scholarly journals The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

2020 ◽  
Vol 19 (2) ◽  
pp. 13-30
Author(s):  
E. Р. Kharchenko
Keyword(s):  
Amino Acid ◽  
Close Contact ◽  
Amino Acid Content ◽  
Infection Process ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Structural Proteins ◽  
Subunit Structure ◽  
S Protein ◽  
Immune Epitope

Relevance. Coronavirus SARS-Cov-2 is a novel virus demonstrating the ability to be trans¬mitted from human-to-human, via respiratory droplets or close contact, and cause the severe acute respiratory syndrome (SARS). The role of its structural proteins in the SARS pathogenesis is unknown.Aim is to characterize the features of the SARS-Cov-2 structural proteins and their changes associated with acquiring other way of transmission and analyze the possibility of heterologous immunity emergence in its infection. Materials and method. For the computer analysis and alignment, the gene sequences of SARS-Cov-2 , SARS-CoV , MERS-CoV и bat CoV HKU3 reference strains were used from the Internet. From the primary structure of their genes it were translated their structural proteins: spike (S), envelope (E),membrane (M), and nucleocapsid (N). The genetic code of structural proteins was also defined. The search of homologous sequences in the SARS-Cov-2 S-protein, surface proteins of other viruses, and human proteins was made to find immune epitope continuum of protein relationships.Results. In the SARS-Cov-2 structural proteins amino acid sequences of M, E, and N-proteins are conservative. The S1 subunit of the S-protein contains some large insertions, significant changes of the amino acid content with the predominance of arginine and lysine which is typical for the surface glycoproteins in the viruses possessing high contagiousness. The S2 subunit is rather conservative and retain negative polarity. The S-protein exhibits the immune epitope relationships with many proteins of viruses and human which may be associated with immune collisions.Conclusion: The SARSCov-2 features are determined by marked changes of the S1 subunit structure in the S-protein which may be responsible for its contagiousness and many immune collisions aggravating infection process.

scholarly journals The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

2020 ◽  
Vol 19 (2) ◽  
pp. 13-30
Author(s):  
E. Р. Kharchenko
Keyword(s):  
Amino Acid ◽  
Close Contact ◽  
Amino Acid Content ◽  
Infection Process ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Structural Proteins ◽  
Subunit Structure ◽  
S Protein ◽  
Immune Epitope

Relevance. Coronavirus SARS-Cov-2 is a novel virus demonstrating the ability to be trans¬mitted from human-to-human, via respiratory droplets or close contact, and cause the severe acute respiratory syndrome (SARS). The role of its structural proteins in the SARS pathogenesis is unknown.Aim is to characterize the features of the SARS-Cov-2 structural proteins and their changes associated with acquiring other way of transmission and analyze the possibility of heterologous immunity emergence in its infection. Materials and method. For the computer analysis and alignment, the gene sequences of SARS-Cov-2 , SARS-CoV , MERS-CoV и bat CoV HKU3 reference strains were used from the Internet. From the primary structure of their genes it were translated their structural proteins: spike (S), envelope (E),membrane (M), and nucleocapsid (N). The genetic code of structural proteins was also defined. The search of homologous sequences in the SARS-Cov-2 S-protein, surface proteins of other viruses, and human proteins was made to find immune epitope continuum of protein relationships.Results. In the SARS-Cov-2 structural proteins amino acid sequences of M, E, and N-proteins are conservative. The S1 subunit of the S-protein contains some large insertions, significant changes of the amino acid content with the predominance of arginine and lysine which is typical for the surface glycoproteins in the viruses possessing high contagiousness. The S2 subunit is rather conservative and retain negative polarity. The S-protein exhibits the immune epitope relationships with many proteins of viruses and human which may be associated with immune collisions.Conclusion: The SARSCov-2 features are determined by marked changes of the S1 subunit structure in the S-protein which may be responsible for its contagiousness and many immune collisions aggravating infection process.

scholarly journals Purification and characterization of a uterine retinol-binding protein in the bitch

1995 ◽  
Vol 311 (2) ◽  
pp. 407-415 ◽  
Author(s):  
W C Buhi ◽  
I M Alvarez ◽  
V M Shille ◽  
M J Thatcher ◽  
J P Harney ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Sequences ◽  
Binding Protein ◽  
Amino Acid Content ◽  
Amino Acid Sequences ◽  
Retinol Binding Protein ◽  
Total Amino Acid ◽  
Major Protein ◽  
Serum Retinol ◽  
Two Dimensional Gel Electrophoresis

