Journal articles: 'Proteine s1'

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Thuong, Ho Thi, Le Thu Ngoc, Nguyen Thu Giang, Trinh Thai Vy, Phan Trong Hoang, Pham Bich Ngoc, Vu Huyen Trang, and Chu Hoang Ha. "Transient expression of recombinant S1 protein of Porcine Epidemic Diarrhea Virus in Nicotiana benthamiana." Vietnam Journal of Biotechnology 19, no. 1 (July 18, 2021): 95–105. http://dx.doi.org/10.15625/1811-4989/14614.

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Porcine Epidemic Diarrhea (PED) is an infectious disease with high mortality especially in suckling piglets. Among the structural proteins of Porcine Epidemic Diarrhea Virus (PEDV), the S protein (including sub-domain S1 and S2), is a homotrimer protein that plays an important role in attaching the viruses to the cell receptors. In particular, the S1 protein is considered as an important sub-component in the development of effective vaccines against PEDV. In this study, for the purpose of expressing S1 in the original form of trimmer and oligomer of trimer based on S-tag and S-protein interactions, the DNA encoding for S1 protein was fused with GCN4pII or GCN4pII-Stag, was then inserted to the pRTRA cloning vector under the control of the 35S CaMV promoter. After that, the whole cassete was inserted into the pCB301 vector and transformed into Agrobacterium tumefaciens for transient expression on Nicotiana benthamiana. The expression of recombinant S1 proteins in tobacco was determined by Western blot. The results showed that the expression levels of S1 trimer and S1 trimer S-tag proteins were equal in plants, which also indicated that S-tag fusion did not affect the expression level of the S1 protein. However, the expression level of S1 proteins was relatively low, reaching 0.005% of total soluble protein. In addition, the expression of S1 trimer S-tag protein and Sprotein-tp protein by co-transformation of two A. tumefaciens strains containing corresponding vectors in plants were also determined by Western blot. This is a premise study for the development of subunit vaccines in plants that prevent the spread of PEDV.

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Gürtler, Lutz. "Überlegungen zur Schutzdauer." Trillium Diagnostik 19, no. 1 (March 18, 2021): 71–72. http://dx.doi.org/10.47184/td.2021.01.07.

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Als Reaktion auf eine SARS-CoV-2-Infektion werden vorwiegend Antikörper gegen die Rezeptor-bindende Domäne des S1-Teils des Spike-Proteins, das Nukleokapsid und die Chymotrypsin-ähnliche Protease gebildet. Die T-Zell-Reaktion richtet sich neben der S1-Domäne und M-, N- und ORF-Protein-Epitope in stärkerem Ausmaß auch gegen die S2-Domäne, was eine Erklärung für den milderen Verlauf bei Kindern sein könnte.

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Hügle, B., R. Hazan, U. Scheer, and W. W. Franke. "Localization of ribosomal protein S1 in the granular component of the interphase nucleolus and its distribution during mitosis." Journal of Cell Biology 100, no. 3 (March 1, 1985): 873–86. http://dx.doi.org/10.1083/jcb.100.3.873.

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Using antibodies to various nucleolar and ribosomal proteins, we define, by immunolocalization in situ, the distribution of nucleolar proteins in the different morphological nucleolar subcompartments. In the present study we describe the nucleolar localization of a specific ribosomal protein (S1) by immunofluorescence and immunoelectron microscopy using a monoclonal antibody (RS1-105). In immunoblotting experiments, this antibody reacts specifically with the largest and most acidic protein of the small ribosomal subunit (S1) and shows wide interspecies cross-reactivity from amphibia to man. Beside its localization in cytoplasmic ribosomes, this protein is found to be specifically localized in the granular component of the nucleolus and in distinct granular aggregates scattered over the nucleoplasm. This indicates that ribosomal protein S1, in contrast to reports on other ribosomal proteins, is not bound to nascent pre-rRNA transcripts but attaches to preribosomes at later stages of rRNA processing and maturation. This protein is not detected in the residual nucleolar structures of cells inactive in rRNA synthesis such as amphibian and avian erythrocytes. During mitosis, the nucleolar material containing ribosomal protein S1 undergoes a remarkable transition and shows a distribution distinct from that of several other nucleolar proteins. In prophase, the nucleolus disintegrates and protein S1 appears in numerous small granules scattered throughout the prophase nucleus. During metaphase and anaphase, a considerable amount of this protein is found in association with the surfaces of all chromosomes and finely dispersed in the cell plasm. In telophase, protein S1-containing material reaccumulates in granular particles in the nucleoplasm of the newly formed nuclei and, finally, in the re-forming nucleoli. These observations indicate that the nucleolus-derived particles containing ribosomal protein S1 are different from cytoplasmic ribosomes and, in the living cell, are selectively recollected after mitosis into the newly formed nuclei and translocated into a specific nucleolar subcompartment, i.e., the granular component. The nucleolar location of ribosomal protein S1 and its rearrangement during mitosis is discussed in relation to the distribution of other nucleolar proteins.

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Deryusheva, Evgenia I., Andrey V. Machulin, Maxim A. Matyunin, and Oxana V. Galzitskaya. "Investigation of the Relationship between the S1 Domain and Its Molecular Functions Derived from Studies of the Tertiary Structure." Molecules 24, no. 20 (October 13, 2019): 3681. http://dx.doi.org/10.3390/molecules24203681.

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S1 domain, a structural variant of one of the “oldest” OB-folds (oligonucleotide/oligosaccharide-binding fold), is widespread in various proteins in three domains of life: Bacteria, Eukaryotes, and Archaea. In this study, it was shown that S1 domains of bacterial, eukaryotic, and archaeal proteins have a low percentage of identity, which indicates the uniqueness of the scaffold and is associated with protein functions. Assessment of the predisposition of tertiary flexibility of S1 domains using computational and statistical tools showed similar structural features and revealed functional flexible regions that are potentially involved in the interaction of natural binding partners. In addition, we analyzed the relative number and distribution of S1 domains in all domains of life and established specific features based on sequences and structures associated with molecular functions. The results correlate with the presence of repeats of the S1 domain in proteins containing the S1 domain in the range from one (bacterial and archaeal) to 15 (eukaryotic) and, apparently, are associated with the need for individual proteins to increase the affinity and specificity of protein binding to ligands.

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Hui-Jun, Lu, He Wen-Qi, Song De-Guang, Liu Li-Guo, Chang Ling-Zhu, Li Zhi-Ping, Chen Ke-Yan, and Gao Feng. "Identification of Porcine haemagglutinating encephalomyelitis virus receptor in PK cell membranes." Chinese Journal of Agricultural Biotechnology 5, no. 1 (April 2008): 87–92. http://dx.doi.org/10.1017/s1479236208002209.

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AbstractTo identify Porcine haemagglutinating encephalomyelitis virus (HEV) 67N receptor in porcine kidney (PK) cell membranes, the S1 protein of HEV was expressed in Pichia pastoris and purified by Ni2+ affinity chromatograph. Polyclonal antibodies to HEV were prepared by immunizing rabbits by injecting the purified S1 protein four times. After SDS–polyacrylamide gel electrophoresis (SDS–PAGE), the PK cell membrane proteins were transferred on to nitrocellulose membrane. A virus overlay protein binding assay (VOPBA) was performed using the recombinant S1 protein to identify the protein binding receptor, HEV-S1. The result showed that HEV-S1 protein bound to one band (about 90 kDa) in PK cell membranes. This result is very important for the study of the pathogenic mechanism of HEV.

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Machulin, Andrey, Evgenia Deryusheva, Mikhail Lobanov, and Oxana Galzitskaya. "Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder." International Journal of Molecular Sciences 20, no. 10 (May 14, 2019): 2377. http://dx.doi.org/10.3390/ijms20102377.

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An important feature of ribosomal S1 proteins is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. For S1 proteins, little is known about the contribution of flexible regions to protein domain function. We exhaustively studied a tendency for intrinsic disorder and flexibility within and between structural domains for all available UniProt S1 sequences. Using charge–hydrophobicity plot cumulative distribution function (CH-CDF) analysis we classified 53% of S1 proteins as ordered proteins; the remaining proteins were related to molten globule state. S1 proteins are characterized by an equal ratio of regions connecting the secondary structure within and between structural domains, which indicates a similar organization of separate S1 domains and multi-domain S1 proteins. According to the FoldUnfold and IsUnstruct programs, in the multi-domain proteins, relatively short flexible or disordered regions are predominant. The lowest percentage of flexibility is in the central parts of multi-domain proteins. Our results suggest that the ratio of flexibility in the separate domains is related to their roles in the activity and functionality of S1: a more stable and compact central part in the multi-domain proteins is vital for RNA interaction, terminals domains are important for other functions.

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Fox, Ted, Patrizia Mason, Andrew C. Storer, and John S. Mort. "Modification of S1 subsite specificity in the cysteine protease cathepsin B." "Protein Engineering, Design and Selection" 8, no. 1 (1995): 53–57. http://dx.doi.org/10.1093/protein/8.1.53.

