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  1. Article ; Online: Flexible, Functional, and Familiar

    Dianita S. Saputri / Songling Li / Floris J. van Eerden / John Rozewicki / Zichang Xu / Hendra S. Ismanto / Ana Davila / Shunsuke Teraguchi / Kazutaka Katoh / Daron M. Standley

    Frontiers in Microbiology, Vol

    Characteristics of SARS-CoV-2 Spike Protein Evolution

    2020  Volume 11

    Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection ... ...

    Abstract The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These “evolutionarily important” residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
    Keywords flexibility ; host like ; molecular evolution ; phylogenetics ; SARS-CoV-2 ; spike protein ; Microbiology ; QR1-502 ; covid19
    Subject code 572
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Table_1_Flexible, Functional, and Familiar

    Dianita S. Saputri / Songling Li / Floris J. van Eerden / John Rozewicki / Zichang Xu / Hendra S. Ismanto / Ana Davila / Shunsuke Teraguchi / Kazutaka Katoh / Daron M. Standley

    Characteristics of SARS-CoV-2 Spike Protein Evolution.DOCX

    2020  

    Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection ... ...

    Abstract The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These “evolutionarily important” residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
    Keywords Microbiology ; Microbial Genetics ; Microbial Ecology ; Mycology ; flexibility ; host like ; molecular evolution ; phylogenetics ; SARS-CoV-2 ; spike protein ; structural modeling ; structure alignment ; covid19
    Subject code 572
    Publishing date 2020-09-17T04:06:55Z
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy

    Khun Zaw Latt / Kenjiro Honda / Myo Thiri / Yuki Hitomi / Yosuke Omae / Hiromi Sawai / Yosuke Kawai / Shunsuke Teraguchi / Kazuko Ueno / Masao Nagasaki / Akihiko Mabuchi / Hajime Kaga / Atsushi Komatsuda / Katsushi Tokunaga / Eisei Noiri

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Volume 9

    Abstract: Abstract The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still ... ...

    Abstract Abstract The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still need to be determined. We used Japanese-specific SNP genotyping array and imputation using 2,048 sequenced Japanese samples to fine-map PLA2R1 region in 98 patients and 413 controls. The most significant SNPs were replicated in a separate sample set of 130 patients and 288 controls. A two-SNP haplotype of intronic and missense SNPs showed the strongest association. The intronic SNP is strongly associated with PLA2R1 expression in the Genotype-Tissue Expression (GTEx) database, and the missense SNP is predicted to alter peptide binding with HLA-DRB1*15:01 by the Immune Epitope Database (IEDB). In HLA region, we performed relative predispositional effect (RPE) tests and identified additional risk alleles in both HLA-DRB1 and HLA-DQB1. We collapsed the risk alleles in each of HLA-DRB1 and HLA-DQB1 into single risk alleles. Reciprocal conditioning of these collapsed risk alleles showed more residual significance for HLA-DRB1 collapsed risk than HLA-DQB1 collapsed risk. These results indicate that changes in the expression levels of structurally different PLA2R protein confer risk for IMN in the presence of risk HLA-DRB1 alleles.
    Keywords Idiopathic Membranous Nephropathy ; Phospholipase A2 Receptor (PLA2R) ; Missense SNPs ; Single Nucleotide Polymorphisms (SNPs) ; Additional Risk Allele ; Medicine ; R ; Science ; Q
    Language English
    Publishing date 2018-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Intrinsic Disorder Mediates Cooperative Signal Transduction in STIM1

    Furukawa, Yukio / Shunsuke Teraguchi / Takahisa Ikegami / Onur Dagliyan / Lin Jin / Damien Hall / Nikolay V. Dokholyan / Keiichi Namba / Shizuo Akira / Tomohiro Kurosaki / Yoshihiro Baba / Daron M. Standley

    Journal of Molecular Biology. 2014 May 15, v. 426

    2014  

    Abstract: Intrinsically disordered domains have been reported to play important roles in signal transduction networks by introducing cooperativity into protein–protein interactions. Unlike intrinsically disordered domains that become ordered upon binding, the EF- ...

    Abstract Intrinsically disordered domains have been reported to play important roles in signal transduction networks by introducing cooperativity into protein–protein interactions. Unlike intrinsically disordered domains that become ordered upon binding, the EF-SAM domain in the stromal interaction molecule (STIM) 1 is distinct in that it is ordered in the monomeric state and partially unfolded in its oligomeric state, with the population of the two states depending on the local Ca2+ concentration. The oligomerization of STIM1, which triggers extracellular Ca2+ influx, exhibits cooperativity with respect to the local endoplasmic reticulum Ca2+ concentration. Although the physiological importance of the oligomerization reaction is well established, the mechanism of the observed cooperativity is not known. Here, we examine the response of the STIM1 EF-SAM domain to changes in Ca2+ concentration using mathematical modeling based on in vitro experiments. We find that the EF-SAM domain partially unfolds and dimerizes cooperatively with respect to Ca2+ concentration, with Hill coefficients and half-maximal activation concentrations very close to the values observed in vivo for STIM1 redistribution and extracellular Ca2+ influx. Our mathematical model of the dimerization reaction agrees quantitatively with our analytical ultracentrifugation-based measurements and previously published free energies of unfolding. A simple interpretation of these results is that Ca2+ loss effectively acts as a denaturant, enabling cooperative dimerization and robust signal transduction. We present a structural model of the Ca2+-unbound EF-SAM domain that is consistent with a wide range of evidence, including resistance to proteolytic cleavage of the putative dimerization portion.
    Keywords calcium ; dimerization ; endoplasmic reticulum ; in vitro studies ; mathematical models ; oligomerization ; protein-protein interactions ; proteolysis ; signal transduction
    Language English
    Dates of publication 2014-0515
    Size p. 2082-2097.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2014.03.006
    Database NAL-Catalogue (AGRICOLA)

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