A major canine endometrial secreted protein (cP6, 23,000-M(r)) was purified by ion-exchange and gel-filtration chromatography and characterized by two-dimensional gel electrophoresis. Anti-[human retinol-binding protein (hRBP)] serum identified cP6 on immunoblot analysis and immunoprecipitated cP6 from culture medium. This major protein was also shown to bind [3H]retinol. N-terminal and internal amino acid sequences were determined and compared with previously identified protein, RNA, or DNA sequences. N-terminal analysis revealed that cP6 had high identity and similarity to serum retinol-binding proteins (RBPs), while internal sequence analysis showed a strong similarity to rat androgen-dependent epididymal protein and beta-lactoglobulins. Amino acid analysis, however, showed significant differences between these proteins and cP6 in both total amino acid content and certain selected amino acids. Immunohistochemical analysis showed staining for RBP only in the uterine luminal epithelium. These studies suggest that bitch endometrium secretes a family of proteins (cP6), some of which bind [3H]retinol, are immunologically related to the RBP family, and have N-terminal and internal sequences with a high similarity to RBP, beta-lactoglobulins and other members of the lipocalin family. This family of proteins may be important in early development for supplying retinol or derivatives to the developing embryo.

The complexity of coagulopathy pathogenesis in COVID-19.

2020 ◽  
Author(s):  
Е.П. Харченко
Keyword(s):  
Antiviral Effect ◽  
Surface Proteins ◽  
Structural Proteins ◽  
Atypical Pneumonia ◽  
Positive Polarity ◽  
S Protein ◽  
Immune Systems ◽  
Hemostasis System ◽  
Relationship Of

Введение. Коронавирус SARS-CoV-2 является новым вирусом, обладающим способностью осуществлять трансмиссию воздушно-капельным путем, вызывая тяжелое течение атипичной пневмонии, нередко сочетающейся с коагулопатиями. Роль структурных белков коронавируса в их патогенезе неизвестна. Цель исследования: с помощью биоинформационного анализа выявить в структурных белках коронавируса SARS-CoV-2 последовательности, гомологичные белкам системы гемостаза, и рассмотреть возможные сценарии их участия в патогенезе коагулопатий при COVID-19, а также объяснить существование вирусостатического эффекта гепарина. Материалы и методы. Для компьютерного анализа были использованы доступные в Интернете базы данных первичных структур белков коронавирусов и их рецепторов, а также поверхностных белков других вирусов, белков системы гемостаза и иммунной системы. Сравнивали аминокислотный состав белков и распределение оснόвных аминокислот (аргинина и лизина) в их первичных последовательностях. С целью выявления пептидного (иммуноэпитопного) родства структурных белков коронавирусов с белками системы гемостаза человека был выполнен поиск гомологичных последовательностей в их белках. Результаты. В структурных белках коронавируса SARS-CoV-2 выявлено множество последовательностей, гомологичных белкам системы гемостаза и иммунной системы. В отличие от коронавирусов SARS-CoV и MERS-CoV, S1-субъединица S-белка коронавируса SARS-CoV-2 имеет положительную полярность. Заключение. Множество последовательностей в структурных белках коронавируса SARS-CoV-2, гомологичных белкам системы гемостаза, потенциально способны вы- зывать различные сценарии патогенеза коагулопатий. Положительная полярность S1-субъединицы S-белка коронавируса SARS-CoV-2 позволяет объяснить неспецифическое взаимодействие ее с гепарином и его вирусостатический (неантикоагулянтный) эффект. Background. The coronavirus SARS-CoV-2 is a new virus capable of human-human transmission and inducing a severe atypical pneumonia often associated with coagulopathy. A role of SARS-CoV-2 structural proteins in coagulopathy pathogenesis is unknown. Objectives: to use a bioinformation analysis to identify SARS-CoV-2 sequences in the structural proteins that are homologous to hemostasis system proteins, regard their possible participation in coagulopathy pathogenesis and explain the antiviral effect of heparin. Materials / Methods. For computer analysis, Internet databases were used of the primary structures of coronavirus proteins and their receptors, as well as surface proteins of other viruses, proteins of hemostasis and immune systems. The amino acid composition of proteins and the distribution of basic amino acids (arginine and lysine) in their primary sequences were compared. For detection of peptide (immunoepitopic) relationship of coronaviruses structural proteins with human hemostasis proteins, a search for homologous sequences in their proteins was performed. Results. Many sequences have been identified in structural proteins of SARS-CoV-2 coronavirus that are homologous to the proteins of hemostasis and immune systems. In contrast with SARS-CoV and MERS-CoV coronaviruses, the S1-subunit of SARS-CoV-2 coronavirus S-protein has a positive polarity. Conclusions. Many sequences in SARS-CoV-2 structural proteins that homologous to hemostasis system proteins are potentially responsible for coagulopathy pathogenesis. The positive polarity of the S1-subunit of SARS-CoV-2 S-protein explains its nonspecific interaction with heparin and its virostatic (non-anticoagulant) effect.