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Jana, Sirsendu, Michael R. Heaven, and Abdu I. Alayash. "Cell-Free Hemoglobin Does Not Attenuate the Effects of SARS-CoV-2 Spike Protein S1 Subunit in Pulmonary Endothelial Cells." International Journal of Molecular Sciences 22, no. 16 (August 22, 2021): 9041. http://dx.doi.org/10.3390/ijms22169041.

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SARS-CoV-2 primarily infects epithelial airway cells that express the host entry receptor angiotensin-converting enzyme 2 (ACE2), which binds to the S1 spike protein on the surface of the virus. To delineate the impact of S1 spike protein interaction with the ACE2 receptor, we incubated the S1 spike protein with human pulmonary arterial endothelial cells (HPAEC). HPAEC treatment with the S1 spike protein caused disruption of endothelial barrier function, increased levels of numerous inflammatory molecules (VCAM-1, ICAM-1, IL-1β, CCL5, CXCL10), elevated mitochondrial reactive oxygen species (ROS), and a mild rise in glycolytic reserve capacity. Because low oxygen tension (hypoxia) is associated with severe cases of COVID-19, we also evaluated treatment with hemoglobin (HbA) as a potential countermeasure in hypoxic and normal oxygen environments in analyses with the S1 spike protein. We found hypoxia downregulated the expression of the ACE2 receptor and increased the critical oxygen homeostatic signaling protein, hypoxia-inducible factor (HIF-1α); however, treatment of the cells with HbA yielded no apparent change in the levels of ACE2 or HIF-1α. Use of quantitative proteomics revealed that S1 spike protein-treated cells have few differentially regulated proteins in hypoxic conditions, consistent with the finding that ACE2 serves as the host viral receptor and is reduced in hypoxia. However, in normoxic conditions, we found perturbed abundance of proteins in signaling pathways related to lysosomes, extracellular matrix receptor interaction, focal adhesion, and pyrimidine metabolism. We conclude that the spike protein alone without the rest of the viral components is sufficient to elicit cell signaling in HPAEC, and that treatment with HbA failed to reverse the vast majority of these spike protein-induced changes.

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Davis, Elisabeth, Dustin Kennedy, Scott A. Halperin, and Song F. Lee. "Role of the Cell Wall Microenvironment in Expression of a Heterologous SpaP-S1 Fusion Protein byStreptococcus gordonii." Applied and Environmental Microbiology 77, no. 5 (December 30, 2010): 1660–66. http://dx.doi.org/10.1128/aem.02178-10.

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ABSTRACTThe charge density in the cell wall microenvironment of Gram-positive bacteria is believed to influence the expression of heterologous proteins. To test this, the expression of a SpaP-S1 fusion protein, consisting of the surface protein SpaP ofStreptococcus mutansand a pertussis toxin S1 fragment, was studied in the live vaccine candidate bacteriumStreptococcus gordonii. Results showed that the parent strain PM14 expressed very low levels of SpaP-S1. By comparison, thedltmutant strain, which has a mutation in thedltoperon preventingd-alanylation of the cell wall lipoteichoic acids, and another mutant strain, OB219(pPM14), which lacks the LPXTG major surface proteins SspA and SspB, expressed more SpaP-S1 than the parent. Both thedltmutant and the OB219(pPM14) strain had a more negatively charged cell surface than PM14, suggesting that the negative charged cell wall played a role in the increase in SpaP-S1 production. Accordingly, the addition of Ca2+, Mg2+, and K+, presumably increasing the positive charge of the cell wall, led to a reduction in SpaP-S1 production, while the addition of bicarbonate resulted in an increase in SpaP-S1 production. The level of SpaP-S1 production could be correlated with the level of PrsA, a peptidyl-prolylcis/transisomerase, in the cells. PrsA expression appears to be regulated by the cell envelope stress two-component regulatory system LiaSR. The results collectively indicate that the charge density of the cell wall microenvironment can modulate heterologous SpaP-S1 protein expression inS. gordoniiand that this modulation is mediated by the level of PrsA, whose expression is regulated by the LiaSR two-component regulatory system.

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INOUE, Akira, Yukitomo ARAO, Akira OMORI, Sachiyo ICHINOSE, Koji NISHIO, Naoki YAMAMOTO, Yosihiro KINOSHITA, and Shiro MITA. "Identification of S1 proteins B2, C1 and D1 as AUF1 isoforms and their major role as heterogeneous nuclear ribonucleoprotein proteins." Biochemical Journal 372, no. 3 (June 15, 2003): 775–85. http://dx.doi.org/10.1042/bj20021719.

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AUF1 (A+U-rich RNA binding factor) participates in the rapid decay of mRNAs in the cytoplasm. It is sometimes called heterogeneous nuclear ribonucleoprotein (hnRNP) D0; however, evidence for its characterization as an hnRNP protein has been scarce. S1 proteins A–D are those selectively extracted at pH 4.9 from isolated nuclei pretreated with either RNase A or DNase I. In the present study we identified S1 (‘first supernatant’) proteins B2, C1 and D1 with p45, p40 and p37 AUF1s respectively, by microsequencing and product analysis of transfected cDNAs. We found, further, that more than 96% of the S1 proteins occurred in the nucleus, and localized largely in RNase-sensitive structures. B2 was confined in the nucleus and C1 directly bound to heterogeneous nuclear RNAs (hnRNAs). These B2 and C1 proteins formed hnRNP structures responsible for the 33 S, and, to lesser extent, the 40 S particles, which were liberated upon mild nucleolytic cleavage. On the other hand, D1 and the remainder of C1 were associated with nuclease-hypersensitive sites of hnRNAs, and comprised the major cytoplasmic AUF1s that may be involved in mRNA decay. Two-dimensional immunoblotting resolved each S1 isoform into up to six spots or more, and suggested that the previous uncertain relationship of hnRNP D0 and hnRNP D is resolved in terms of charge differences and differential splicing arising from one gene. The present results thus indicate that S1 proteins B2, C1 and D1 are identical with AUF1 proteins, but largely occur as hnRNP proteins in the nucleus. That hnRNP D0 is indeed an hnRNP protein was verified.

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Lee, Song F., Yi-Jing Li, and Scott A. Halperin. "Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii." Microbiology 155, no. 11 (November 1, 2009): 3581–88. http://dx.doi.org/10.1099/mic.0.030064-0.

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One of the limitations facing the development of Streptococcus gordonii into a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons in S. gordonii and seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains of S. gordonii expressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or the Toxoplasma gondii cyclophilin C18 protein. These three heterologous proteins contained high percentages of amino acids encoded by rare codons. The results showed that the production of SpaP/S1, anti-CR1 scFv and C18 increased by 2.7-, 120- and 10-fold, respectively, over the control strains. In contrast, the production of the streptococcal SpaP protein without the pertussis toxin S1 fragment was not affected by tRNA gene supplementation, indicating that the increased production of SpaP/S1 protein was due to the ability to overcome the limitation caused by rare codons required for the S1 fragment. The increase in anti-CR1 scFv production was also observed in Streptococcus mutans following tRNA gene supplementation. Collectively, the findings in the present study demonstrate for the first time, to the best of our knowledge, that codon-usage bias exists in Streptococcus spp. and the limitation of heterologous protein expression caused by codon-usage bias can be overcome by tRNA supplementation.

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Fujii, Taiki, Kazuhiro Fukano, Keita Hirano, Akinori Mimura, Miyu Terauchi, Shin-ichi Etoh, and Akihiro Iida. "A new serine protease family with elastase activity is produced by Streptomyces bacteria." Microbiology 166, no. 3 (March 1, 2020): 253–61. http://dx.doi.org/10.1099/mic.0.000880.

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We found an elastolytic activity in the culture supernatant of Streptomyces sp. P-3, and the corresponding enzyme (streptomycetes elastase, SEL) was purified to apparent homogeneity from the culture supernatant. The molecular mass of purified SEL was approximately 18 kDa as judged by SDS-PAGE analysis and gel-filtration chromatography. Utilizing information from N-terminal amino acid sequencing of SEL and mass spectrometry of SEL tryptic fragments, we succeeded in cloning the gene-encoding SEL. The cloned SEL gene contains a 726 bp ORF, which encodes a 241 amino acid polypeptide containing a putative signal peptide for secretion (28 amino acid) and pro-sequence (14 amino acid). Although the deduced primary structure of SEL has sequence similarity to proteins in the S1 protease family, the amino acid sequence shares low identity (< 31.5 %) with any known elastase. SEL efficiently hydrolyses synthetic peptides having Ala or Val in the P1 position such as N-succinyl-Ala-Ala-(Pro or Val)-Ala-p-nitroanilide (pNA), whereas reported proteases by streptomycetes having elastolytic activity prefer large residues, such as Phe and Leu. Compared of kcat/Km ratios for Suc-Ala-Ala-Val-Ala-pNA and Suc-Ala-Ala-Pro-Ala-pNA with subtilisin YaB, which has high elastolytic activity, Streptomyces sp. P-3 SEL exhibits 12- and 121-fold higher, respectively. Phylogenetic analyses indicate that the predicted SEL protein, together with predicted proteins in streptomycetes, constitutes a novel group within the S1 serine protease family. These characteristics suggest that SEL-like proteins are new members of the S1 serine protease family, which display elastolytic activity.

