlings ◽  
A J Barrett
Keyword(s):  
Escherichia Coli ◽  
Statistical Analysis ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Amino Acid Sequences

On the basis of a statistical analysis of an alignment of the amino acid sequences, a new superfamily of metalloendopeptidases is proposed, consisting of human insulinase, Escherichia coli protease III and mitochondrial processing endopeptidases from Saccharomyces and Neurospora. These enzymes do not contain the ‘HEXXH’ consensus sequence found in all previously recognized zinc metalloendopeptidases.

scholarly journals Expression analysis of a Cucurbita cDNA encoding endonuclease.

1995 ◽  
Vol 42 (2) ◽  
pp. 183-189 ◽  
Author(s):  
J Szopa
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Northern Blot Analysis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Nuclease Activity ◽  
Amino Acid Sequences ◽  
Cell Nuclei ◽  
Consensus Sequences ◽  
Mrna Content ◽  
Membrane Binding Sites

The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3 protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber.

The ‘30K’ superfamily of viral movement proteins

Microbiology ◽  
2000 ◽  
Vol 81 (1) ◽  
pp. 257-266 ◽  
Author(s):  
Ulrich Melcher
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Consensus Sequence ◽  
Amino Acid Sequences ◽  
Movement Proteins ◽  
Consensus Sequences ◽  
Viral Movement ◽  
Secondary Structure Predictions ◽  
Α Helix

Relationships among the amino acid sequences of viral movement proteins related to the 30 kDa (‘30K’) movement protein of tobacco mosaic virus – the 30K superfamily – were explored. Sequences were grouped into 18 families. A comparison of secondary structure predictions for each family revealed a common predicted core structure flanked by variable N- and C-terminal domains. The core consisted of a series of β-elements flanked by an α-helix on each end. Consensus sequences for each of the families were generated and aligned with one another. From this alignment an overall secondary structure prediction was generated and a consensus sequence that can recognize each family in database searches was obtained. The analysis led to criteria that were used to evaluate other virus-encoded proteins for possible membership of the 30K superfamily. A rhabdoviral and a tenuiviral protein were identified as 30K superfamily members, as were plant-encoded phloem proteins. Parsimony analysis grouped tubule-forming movement proteins separate from others. Establishment of the alignment of residues of diverse families facilitates comparison of mutagenesis experiments done on different movement proteins and should serve as a guide for further such experiments.

Correlated mutations in hydroxysteroid dehydrogenases family

2017 ◽  
Vol 13 (1) ◽  
Author(s):  
Agata Żyźniewska ◽  
Jacek Leluk ◽  
Gabriela Żaroffe
Keyword(s):  
Amino Acid ◽  
Consensus Sequence ◽  
Hydroxysteroid Dehydrogenase ◽  
Amino Acid Sequences ◽  
Multiple Sequence ◽  
Hydroxysteroid Dehydrogenases ◽  
Uniprot Database ◽  
Correlated Mutations ◽  
Almost All ◽  
Degree Of Similarity

AbstractBackgroundHydroxysteroid dehydrogenase enzymes belong to the short-chain dehydrogenase/reductase (SDR) superfamily and aldo-keto reductases (AKRs). SDR is involved in the metabolism of many compounds (hormones, lipids, etc.) and is present in almost all studied genomes. Two hundred members of hydroxysteroid dehydrogenases have been analysed in terms of natural mutational variability. The second superfamily comprises AKR superfamily group enzymes whose function is catalysing the oxidation and reduction of many substrates by binding NAD(P)H as a cofactor. This kind of study is the first approach for the hydroxysteroid dehydrogenase family. This information grants practical meaning to designing potential specific drugs to fight specific diseases caused by mutations.MethodsIn the research, amino acid sequences of representatives of the hydroxysteroid dehydrogenase family were extracted from the UniProt database. In total, the analysed 200 sequences with the highest degree of similarity were shown by BLAST searches. In the sequence analyses, we used the following software: ClustalX (multiple sequence alignment), Consensus Constructor (creating consensus sequence), and CORM (finding correlated mutations).ResultsThe CORM program identified potential sites of correlated mutations in hydroxysteroid dehydrogenases. This program generated 18 tables of results that contain the amino acid positions of mutations. Seven of these are presented in this paper.ConclusionsThe primary structure of the hydroxysteroid dehydrogenase family shows high variation.

scholarly journals A new member of the chalcone synthase (CHS) family in sugarcane

2001 ◽  
Vol 24 (1-4) ◽  
pp. 257-261 ◽  
Author(s):  
Miriam G.G. Contessotto ◽  
Claudia B. Monteiro-Vitorello ◽  
Pilar D.S.C. Mariani ◽  
Luiz L. Coutinho
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Chalcone Synthase ◽  
Expressed Sequence Tag ◽  
Consensus Sequence ◽  
Stilbene Synthase ◽  
Amino Acid Sequences ◽  
Group 2 ◽  
Expressed Sequence ◽  
Group 1