scholarly journals Sequence Conservation and Antigenic Variation of the Structural Proteins of Equine Rhinitis A Virus

2001 ◽  
Vol 75 (21) ◽  
pp. 10550-10556 ◽  
Author(s):  
Annalisa Varrasso ◽  
Heidi E. Drummer ◽  
Jin-an Huang ◽  
Rachel A. Stevenson ◽  
Nino Ficorilli ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Antigenic Variation ◽  
Amino Acid Sequences ◽  
Sequence Conservation ◽  
Structural Proteins ◽  
Serum Neutralization ◽  
Prototype Virus

ABSTRACT The nucleotide and deduced amino acid sequences of the P1 region of the genomes of 10 independent equine rhinitis A virus (ERAV) isolates were determined and found to be very closely related. A panel of seven monoclonal antibodies to the prototype virus ERAV.393/76 that bound to nonneutralization epitopes conserved among all 10 isolates was raised. In serum neutralization assays, rabbit polyclonal sera and sera from naturally and experimentally infected horses reacted in a consistent and discriminating manner with the 10 isolates, which indicated the existence of variation in the neutralization epitopes of these viruses.

scholarly journals Identification and Characterization of Novel Surface Proteins in Lactobacillus johnsonii and Lactobacillus gasseri

2002 ◽  
Vol 68 (12) ◽  
pp. 6172-6181 ◽  
Author(s):  
Marco Ventura ◽  
Ivana Jankovic ◽  
D. Carey Walker ◽  
R. David Pridmore ◽  
Ralf Zink
Keyword(s):  
Amino Acid ◽  
Blot Analysis ◽  
Surface Protein ◽  
Promoter Sequence ◽  
Amino Acid Sequences ◽  
Surface Proteins ◽  
Lactobacillus Johnsonii ◽  
Intact Cells ◽  
Lactobacillus Gasseri ◽  
Cell Extracts

ABSTRACT We have identified and sequenced the genes encoding the aggregation-promoting factor (APF) protein from six different strains of Lactobacillus johnsonii and Lactobacillus gasseri. Both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. Multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. Northern blot analysis showed that both genes are transcribed, reaching their maximum expression during the exponential phase. Primer extension analysis revealed that apf1 and apf2 harbor a putative promoter sequence that is conserved in all of the genes. Western blot analysis of the LiCl cell extracts showed that APF proteins are located on the cell surface. Intact cells of L. johnsonii revealed the typical cell wall architecture of S-layer-carrying gram-positive eubacteria, which could be selectively removed with LiCl treatment. In addition, the amino acid composition, physical properties, and genetic organization were found to be quite similar to those of S-layer proteins. These results suggest that APF is a novel surface protein of the Lactobacillus acidophilus B-homology group which might belong to an S-layer-like family.

scholarly journals The α- and β-subunits of the Human UDP-N-acetylglucosamine:Lysosomal Enzyme Phosphotransferase Are Encoded by a Single cDNA

2005 ◽  
Vol 280 (43) ◽  
pp. 36141-36149 ◽  
Author(s):  
Mariko Kudo ◽  
Ming Bao ◽  
Anil D'Souza ◽  
Fu Ying ◽  
Huaqin Pan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Domain ◽  
Amino Acid Sequences ◽  
Subunit Structure ◽  
Bac Clone ◽  
Significant Similarity ◽  
Α Subunit ◽  
Γ Subunit ◽  
Mannose 6 Phosphate ◽  
Α And Β Subunits