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Dong, Bo, Wei Gao, Huijun Lu, Kui Zhao, Ning Ding, Wenfeng Liu, Jiakuan Zhao, et al. "A Small Region of Porcine Hemagglutinating Encephalomyelitis Virus Spike Protein Interacts with the Neural Cell Adhesion Molecule." Intervirology 58, no. 2 (2015): 130–37. http://dx.doi.org/10.1159/000381060.

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Objective: The spike (S) protein of porcine hemagglutinating encephalomyelitis virus (PHEV) may mediate infection by binding to a cellular neural cell adhesion molecule (NCAM). This study aimed to identify the crucial domain of the S1 subunit of the S protein that interacts with NCAM. Methods: Three truncated segments (S1-291, S277-794 and S548-868) of the S gene of PHEV and the NCAM gene were cloned individually into the Escherichia coli expression vectors and yeast two-hybrid expression vectors. The interaction between S1-291, S277-794, S548-868 and NCAM were detected by a GST pull-down experiment and yeast two-hybrid assay. Results: Three fusion proteins (S1-291, S277-794 and S548-868) were screened for their interactions with NCAM by protein-protein interaction assays. The results of these assays clarified that S277-794 interacted with NCAM, while S1-291 and S548-868 did not. Conclusions: A small fragment (258-amino-acid fragment, residues 291-548) on the PHEV S protein was posited to be the minimum number of amino acids necessary to interact with NCAM. This fragment may be the receptor-binding domain that mediates PHEV binding to NCAM.

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Shinzawa-Itoh, Kyoko, Shinya Yoshikawa, and Tomitake Tsukihara. "S1f1-2 Crystallization of membrane protein complexes(S1-f1: "Structural chemical studies on physiological functions of proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S109. http://dx.doi.org/10.2142/biophys.46.s109_4.

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Shiraishi, Kenji, Katsumasa Kamiya, Shuji Yamamoto, Mauro Boero, Masaru Tateno, and Atsushi Oshiyama. "S1f1-7 Theoretical approaches for protein function(S1-f1: "Structural chemical studies on physiological functions of proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S111. http://dx.doi.org/10.2142/biophys.46.s111_1.

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Johnson, M. D., G. M. Housey, P. T. Kirschmeier, and I. B. Weinstein. "Molecular cloning of gene sequences regulated by tumor promoters and mitogens through protein kinase C." Molecular and Cellular Biology 7, no. 8 (August 1987): 2821–29. http://dx.doi.org/10.1128/mcb.7.8.2821.

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cDNA clones representing genes whose expression is modulated by treatment with mitogens and tumor promoters were isolated and characterized. TPA-S1 corresponds to an mRNA species whose abundance was increased markedly within 1 h of exposure to the tumor promoter 12-O-tetradecanoyl phorbol-13-acetate (TPA), and TPA-R1 represents an mRNA that was decreased in TPA-treated cells. The induction of TPA-S1 was blocked by actinomycin D but was not affected by cycloheximide, and it was specific for phorbol esters with tumor-promoting activity. The role of protein kinase C in the induction of TPA-S1 is supported by the following lines of evidence. (i) Agents that activated protein kinase C (TPA, platelet-derived growth factor, and diacylglycerol) also increased TPA-S1 mRNA levels. (ii) A potent PKC inhibitor blocked the induction of TPA-S1. (iii) Down-regulation of PKC activity, by treatment of cells with TPA for 24 h, resulted in a loss of responsiveness to TPA-S1 induction by subsequent TPA treatment. DNA sequence analysis of TPA-S1 predicts a cysteine-rich, secreted protein with a molecular weight of 22.6 X 10(3) that exhibits homology with sequences representing a protein with human erythroid-potentiating activity and protease inhibitory activity.

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Johnson, M. D., G. M. Housey, P. T. Kirschmeier, and I. B. Weinstein. "Molecular cloning of gene sequences regulated by tumor promoters and mitogens through protein kinase C." Molecular and Cellular Biology 7, no. 8 (August 1987): 2821–29. http://dx.doi.org/10.1128/mcb.7.8.2821-2829.1987.

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cDNA clones representing genes whose expression is modulated by treatment with mitogens and tumor promoters were isolated and characterized. TPA-S1 corresponds to an mRNA species whose abundance was increased markedly within 1 h of exposure to the tumor promoter 12-O-tetradecanoyl phorbol-13-acetate (TPA), and TPA-R1 represents an mRNA that was decreased in TPA-treated cells. The induction of TPA-S1 was blocked by actinomycin D but was not affected by cycloheximide, and it was specific for phorbol esters with tumor-promoting activity. The role of protein kinase C in the induction of TPA-S1 is supported by the following lines of evidence. (i) Agents that activated protein kinase C (TPA, platelet-derived growth factor, and diacylglycerol) also increased TPA-S1 mRNA levels. (ii) A potent PKC inhibitor blocked the induction of TPA-S1. (iii) Down-regulation of PKC activity, by treatment of cells with TPA for 24 h, resulted in a loss of responsiveness to TPA-S1 induction by subsequent TPA treatment. DNA sequence analysis of TPA-S1 predicts a cysteine-rich, secreted protein with a molecular weight of 22.6 X 10(3) that exhibits homology with sequences representing a protein with human erythroid-potentiating activity and protease inhibitory activity.

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Le Seyec, J., P. Chouteau, I. Cannie, C. Guguen-Guillouzo, and P. Gripon. "Infection Process of the Hepatitis B Virus Depends on the Presence of a Defined Sequence in the Pre-S1 Domain." Journal of Virology 73, no. 3 (March 1, 1999): 2052–57. http://dx.doi.org/10.1128/jvi.73.3.2052-2057.1999.

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ABSTRACT During the life cycle of hepatitis B virus (HBV), the large envelope protein (L) plays a pivotal role. Indeed, this polypeptide is essential for viral assembly and probably for the infection process. By performing mutagenesis experiments, we have previously excluded a putative involvement of the pre-S2 domain of the L protein in viral infectivity. In the present study, we have evaluated the role of the pre-S1 region in HBV infection. For this purpose, 21 mutants of the L protein were created. The entire pre-S1 domain was covered by contiguous deletions of 5 amino acids. First, after transfection into HepG2 cells, the efficient expression of both glycosylated and unglycosylated L mutant proteins was verified. The secretion rate of envelope proteins was modified positively or negatively by deletions, indicating that the pre-S1 domain contains several regulating sequences able to influence the surface protein secretion. The ability of mutant proteins to support the production of virions was then studied. Only the four C-terminal deletions, covering the 17 amino acids suspected to interact with the cytoplasmic nucleocapsids, inhibited virion release. Finally, the presence of the modified pre-S1 domain at the external side of all secreted virions was confirmed, and their infectivity was assayed on normal human hepatocytes in primary culture. Only a short sequence including amino acids 78 to 87 tolerates internal deletions without affecting viral infectivity. These results confirm the involvement of the L protein in the infection step and demonstrate that the sequence between amino acids 3 and 77 is involved in this process.

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Zyrianova, Irina. "Phylogenetic analysis of the betacoronavirus S1 subunit." F1000Research 9 (December 3, 2020): 1389. http://dx.doi.org/10.12688/f1000research.27681.1.

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The ongoing pandemic outbreak of coronavirus disease 2019 (COVID-19) has been caused by the new betacoronavirus (BetaCoV) severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Together with other epidemic outbreaks of BetaCoV infectious diseases (Severe Acute Respiratory Syndrome (SARS) in 2002-2003 in China and Middle East Respiratory Syndrome (MERS) in 2012 in the Middle East, which have been caused by SARS-CoV and MERS-CoV, respectively), these events have generated interest in the coronaviruses (CoVs). Although many phylogenetic analyzes have been reported at a gene or protein level, there is no study as yet encompassing the many sequences publicly available for BetaCoVs, including those that have been manipulated in the lab. In this study, the phylogenetic analysis of 679 different S1 protein sequences of BetaCoVs from a total of 1595, which are publicly available in GenBank from the beginning of the pandemic event to April 2020, has been carried out. The S1 subunit is one part of the S (spike) protein, one of three CoV envelope proteins. The S1 subunit contains a host cell receptor binding domain. This domain is essential in the initiation of the infectious process. Therefore, its phylogenetic analysis is very important for studying CoV evolution. The phylogenetic analysis of BetaCoV S1 protein presented herein shows the evolutionary history of BetaCoVs from bovine CoV to SARS-CoV-2.

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McClain, Mark S., Ping Cao, Hideki Iwamoto, Arlene D. Vinion-Dubiel, Gabor Szabo, Zhifeng Shao, and Timothy L. Cover. "A 12-Amino-Acid Segment, Present in Type s2 but Not Type s1 Helicobacter pylori VacA Proteins, Abolishes Cytotoxin Activity and Alters Membrane Channel Formation." Journal of Bacteriology 183, no. 22 (November 15, 2001): 6499–508. http://dx.doi.org/10.1128/jb.183.22.6499-6508.2001.