Sequences from the sugarcane expressed sequence tag (SUCEST) database were analyzed based on their identities to genes encoding chalcone-synthase-like enzymes. The sorghum (Sorghum bicolor) chalcone-synthase (CHS, EC 2.3.1.74) protein sequence (gi|12229613) was used to search the SUCEST database for clusters of sequencing reads that were most similar to chalcone synthase. We found 121 reads with homology to sorghum chalcone synthase, which we were then able to sort into 14 clusters which themselves were divided into two groups (group 1 and group 2) based on the similarity of their deduced amino acid sequences. Clusters in group 1 were more similar to the sorghum enzyme than those in group 2, having the consensus sequence of the active site of chalcone and stilbene synthase. Analysis of gene expression (based on the number of reads from a specific library present in each group) indicated that most of the group 1 reads were from sugarcane flower and root libraries. Group 2 clusters were more similar to the amino acid sequence of an uncharacterized pathogen-induced protein (PI1, gi|9855801) from the S. bicolor expressed sequence tag (EST) database. The group 2 clusters sequences and PI1 proteins are 90% identical, having two amino acid changes at the chalcone and stilbene synthase consensi but conserving the cysteine residue at the active site. The PI1 EST has not been previously associated with chalcone synthase and has a different consensus sequence from the previously described chalcone synthase of sorghum. Most of the group 2 reads were from libraries prepared from sugarcane roots and plants infected with Herbaspirillum rubrisubalbicans and Gluconacetobacter diazotroficans. Our results indicate that we have identified a sugarcane chalcone synthase similar to the pathogen-induced PI1 protein found in the sorghum cDNA libraries, and it appears that both proteins represent new members of the chalcone and stilbene synthase super-family.

scholarly journals Identification of calreticulin isoforms in the central nervous system

1992 ◽  
Vol 287 (2) ◽  
pp. 579-581 ◽  
Author(s):  
S Treves ◽  
F Zorzato ◽  
T Pozzan
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Amino Acid ◽  
Xenopus Laevis ◽  
Consensus Sequence ◽  
Amino Acid Level ◽  
Amino Acid Sequences ◽  
Open Questions ◽  
Mammalian Liver ◽  
The Central Nervous System

In the present paper we report the cloning and sequencing of the cDNA encoding two calreticulin isoforms from Xenopus laevis central nervous system. The two isoforms display 93% identity at the amino acid level. The predicted amino acid sequences of the amphibian calreticulins are very similar (76%) to those of mammalian liver and skeletal muscle. Xenopus laevis calreticulins are characterized by a very acidic c-terminal domain endowed with the endoplasmic-reticulum retention signal KDEL. The cDNAs of both clones encode an N-glycosylation consensus sequence. A third clone of calreticulin was also identified. The restriction map of this clone was clearly distinct from that of the two sequenced clones. These results indicate the existence of multiple calreticulin isoforms in the central nervous system and open questions about their functional role in different cells and/or subcellular compartments.

scholarly journals Localization of the essential histidine and carboxylate group in d-xylose isomerases

1990 ◽  
Vol 265 (3) ◽  
pp. 699-705 ◽  
Author(s):  
W Vangrysperre ◽  
J Van Damme ◽  
J Vandekerckhove ◽  
C K De Bruyne ◽  
R Cornelis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Peptide Mapping ◽  
Ph Dependence ◽  
Consensus Sequence ◽  
Amino Acid Sequences ◽  
Specific Class ◽  
Active Site Residues ◽  
Bacterial Strains ◽  
Active Centre ◽  
Hydrogen Bond Formation

D-Xylose isomerases from different bacterial strains were chemically modified with histidine and carboxylate-specific reagents. The active-site residues were identified by amino acid sequence analysis of peptides recognized by differential peptide mapping on ligand-protected and unprotected derivatized enzyme. Both types of modified residues were found to cluster in a region with consensus sequence: Phe-His-Asp-Xaa-Asp-Xaa-Xaa-Pro-Xaa-Gly, conserved in all D-xylose isomerases studied so far. These results are consistent with the recently published X-ray data of the enzyme active centre from Streptomyces rubiginosus showing hydrogen bond formation between Asp-57 and His-54 which locks the latter in one tautomeric form. A study of the pH-dependence of the kinetic parameters suggests the participation of a histidine group in the substrate-binding but not in the isomerization process. Comparison of the N-terminal amino acid sequences of several D-xylose isomerases further revealed a striking homology among the Actinomycetaceae enzymes and identifies them as a specific class of D-xylose isomerases.

Sign in / Sign up

Export Citation Format

Share Document