Lysosomal enzymes are targeted to the lysosome through binding to mannose 6-phosphate receptors because their glycans are modified with mannose 6-phosphate. This modification is catalyzed by UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase). Bovine GlcNAc-phosphotransferase was isolated using monoclonal antibody affinity chromatography, and an α2β2γ2-subunit structure was proposed. Although cDNA encoding the γ-subunit has been described, cDNAs for the α- and β-subunits have not. Using partial amino acid sequences from the bovine α- and β-subunits, we have isolated a human cDNA that encodes both the α- and β-subunits. Both subunits contain a single predicted membrane-spanning domain. The α- and β-subunits appear to be generated by a proteolytic cleavage at the Lys928-Asp929 bond. Transfection of 293T cells with the α/β-subunits-precursor cDNA with or without the γ-subunit cDNA results in a 3.6- or 17-fold increase in GlcNAc-phosphotransferase activity in cell lysates, suggesting that the precursor cDNA contains the catalytic domain. The sequence lacks significant similarity with any described vertebrate enzyme except for two Notch-like repeats in the α-subunit. However, a 112-amino acid sequence is highly similar to a group of bacterial capsular polymerases (46% identity). A BAC clone containing the gene that spanned 85.3 kb and was composed of 21 exons was sequenced and localized to chromosome 12q23. We now report the cloning of both the cDNA and genomic DNA of the precursor of Glc-NAc-phosphotransferase. The completion of cloning all three subunits of GlcNAc-phosphotransferase allows expression of recombinant enzyme and dissection of lysosomal targeting disorders.

scholarly journals Expression and characterisation of the ryegrass mottle virus non-structural proteins

2010 ◽  
Vol 64 (5-6) ◽  
pp. 215-222
Author(s):  
Ina Baļķe ◽  
Gunta Resēviča ◽  
Dace Skrastiņa ◽  
Andris Zeltiņš
Keyword(s):  
Amino Acid ◽  
Expression System ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Mottle Virus ◽  
Expression Vectors ◽  
Structural Protein ◽  
E Coli

Expression and characterisation of the ryegrass mottle virus non-structural proteins The Ryegrass mottle virus (RGMoV) single-stranded RNA genome is organised into four open reading frames (ORF) which encode several proteins: ORF1 encodes protein P1, ORF2a contains the membrane-associated 3C-like serine protease, genome-linked protein VPg and a P16 protein gene. ORF2b encodes replicase RdRP and the only structural protein, coat protein, is synthesised from ORF3. To obtain the non-structural proteins in preparative quantities and to characterise them, the corresponding RGMoV gene cDNAs were cloned in pET- and pColdI-derived expression vectors and overexpressed in several E. coli host cells. For protease and RdRP, the best expression system containing pColdI vector and E. coli WK6 strain was determined. VPg and P16 proteins were obtained from the pET- or pACYC- vectors and E. coli BL21 (DE3) host cells and purified using Ni-Sepharose affinity chromatography. Attempts to crystallize VPg and P16 were unsuccessful, possibly due to non-structured amino acid sequences in both protein structures. Methods based on bioinformatic analysis indicated that the entire VPg domain and the C-terminal part of the P16 contain unstructured amino acid stretches, which possibly prevented the formation of crystals.

scholarly journals Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site

2002 ◽  
Vol 83 (12) ◽  
pp. 3075-3084 ◽  
Author(s):  
Afjal Hossain Khan ◽  
Kouichi Morita ◽  
Maria del Carmen Parquet ◽  
Futoshi Hasebe ◽  
Edward G. M. Mathenge ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chikungunya Virus ◽  
Genomic Sequence ◽  
Adenine Nucleotides ◽  
Repeated Sequence ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Sequence Elements

In this study, the complete genomic sequence of chikungunya virus (CHIK; S27 African prototype) was determined and the presence of an internal polyadenylation [I-poly(A)] site was confirmed within the 3′ non-translated region (NTR) of this strain. The complete genome was 11805 nucleotides in length, excluding the 5′ cap nucleotide, an I-poly(A) tract and the 3′ poly(A) tail. It comprised two long open reading frames that encoded the non-structural (2474 amino acids) and structural polyproteins (1244 amino acids). The genetic location of the non-structural and structural proteins was predicted by comparing the deduced amino acid sequences with the known cleavage sites of other alphaviruses, located at the C-terminal region of their virus-encoded proteins. In addition, predicted secondary structures were identified within the 5′ NTR and repeated sequence elements (RSEs) within the 3′ NTR. Amino acid sequence homologies, phylogenetic analysis of non-structural and structural proteins and characteristic RSEs revealed that although CHIK is closely related to o’nyong-nyong virus, it is in fact a distinct virus. The existence of I-poly(A) fragments with different lengths (e.g. 19, 36, 43, 91, 94 and 106 adenine nucleotides) at identical initiation positions for each clone strongly suggests that the polymerase of the alphaviruses has a capacity to create poly(A) by a template-dependant mechanism such as ‘polymerase slippage’, as has been reported for vesicular stomatitis virus.

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