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ABSTRACT Helicobacter pylori, a gram-negative bacterium associated with gastritis, peptic ulceration, and gastric adenocarcinoma in humans, secretes a protein toxin, VacA, that causes vacuolar degeneration of epithelial cells. Several different families of H. pylori vacA alleles can be distinguished based on sequence diversity in the “middle” region (i.e., m1 and m2) and in the 5′ end of the gene (i.e., s1 and s2). Type s2 VacA toxins contain a 12-amino-acid amino-terminal hydrophilic segment, which is absent from type s1 toxins. To examine the functional properties of VacA toxins containing this 12-amino-acid segment, we analyzed a wild-type s1/m1 VacA and a chimeric s2/m1 VacA protein. Purified s1/m1 VacA from H. pylori strain 60190 induced vacuolation in HeLa and Vero cells, whereas the chimeric s2/m1 toxin (in which the s1 sequence of VacA from strain 60190 was replaced with the s2 sequence from strain Tx30a) lacked detectable cytotoxic activity. Type s1/m1 VacA from strain 60190 formed membrane channels in a planar lipid bilayer assay at a significantly higher rate than did s2/m1 VacA. However, membrane channels formed by type s1 VacA and type s2 VacA proteins exhibited similar anion selectivities (permeability ratio, PCl/PNa = 5). When an equimolar mixture of the chimeric s2/m1 toxin and the wild-type s1/m1 toxin was added to HeLa cells, the chimeric toxin completely inhibited the activity of the s1/m1 toxin. Thus, the s2/m1 toxin exhibited a dominant-negative phenotype similar to that of a previously described mutant toxin, VacA-(Δ6–27). Immunoprecipitation experiments indicated that both s2/m1 VacA and VacA-(Δ6–27) could physically interact with a c-myc epitope-tagged s1/m1 VacA, which suggests that the dominant-negative phenotype results from the formation of heterooligomeric VacA complexes with defective functional activity. Despite detectable differences in the channel-forming activities and cytotoxic properties of type s1 and type s2 VacA proteins, the conservation of type s2 sequences in many H. pyloriisolates suggests that type s2 VacA proteins retain an important biological activity.

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Yamayoshi, Seiya, Mariko Watanabe, Hideo Goto, and Yoshihiro Kawaoka. "Identification of a Novel Viral Protein Expressed from the PB2 Segment of Influenza A Virus." Journal of Virology 90, no. 1 (October 21, 2015): 444–56. http://dx.doi.org/10.1128/jvi.02175-15.

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ABSTRACTOver the past 2 decades, several novel influenza virus proteins have been identified that modulate viral infectionsin vitroand/orin vivo. The PB2 segment, which is one of the longest influenza A virus segments, is known to encode only one viral protein, PB2. In the present study, we used reverse transcription-PCR (RT-PCR) targeting viral mRNAs transcribed from the PB2 segment to look for novel viral proteins encoded by spliced mRNAs. We identified a new viral protein, PB2-S1, encoded by a novel spliced mRNA in which the region corresponding to nucleotides 1513 to 1894 of the PB2 mRNA is deleted. PB2-S1 was detected in virus-infected cells and in cells transfected with a protein expression plasmid encoding PB2. PB2-S1 localized to mitochondria, inhibited the RIG-I-dependent interferon signaling pathway, and interfered with viral polymerase activity (dependent on its PB1-binding capability). The nucleotide sequences around the splicing donor and acceptor sites for PB2-S1 were highly conserved among pre-2009 human H1N1 viruses but not among human H1N1pdm and H3N2 viruses. PB2-S1-deficient viruses, however, showed growth kinetics in MDCK cells and virulence in mice similar to those of wild-type virus. The biological significance of PB2-S1 to the replication and pathogenicity of seasonal H1N1 influenza A viruses warrants further investigation.IMPORTANCETranscriptome analysis of cells infected with influenza A virus has improved our understanding of the host response to viral infection, because such analysis yields considerable information about bothin vitroandin vivoviral infections. However, little attention has been paid to transcriptomes derived from the viral genome. Here we focused on the splicing of mRNA expressed from the PB2 segment and identified a spliced viral mRNA encoding a novel viral protein. This result suggests that other, as yet unidentified viral proteins encoded by spliced mRNAs could be expressed in virus-infected cells. A viral transcriptome including the viral spliceosome should be evaluated to gain new insights into influenza virus infection.

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Ryu, Chun Jeih, Dae-Yeon Cho, Philippe Gripon, Hee Sun Kim, Christiane Guguen-Guillouzo, and Hyo Jeong Hong. "An 80-Kilodalton Protein That Binds to the Pre-S1 Domain of Hepatitis B Virus." Journal of Virology 74, no. 1 (January 1, 2000): 110–16. http://dx.doi.org/10.1128/jvi.74.1.110-116.2000.

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ABSTRACT It has been suggested that hepatitis B virus (HBV) binds to a receptor on the plasma membrane of human hepatocytes via the pre-S1 domain of the large envelope protein as an initial step in HBV infection. However, the nature of the receptor remains controversial. In an attempt to identify a cell surface receptor for HBV, purified recombinant fusion protein of the pre-S1 domain of HBV with glutathioneS-transferase (GST), expressed in Escherichia coli, was used as a ligand. The surface of human hepatocytes or HepG2 cells was biotinylated, and the cell lysate (precleared lysate) which did not bind to GST and glutathione-Sepharose beads was used as a source of receptor molecules. The precleared lysate of the biotinylated cells was incubated with the GST–pre-S1 fusion protein, and the bound proteins were visualized by Western blotting and enhanced chemiluminescence. An approximately 80-kDa protein (p80) was shown to bind specifically to the pre-S1 domain of the fusion protein. The receptor binding assay using serially or internally deleted segments of pre-S1 showed that amino acid residues 12 to 20 and 82 to 90 are essential for the binding of pre-S1 to p80. p80 also bound specifically to the pre-S1 of native HBV particles. Analysis of the tissue and species specificity of p80 expression in several available human primary cultures and cell lines of different tissue origin showed that p80 expression is not restricted to human hepatocytes. Taken together the results suggest that p80 may be a component of the viral entry machinery.

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Li, Fang. "Receptor Recognition Mechanisms of Coronaviruses: a Decade of Structural Studies." Journal of Virology 89, no. 4 (November 26, 2014): 1954–64. http://dx.doi.org/10.1128/jvi.02615-14.

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Receptor recognition by viruses is the first and essential step of viral infections of host cells. It is an important determinant of viral host range and cross-species infection and a primary target for antiviral intervention. Coronaviruses recognize a variety of host receptors, infect many hosts, and are health threats to humans and animals. The receptor-binding S1 subunit of coronavirus spike proteins contains two distinctive domains, the N-terminal domain (S1-NTD) and the C-terminal domain (S1-CTD), both of which can function as receptor-binding domains (RBDs). S1-NTDs and S1-CTDs from three major coronavirus genera recognize at least four protein receptors and three sugar receptors and demonstrate a complex receptor recognition pattern. For example, highly similar coronavirus S1-CTDs within the same genus can recognize different receptors, whereas very different coronavirus S1-CTDs from different genera can recognize the same receptor. Moreover, coronavirus S1-NTDs can recognize either protein or sugar receptors. Structural studies in the past decade have elucidated many of the puzzles associated with coronavirus-receptor interactions. This article reviews the latest knowledge on the receptor recognition mechanisms of coronaviruses and discusses how coronaviruses have evolved their complex receptor recognition pattern. It also summarizes important principles that govern receptor recognition by viruses in general.

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Grishin, Sergei Y., Evgeniya I. Deryusheva, Andrey V. Machulin, Olga M. Selivanova, Anna V. Glyakina, Elena Y. Gorbunova, Leila G. Mustaeva, et al. "Amyloidogenic Propensities of Ribosomal S1 Proteins: Bioinformatics Screening and Experimental Checking." International Journal of Molecular Sciences 21, no. 15 (July 22, 2020): 5199. http://dx.doi.org/10.3390/ijms21155199.

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Structural S1 domains belong to the superfamily of oligosaccharide/oligonucleotide-binding fold domains, which are highly conserved from prokaryotes to higher eukaryotes and able to function in RNA binding. An important feature of this family is the presence of several copies of the structural domain, the number of which is determined in a strictly limited range from one to six. Despite the strong tendency for the aggregation of several amyloidogenic regions in the family of the ribosomal S1 proteins, their fibril formation process is still poorly understood. Here, we combined computational and experimental approaches for studying some features of the amyloidogenic regions in this protein family. The FoldAmyloid, Waltz, PASTA 2.0 and Aggrescan programs were used to assess the amyloidogenic propensities in the ribosomal S1 proteins and to identify such regions in various structural domains. The thioflavin T fluorescence assay and electron microscopy were used to check the chosen amyloidogenic peptides’ ability to form fibrils. The bioinformatics tools were used to study the amyloidogenic propensities in 1331 ribosomal S1 proteins. We found that amyloidogenicity decreases with increasing sizes of proteins. Inside one domain, the amyloidogenicity is higher in the terminal parts. We selected and synthesized 11 amyloidogenic peptides from the Escherichia coli and Thermus thermophilus ribosomal S1 proteins and checked their ability to form amyloids using the thioflavin T fluorescence assay and electron microscopy. All 11 amyloidogenic peptides form amyloid-like fibrils. The described specific amyloidogenic regions are actually responsible for the fibrillogenesis process and may be potential targets for modulating the amyloid properties of bacterial ribosomal S1 proteins.

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Kurpe, Stanislav, Sergei Grishin, Alexey Surin, Olga Selivanova, Roman Fadeev, Ulyana Dzhus, Elena Gorbunova, Leila Mustaeva, Vyacheslav Azev, and Oxana Galzitskaya. "Antimicrobial and Amyloidogenic Activity of Peptides Synthesized on the Basis of the Ribosomal S1 Protein from Thermus Thermophilus." International Journal of Molecular Sciences 21, no. 17 (September 2, 2020): 6382. http://dx.doi.org/10.3390/ijms21176382.

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Controlling the aggregation of vital bacterial proteins could be one of the new research directions and form the basis for the search and development of antibacterial drugs with targeted action. Such approach may be considered as an alternative one to antibiotics. Amyloidogenic regions can, like antibacterial peptides, interact with the “parent” protein, for example, ribosomal S1 protein (specific only for bacteria), and interfere with its functioning. The aim of the work was to search for peptides based on the ribosomal S1 protein from T. thermophilus, exhibiting both aggregation and antibacterial properties. The biological system of the response of Gram-negative bacteria T. thermophilus to the action of peptides was characterized. Among the seven studied peptides, designed based on the S1 protein sequence, the R23I (modified by the addition of HIV transcription factor fragment for bacterial cell penetration), R23T (modified), and V10I (unmodified) peptides have biological activity that inhibits the growth of T. thermophilus cells, that is, they have antimicrobial activity. But, only the R23I peptide had the most pronounced activity comparable with the commercial antibiotics. We have compared the proteome of peptide-treated and intact T. thermophilus cells. These important data indicate a decrease in the level of energy metabolism and anabolic processes, including the processes of biosynthesis of proteins and nucleic acids. Under the action of 20 and 50 μg/mL R23I, a decrease in the number of proteins in T. thermophilus cells was observed and S1 ribosomal protein was absent. The obtained results are important for understanding the mechanism of amyloidogenic peptides with antimicrobial activity and can be used to develop new and improved analogues.

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Gudima, Severin, Yiping He, Ning Chai, Volker Bruss, Stephan Urban, William Mason, and John Taylor. "Primary Human Hepatocytes Are Susceptible to Infection by Hepatitis Delta Virus Assembled with Envelope Proteins of Woodchuck Hepatitis Virus." Journal of Virology 82, no. 15 (May 21, 2008): 7276–83. http://dx.doi.org/10.1128/jvi.00576-08.

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ABSTRACT Hepatitis B virus (HBV) and hepatitis delta virus (HDV) share the HBV envelope proteins. When woodchucks chronically infected with woodchuck hepatitis virus (WHV) are superinfected with HDV, they produce HDV with a WHV envelope, wHDV. Several lines of evidence are provided that wHDV infects not only cultured primary woodchuck hepatocytes (PWH) but also primary human hepatocytes (PHH). Surprisingly, HBV-enveloped HDV (hHDV) and wHDV infected PHH with comparable efficiencies; however, hHDV did not infect PWH. The basis for these host range specificities was investigated using as inhibitors peptides bearing species-specific pre-S (where S is the small envelope protein) sequences. It was found that pre-S1 contributed to the ability of wHDV to infect both PHH and PWH. In addition, the inability of hHDV to infect PWH was not overcome using a chimeric form of hHDV containing WHV S protein, again supporting the essential role of pre-S1 in infection of target cells. One interpretation of these data is that host range specificity of HDV is determined entirely by pre-S1 and that the WHV and HBV pre-S1 proteins recognize different receptors on PHH.

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Xu, N., K. M. Coulter, J. E. Krochko, and J. D. Bewley. "Morphological stages and storage protein accumulation in developing alfalfa (Medicago sativa L.) seeds." Seed Science Research 1, no. 2 (June 1991): 119–25. http://dx.doi.org/10.1017/s0960258500000751.

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AbstractIdentification of discrete stages during embryogenesis is important for the consistent and repeatable selection of seeds having similar developmental characteristics. A timetable for staging developing seeds of alfalfa (Medicago sativa L.) has been developed. Morphological characteristics, fresh and dry weights, SDSpolyacrylamide gel electrophoretic protein patterns and total protein content were recorded at various times between fertilization and 36 d after pollination (maturity), stages I–IX. A full complement of storage proteins (2S, 7S, 11S) is synthesized in both developing cotyledons and radicles. Low-salt soluble (S1) and high-salt soluble (S2) storage proteins first appear during embryo elongation. The proportional amounts of some S1 storage proteins change during alfalfa seed development. Markers are thus provided as uniform reference points for staging from the time of anthesis to seed shedding.

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Schuh, Claus D., Marcello Polesel, Evgenia Platonova, Dominik Haenni, Alkaly Gassama, Natsuko Tokonami, Susan Ghazi, et al. "Combined Structural and Functional Imaging of the Kidney Reveals Major Axial Differences in Proximal Tubule Endocytosis." Journal of the American Society of Nephrology 29, no. 11 (October 9, 2018): 2696–712. http://dx.doi.org/10.1681/asn.2018050522.

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BackgroundThe kidney proximal convoluted tubule (PCT) reabsorbs filtered macromolecules via receptor-mediated endocytosis (RME) or nonspecific fluid phase endocytosis (FPE); endocytosis is also an entry route for disease-causing toxins. PCT cells express the protein ligand receptor megalin and have a highly developed endolysosomal system (ELS). Two PCT segments (S1 and S2) display subtle differences in cellular ultrastructure; whether these translate into differences in endocytotic function has been unknown.MethodsTo investigate potential differences in endocytic function in S1 and S2, we quantified ELS protein expression in mouse kidney PCTs using real-time quantitative polymerase chain reaction and immunostaining. We also used multiphoton microscopy to visualize uptake of fluorescently labeled ligands in both living animals and tissue cleared using a modified CLARITY approach.ResultsUptake of proteins by RME occurs almost exclusively in S1. In contrast, dextran uptake by FPE takes place in both S1 and S2, suggesting that RME and FPE are discrete processes. Expression of key ELS proteins, but not megalin, showed a bimodal distribution; levels were far higher in S1, where intracellular distribution was also more polarized. Tissue clearing permitted imaging of ligand uptake at single-organelle resolution in large sections of kidney cortex. Analysis of segmented tubules confirmed that, compared with protein uptake, dextran uptake occurred over a much greater length of the PCT, although individual PCTs show marked heterogeneity in solute uptake length and three-dimensional morphology.ConclusionsStriking axial differences in ligand uptake and ELS function exist along the PCT, independent of megalin expression. These differences have important implications for understanding topographic patterns of kidney diseases and the origins of proteinuria.

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Ito, Yutaka, Kaori Kurashima-Ito, Kayano Moromisato, Takao Inoue, Kaoru Nishimura, Jonathan Heddle, Jeremy Tame, and Masaki Mishima. "S1f2-1 NMR studies of periplasmic binding proteins(S1-f2: "Functions and dynamics of protein systems in various aspect",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S119. http://dx.doi.org/10.2142/biophys.46.s119_1.

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Le Duff, Yann, Matthieu Blanchet, and Camille Sureau. "The Pre-S1 and Antigenic Loop Infectivity Determinants of the Hepatitis B Virus Envelope Proteins Are Functionally Independent." Journal of Virology 83, no. 23 (September 16, 2009): 12443–51. http://dx.doi.org/10.1128/jvi.01594-09.

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ABSTRACT The hepatitis B virus (HBV) envelope proteins bear two determinants of viral entry: a receptor-binding site (RBS) in the pre-S1 domain of the large envelope protein and a conformation-dependent determinant, of unknown function, in the antigenic loop (AGL) of the small, middle, and large envelope proteins. Using an in vitro infection assay consisting of susceptible HepaRG cells and the hepatitis delta virus (HDV) as a surrogate of HBV, we first investigated whether subelements of the pre-S1 determinant (amino acids 2 to 75), i.e., the N-terminal myristoyl anchor, subdomain 2-48 (RBS), and subdomain 49-75, were functionally separable. In transcomplementation experiments, coexpression of two distinct infectivity-deficient pre-S1 mutants at the surface of HDV virions failed to restore infectivity, indicating that the myristoyl anchor, the 2-48 RBS, and the 49-75 sequence, likely cooperate in cis at viral entry. Furthermore, we showed that as much as 52% of total pre-S1 in the HDV envelope could bear infectivity-deficient lesions without affecting entry, indicating that a small number of pre-S1 polypeptides—estimated at three to four per virion—is sufficient for infectivity. We next investigated the AGL activity in the small or large envelope protein background (S- and L-AGL, respectively) and found that lesions in S-AGL were more deleterious to infectivity than in L-AGL, a difference that reflects the relative stoichiometry of the small and large envelope proteins in the viral envelope. Finally, we showed that C147S, an AGL infectivity-deficient substitution, exerted a dominant-negative effect on infectivity, likely reflecting an involvement of C147 in intermolecular disulfide bonds.

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Dale, Glenn E., Clemens Broger, Hanno Langen, Allan D' Arcy, and Dietrich Stüber. "Improving protein solubility through rationally designed amino acid replacements: solubilization of the trimethoprim-resistant type S1 dihydrofolate reductase." "Protein Engineering, Design and Selection" 7, no. 7 (1994): 933–39. http://dx.doi.org/10.1093/protein/7.7.933.

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Sukhodolets, M. V. "Ribosomal protein S1 promotes transcriptional cycling." RNA 12, no. 8 (June 29, 2006): 1505–13. http://dx.doi.org/10.1261/rna.2321606.

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van den Brink, Edward N., Jan ter Meulen, Freek Cox, Mandy A. C. Jongeneelen, Alexandra Thijsse, Mark Throsby, Wilfred E. Marissen, et al. "Molecular and Biological Characterization of Human Monoclonal Antibodies Binding to the Spike and Nucleocapsid Proteins of Severe Acute Respiratory Syndrome Coronavirus." Journal of Virology 79, no. 3 (February 1, 2005): 1635–44. http://dx.doi.org/10.1128/jvi.79.3.1635-1644.2005.

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ABSTRACT Human monoclonal antibodies (MAbs) were selected from semisynthetic antibody phage display libraries by using whole irradiated severe acute respiratory syndrome (SARS) coronavirus (CoV) virions as target. We identified eight human MAbs binding to virus and infected cells, six of which could be mapped to two SARS-CoV structural proteins: the nucleocapsid (N) and spike (S) proteins. Two MAbs reacted with N protein. One of the N protein MAbs recognized a linear epitope conserved between all published human and animal SARS-CoV isolates, and the other bound to a nonlinear N epitope. These two N MAbs did not compete for binding to SARS-CoV. Four MAbs reacted with the S glycoprotein, and three of these MAbs neutralized SARS-CoV in vitro. All three neutralizing anti-S MAbs bound a recombinant S1 fragment comprising residues 318 to 510, a region previously identified as the SARS-CoV S receptor binding domain; the nonneutralizing MAb did not. Two strongly neutralizing anti-S1 MAbs blocked the binding of a recombinant S fragment (residues 1 to 565) to SARS-CoV-susceptible Vero cells completely, whereas a poorly neutralizing S1 MAb blocked binding only partially. The MAb ability to block S1-receptor binding and the level of neutralization of the two strongly neutralizing S1 MAbs correlated with the binding affinity to the S1 domain. Finally, epitope mapping, using recombinant S fragments (residues 318 to 510) containing naturally occurring mutations, revealed the importance of residue N479 for the binding of the most potent neutralizing MAb, CR3014. The complete set of SARS-CoV MAbs described here may be useful for diagnosis, chemoprophylaxis, and therapy of SARS-CoV infection and disease.

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Reguera, Juan, Desiderio Ordoño, César Santiago, Luis Enjuanes, and José M. Casasnovas. "Antigenic modules in the N-terminal S1 region of the transmissible gastroenteritis virus spike protein." Journal of General Virology 92, no. 5 (May 1, 2011): 1117–26. http://dx.doi.org/10.1099/vir.0.027607-0.

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The N-terminal S1 region of the transmissible gastroenteritis virus (TGEV) spike (S) glycoprotein contains four antigenic sites (C, B, D and A, from the N- to the C-terminal end) and is engaged in host-cell receptor recognition. The most N-terminal portion of the S1 region, which comprises antigenic sites C and B, is needed for the enteric tropism of TGEV, whereas the major antigenic site A at the C-terminal moiety is required for both respiratory and enteric cell tropism, and is engaged in recognition of the aminopeptidase N (APN) receptor. This study determined the kinetics for binding of a soluble S1 protein to the APN protein. Moreover, the S1 region of the TGEV S protein was dissected, with the aim of identifying discrete modules displaying unique antigenic sites and receptor-binding functions. Following protease treatments and mammalian cell expression methods, four modules or domains (D1–D4) were defined at the S1 region. Papain treatment identified an N-terminal domain (D1) resistant to proteolysis, whereas receptor binding defined a soluble and functional APN receptor-binding domain (D3). This domain was recognized by neutralizing antibodies belonging to the antigenic site A and therefore could be used as an immunogen for the prevention of viral infection. The organization of the four modules in the S1 region of the TGEV S glycoprotein is discussed.

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Chai, Ning, Severin Gudima, Jinhong Chang, and John Taylor. "Immunoadhesins Containing Pre-S Domains of Hepatitis B Virus Large Envelope Protein Are Secreted and Inhibit Virus Infection." Journal of Virology 81, no. 10 (February 28, 2007): 4912–18. http://dx.doi.org/10.1128/jvi.02865-06.

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ABSTRACT Hepatitis B virus (HBV) replication produces three envelope proteins (L, M, and S) that have a common C terminus. L, the largest, contains a domain, pre-S1, not present on M. Similarly M contains a domain, pre-S2, not present on S. The pre-S1 region has important functions in the HBV life cycle. Thus, as an approach to studying these roles, the pre-S1 and/or pre-S2 sequences of HBV (serotype adw2, genotype A) were expressed as N-terminal fusions to the Fc domain of a rabbit immunoglobulin G chain. Such proteins, known as immunoadhesins (IA), were highly expressed following transfection of cultured cells and, when the pre-S1 region was present, >80% were secreted. The IA were myristoylated at a glycine penultimate to the N terminus, although mutation studies showed that this modification was not needed for secretion. As few as 30 amino acids from the N terminus of pre-S1 were both necessary and sufficient to drive secretion of IA. Even expression of pre-S1 plus pre-S2, in the absence of an immunoglobulin chain, led to efficient secretion. Overall, these studies demonstrate an unexpected ability of the N terminus of pre-S1 to promote protein secretion. In addition, some of these secreted IA, at nanomolar concentrations, inhibited infection of primary human hepatocytes either by hepatitis delta virus (HDV), a subviral agent that uses HBV envelope proteins, or HBV. These IA have potential to be part of antiviral therapies against chronic HDV and HBV, and may help understand the attachment and entry mechanisms used by these important human pathogens.

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Nara, Masayuki. "S1f1-5 Infrared Spectroscopic Analyses of calcium-binding protein structure(S1-f1: "Structural chemical studies on physiological functions of proteins",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S110. http://dx.doi.org/10.2142/biophys.46.s110_3.

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Ambepitiya Wickramasinghe, I. N., R. P. de Vries, E. A. W. S. Weerts, S. J. van Beurden, W. Peng, R. McBride, M. Ducatez, et al. "Novel Receptor Specificity of Avian Gammacoronaviruses That Cause Enteritis." Journal of Virology 89, no. 17 (June 10, 2015): 8783–92. http://dx.doi.org/10.1128/jvi.00745-15.

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ABSTRACTViruses exploit molecules on the target membrane as receptors for attachment and entry into host cells. Thus, receptor expression patterns can define viral tissue tropism and might to some extent predict the susceptibility of a host to a particular virus. Previously, others and we have shown that respiratory pathogens of the genusGammacoronavirus, including chicken infectious bronchitis virus (IBV), require specific α2,3-linked sialylated glycans for attachment and entry. Here, we studied determinants of binding of enterotropic avian gammacoronaviruses, including turkey coronavirus (TCoV), guineafowl coronavirus (GfCoV), and quail coronavirus (QCoV), which are evolutionarily distant from respiratory avian coronaviruses based on the viral attachment protein spike (S1). We profiled the binding of recombinantly expressed S1 proteins of TCoV, GfCoV, and QCoV to tissues of their respective hosts. Protein histochemistry showed that the tissue binding specificity of S1 proteins of turkey, quail, and guineafowl CoVs was limited to intestinal tissues of each particular host, in accordance with the reported pathogenicity of these virusesin vivo. Glycan array analyses revealed that, in contrast to the S1 protein of IBV, S1 proteins of enteric gammacoronaviruses recognize a unique set of nonsialylated type 2 poly-N-acetyl-lactosamines. Lectin histochemistry as well as tissue binding patterns of TCoV S1 further indicated that these complex N-glycans are prominently expressed on the intestinal tract of various avian species. In conclusion, our data demonstrate not only that enteric gammacoronaviruses recognize a novel glycan receptor but also that enterotropism may be correlated with the high specificity of spike proteins for such glycans expressed in the intestines of the avian host.IMPORTANCEAvian coronaviruses are economically important viruses for the poultry industry. While infectious bronchitis virus (IBV), a respiratory pathogen of chickens, is rather well known, other viruses of the genusGammacoronavirus, including those causing enteric disease, are hardly studied. In turkey, guineafowl, and quail, coronaviruses have been reported to be the major causative agent of enteric diseases. Specifically, turkey coronavirus outbreaks have been reported in North America, Europe, and Australia for several decades. Recently, a gammacoronavirus was isolated from guineafowl with fulminating disease. To date, it is not clear why these avian coronaviruses are enteropathogenic, whereas other closely related avian coronaviruses like IBV cause respiratory disease. A comprehensive understanding of the tropism and pathogenicity of these viruses explained by their receptor specificity and receptor expression on tissues was therefore needed. Here, we identify a novel glycan receptor for enteric avian coronaviruses, which will further support the development of vaccines.

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Hung, S. H., and L. Hedstrom. "Converting trypsin to elastase: substitution of the S1 site and adjacent loops reconstitutes esterase specificity but not amidase activity." Protein Engineering Design and Selection 11, no. 8 (August 1, 1998): 669–73. http://dx.doi.org/10.1093/protein/11.8.669.

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Ravichandran, Supriya, Elizabeth M. Coyle, Laura Klenow, Juanjie Tang, Gabrielle Grubbs, Shufeng Liu, Tony Wang, Hana Golding, and Surender Khurana. "Antibody signature induced by SARS-CoV-2 spike protein immunogens in rabbits." Science Translational Medicine 12, no. 550 (June 8, 2020): eabc3539. http://dx.doi.org/10.1126/scitranslmed.abc3539.

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Multiple vaccine candidates against SARS-CoV-2 based on viral spike protein are under development. However, there is limited information on the quality of antibody responses generated with these vaccine modalities. To better understand antibody responses induced by spike protein–based vaccines, we performed a qualitative study by immunizing rabbits with various SARS-CoV-2 spike protein antigens: S ectodomain (S1+S2; amino acids 16 to 1213), which lacks the cytoplasmic and transmembrane domains (CT-TM), the S1 domain (amino acids 16 to 685), the receptor binding domain (RBD) (amino acids 319 to 541), and the S2 domain (amino acids 686 to 1213, lacking the RBD, as control). Resulting antibody quality and function were analyzed by enzyme-linked immunosorbent assay (ELISA), RBD competition assay, surface plasmon resonance (SPR) against different spike proteins in native conformation, and neutralization assays. All three antigens (S1+S2 ectodomain, S1 domain, and RBD), but not S2, generated strong neutralizing antibodies against SARS-CoV-2. Vaccination-induced antibody repertoire was analyzed by SARS-CoV-2 spike genome fragment phage display libraries (SARS-CoV-2 GFPDL), which identified immunodominant epitopes in the S1, S1-RBD, and S2 domains. Furthermore, these analyses demonstrated that the RBD immunogen elicited a higher antibody titer with five-fold higher affinity antibodies to native spike antigens compared with other spike antigens, and antibody affinity correlated strongly with neutralization titers. These findings may help guide rational vaccine design and facilitate development and evaluation of effective therapeutics and vaccines against COVID-19 disease.

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Montalto, G., J. Bonicel, L. Multigner, M. Rovery, H. Sarles, and A. De Caro. "Partial amino acid sequence of human pancreatic stone protein, a novel pancreatic secretory protein." Biochemical Journal 238, no. 1 (August 15, 1986): 227–32. http://dx.doi.org/10.1042/bj2380227.

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Pancreatic stone protein (PSP) is the major organic component of human pancreatic stones. With the use of monoclonal antibody immunoadsorbents, five immunoreactive forms (PSP-S) with close Mr values (14,000-19,000) were isolated from normal pancreatic juice. By CM-Trisacryl M chromatography the lowest-Mr form (PSP-S1) was separated from the others and some of its molecular characteristics were investigated. The Mr of the PSP-S1 polypeptide chain calculated from the amino acid composition was about 16,100. The N-terminal sequences (40 residues) of PSP and PSP-S1 are identical, which suggests that the peptide backbone is the same for both of these polypeptides. The PSP-S1 sequence was determined up to residue 65 and was found to be different from all other known protein sequences.

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Soede, Ron D. M., Yvonne M. Wijnands, Marga Kamp, Martin A. van der Valk, and Ed Roos. "Gi and Gq/11 proteins are involved in dissemination of myeloid leukemia cells to the liver and spleen, whereas bone marrow colonization involves Gq/11 but not Gi." Blood 96, no. 2 (July 15, 2000): 691–98. http://dx.doi.org/10.1182/blood.v96.2.691.

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Abstract The migration of leukocytes into tissues is regulated by chemokines and other chemotactic factors that act on receptors that signal through Gi proteins. It seems likely that the colonization of tissues during dissemination of hematopoietic tumor cells is similarly regulated. In fact, dissemination of a T-cell hybridoma, a model for T lymphoma, was blocked when Gi proteins were inactivated by the S1 catalytic subunit of pertussis toxin that had been transfected into those cells. Pertussis toxin S1 blocked dissemination of MDAY-D2 murine myeloid leukemia cells to the liver and spleen, as in T-cell hybridoma cells, but it did not prevent bone marrow colonization. In contrast, overexpression of a function-defective mutant of the Gq/11 protein blocked dissemination to the bone marrow and also prevented Gq/11 dissemination to the liver and spleen. This indicates that the influx of these myeloid cells into all tissues requires the Gq/11 protein in addition to the Gi protein in the liver and spleen.

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Soede, Ron D. M., Yvonne M. Wijnands, Marga Kamp, Martin A. van der Valk, and Ed Roos. "Gi and Gq/11 proteins are involved in dissemination of myeloid leukemia cells to the liver and spleen, whereas bone marrow colonization involves Gq/11 but not Gi." Blood 96, no. 2 (July 15, 2000): 691–98. http://dx.doi.org/10.1182/blood.v96.2.691.014k48_691_698.

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The migration of leukocytes into tissues is regulated by chemokines and other chemotactic factors that act on receptors that signal through Gi proteins. It seems likely that the colonization of tissues during dissemination of hematopoietic tumor cells is similarly regulated. In fact, dissemination of a T-cell hybridoma, a model for T lymphoma, was blocked when Gi proteins were inactivated by the S1 catalytic subunit of pertussis toxin that had been transfected into those cells. Pertussis toxin S1 blocked dissemination of MDAY-D2 murine myeloid leukemia cells to the liver and spleen, as in T-cell hybridoma cells, but it did not prevent bone marrow colonization. In contrast, overexpression of a function-defective mutant of the Gq/11 protein blocked dissemination to the bone marrow and also prevented Gq/11 dissemination to the liver and spleen. This indicates that the influx of these myeloid cells into all tissues requires the Gq/11 protein in addition to the Gi protein in the liver and spleen.

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Barrera, Azeneth, Bernadette Guerra, Lena Notvall, and Robert E. Lanford. "Mapping of the Hepatitis B Virus Pre-S1 Domain Involved in Receptor Recognition." Journal of Virology 79, no. 15 (August 1, 2005): 9786–98. http://dx.doi.org/10.1128/jvi.79.15.9786-9798.2005.

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ABSTRACT Hepatitis B virus (HBV) and woolly monkey hepatitis B virus (WMHBV) are primate hepadnaviruses that display restricted tissue and host tropisms. Hepatitis D virus (HDV) particles pseudotyped with HBV and WMHBV envelopes (HBV-HDV and WM-HDV) preferentially infect human and spider monkey hepatocytes, respectively, thereby confirming host range bias in vitro. The analysis of chimeric HBV and WMHBV large (L) envelope proteins suggests that the pre-S1 domain may comprise two regions that affect infectivity: one within the amino-terminal 40 amino acids of pre-S1 and one downstream of this region. In the present study, we further characterized the role of the amino terminus of pre-S1 in infectivity by examining the ability of synthetic peptides to competitively block HDV infection of primary human and spider monkey hepatocytes. A synthetic peptide representing the first 45 residues of the pre-S1 domain of the HBV L protein blocked infectivity of HBV-HDV and WM-HDV, with a requirement for myristylation of the amino terminal residue. Competition studies with truncated peptides suggested that pre-S1 residues 5 to 20 represent the minimal domain for inhibition of HDV infection and, thus, presumably represent the residues involved in virus-host receptor interaction. Recombinant pre-S1 proteins expressed in insect cells blocked infection with HBV-HDV and WM-HDV at a concentration of 1 nanomolar. The ability of short pre-S1 peptides to efficiently inhibit HDV infection suggests that they represent suitable ligands for identification of the HBV receptor and that a pre-S1 mimetic may represent a rational therapy for the treatment of HBV infection.

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Shmulevitz, Maya, Zareen Yameen, Sandra Dawe, Jingyun Shou, David O’Hara, Ian Holmes, and Roy Duncan. "Sequential Partially Overlapping Gene Arrangement in the Tricistronic S1 Genome Segments of Avian Reovirus and Nelson Bay Reovirus: Implications for Translation Initiation." Journal of Virology 76, no. 2 (January 15, 2002): 609–18. http://dx.doi.org/10.1128/jvi.76.2.609-618.2002.

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ABSTRACT Previous studies of the avian reovirus strain S1133 (ARV-S1133) S1 genome segment revealed that the open reading frame (ORF) encoding the ςC viral cell attachment protein initiates over 600 nucleotides distal from the 5′ end of the S1 mRNA and is preceded by two predicted small nonoverlapping ORFs. To more clearly define the translational properties of this unusual polycistronic RNA, we pursued a comparative analysis of the S1 genome segment of the related Nelson Bay reovirus (NBV). Sequence analysis indicated that the 3′-proximal ORF present on the NBV S1 genome segment also encodes a ςC homolog, as evidenced by the presence of an extended N-terminal heptad repeat characteristic of the coiled-coil region common to the cell attachment proteins of reoviruses. Most importantly, the NBV S1 genome segment contains two conserved ORFs upstream of the ςC coding region that are extended relative to the predicted ORFs of ARV-S1133 and are arranged in a sequential, partially overlapping fashion. Sequence analysis of the S1 genome segments of two additional strains of ARV indicated a similar overlapping tricistronic gene arrangement as predicted for the NBV S1 genome segment. Expression analysis of the ARV S1 genome segment indicated that all three ORFs are functional in vitro and in virus-infected cells. In addition to the previously described p10 and ςC gene products, the S1 genome segment encodes from the central ORF a 17-kDa basic protein (p17) of no known function. Optimizing the translation start site of the ARV p10 ORF lead to an approximately 15-fold increase in p10 expression with little or no effect on translation of the downstream ςC ORF. These results suggest that translation initiation complexes can bypass over 600 nucleotides and two functional overlapping upstream ORFs in order to access the distal ςC start site.

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Norton, Raymond S., Shenggen Yao, Zhihe Kuang, Indu Chandrashekaran, Kerrie A. McNeil, Briony E. Forbes, John C. Wallace, et al. "S1f2-6 Structure, dynamics and function in proteins : flexibility matters(S1-f2: "Functions and dynamics of protein systems in various aspect",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S120. http://dx.doi.org/10.2142/biophys.46.s120_2.

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Cho, Dae-Yeon, Gi-Hyeok Yang, Chun Jeih Ryu, and Hyo Jeong Hong. "Molecular Chaperone GRP78/BiP Interacts with the Large Surface Protein of Hepatitis B Virus In Vitro and In Vivo." Journal of Virology 77, no. 4 (February 15, 2003): 2784–88. http://dx.doi.org/10.1128/jvi.77.4.2784-2788.2003.

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ABSTRACT The proper folding and assembly of viral envelope proteins are mediated by host chaperones. In this study, we demonstrated that an endoplasmic reticulum luminal chaperone GRP78/BiP bound specifically to the pre-S1 domain of the L protein in vitro and in vivo where complete viral particles were secreted, suggesting that GRP78/BiP plays an essential role in the proper folding of the L protein and/or assembly of viral envelope proteins.

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47

Li, Fang, Marcelo Berardi, Wenhui Li, Michael Farzan, Philip R. Dormitzer, and Stephen C. Harrison. "Conformational States of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Ectodomain." Journal of Virology 80, no. 14 (July 15, 2006): 6794–800. http://dx.doi.org/10.1128/jvi.02744-05.

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ABSTRACT The severe acute respiratory syndrome coronavirus enters cells through the activities of a spike protein (S) which has receptor-binding (S1) and membrane fusion (S2) regions. We have characterized four sequential states of a purified recombinant S ectodomain (S-e) comprising S1 and the ectodomain of S2. They are S-e monomers, uncleaved S-e trimers, cleaved S-e trimers, and dissociated S1 monomers and S2 trimer rosettes. Lowered pH induces an irreversible transition from flexible, L-shaped S-e monomers to clove-shaped trimers. Protease cleavage of the trimer occurs at the S1-S2 boundary; an ensuing S1 dissociation leads to a major rearrangement of the trimeric S2 and to formation of rosettes likely to represent clusters of elongated, postfusion trimers of S2 associated through their fusion peptides. The states and transitions of S suggest conformational changes that mediate viral entry into cells.

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48

Barile, Elisa, Carlo Baggio, Luca Gambini, Sergey A. Shiryaev, Alex Y. Strongin, and Maurizio Pellecchia. "Potential Therapeutic Targeting of Coronavirus Spike Glycoprotein Priming." Molecules 25, no. 10 (May 22, 2020): 2424. http://dx.doi.org/10.3390/molecules25102424.

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Processing of certain viral proteins and bacterial toxins by host serine proteases is a frequent and critical step in virulence. The coronavirus spike glycoprotein contains three (S1, S2, and S2′) cleavage sites that are processed by human host proteases. The exact nature of these cleavage sites, and their respective processing proteases, can determine whether the virus can cross species and the level of pathogenicity. Recent comparisons of the genomes of the highly pathogenic SARS-CoV2 and MERS-CoV, with less pathogenic strains (e.g., Bat-RaTG13, the bat homologue of SARS-CoV2) identified possible mutations in the receptor binding domain and in the S1 and S2′ cleavage sites of their spike glycoprotein. However, there remains some confusion on the relative roles of the possible serine proteases involved for priming. Using anthrax toxin as a model system, we show that in vivo inhibition of priming by pan-active serine protease inhibitors can be effective at suppressing toxicity. Hence, our studies should encourage further efforts in developing either pan-serine protease inhibitors or inhibitor cocktails to target SARS-CoV2 and potentially ward off future pandemics that could develop because of additional mutations in the S-protein priming sequence in coronaviruses.

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Chambers, James P., Jieh Yu, James J. Valdes, and Bernard P. Arulanandam. "SARS-CoV-2, Early Entry Events." Journal of Pathogens 2020 (November 24, 2020): 1–11. http://dx.doi.org/10.1155/2020/9238696.

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Viruses are obligate intracellular parasites, and host cell entry is the first step in the viral life cycle. The SARS-CoV-2 (COVID-19) entry process into susceptible host tissue cells is complex requiring (1) attachment of the virus via the conserved spike (S) protein receptor-binding motif (RBM) to the host cell angiotensin-converting-enzyme 2 (ACE2) receptor, (2) S protein proteolytic processing, and (3) membrane fusion. Spike protein processing occurs at two cleavage sites, i.e., S1/S2 and S 2 ′ . Cleavage at the S1/S2 and S 2 ′ sites ultimately gives rise to generation of competent fusion elements important in the merging of the host cell and viral membranes. Following cleavage, shedding of the S1 crown results in significant conformational changes and fusion peptide repositioning for target membrane insertion and fusion. Identification of specific protease involvement has been difficult due to the many cell types used and studied. However, it appears that S protein proteolytic cleavage is dependent on (1) furin and (2) serine protease transmembrane protease serine 2 proteases acting in tandem. Although at present not clear, increased SARS-CoV-2 S receptor-binding motif binding affinity and replication efficiency may in part account for observed differences in infectivity. Cleavage of the ACE2 receptor appears to be yet another layer of complexity in addition to forfeiture and/or alteration of ACE2 function which plays an important role in cardiovascular and immune function.

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Arlt, Alexander, Jörg Minkenberg, Marie-Luise Kruse, Frauke Grohmann, Ulrich R. Fölsch, and Heiner Schäfer. "Immediate early gene-X1 interferes with 26 S proteasome activity by attenuating expression of the 19 S proteasomal components S5a/Rpn10 and S1/Rpn2." Biochemical Journal 402, no. 2 (February 12, 2007): 367–75. http://dx.doi.org/10.1042/bj20061072.

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The stress response gene IEX-1 (immediate early gene-X-1) is involved in the regulation of cell growth and cellular viability. To some extent, these effects include an interference with the proteasomal turnover of certain regulatory proteins. Here, we show that IEX-1 directly attenuates the activity and formation of the 26 S proteasome in HEK-293 cells (human embryonic kidney cells). We further demonstrate that IEX-1 reduces the overall expression levels of certain protein components of the 19 S proteasomal subunit such as S5a/Rpn10 and S1/Rpn2, whereas the expression of other proteasomal proteins was less or not affected. In contrast with direct apoptotic stimuli, such as the anti-cancer drug etoposide, leading to caspase-dependent degradation of S1 and S5a, the effect of IEX-1 is independent of proteolytic cleavage of these proteins. Furthermore, the decreasing effect of IEX-1 on S5a and S1 expression is still seen in the presence of cycloheximide, but not in the presence of actinomycin D, and quantitative real-time PCR revealed lower mRNA levels of S5a and S1 in IEX-1-overexpressing cells, suggesting an interference of IEX-1 with the gene transcription of S5a and S1. Additionally, luciferase assays confirmed an interference of IEX-1 with the activity of the S5a promoter. These findings indicate a role of IEX-1 in the maintenance and assembly of the 26 S proteasome, obviously involving an altered gene expression of certain proteasomal proteins. Thereby, IEX-1 may essentially modulate signalling pathways related to 26 S proteasome activity and involved in cellular growth control and apoptosis.

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Journal articles on the topic 'Proteine s1'

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