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  1. Article ; Online: Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions.

    Barik, Sailen

    International journal of molecular sciences

    2023  Volume 24, Issue 4

    Abstract: The stringent response, originally identified ... ...

    Abstract The stringent response, originally identified in
    MeSH term(s) Animals ; Guanosine Pentaphosphate/genetics ; Guanosine Pentaphosphate/metabolism ; Guanosine Tetraphosphate/metabolism ; Ligands ; Escherichia coli/metabolism ; Guanosine ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/metabolism
    Chemical Substances Guanosine Pentaphosphate (38918-96-6) ; Guanosine Tetraphosphate (33503-72-9) ; Ligands ; Guanosine (12133JR80S) ; Bacterial Proteins
    Language English
    Publishing date 2023-02-16
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24043999
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Suppression of Innate Immunity by the Hepatitis C Virus (HCV): Revisiting the Specificity of Host-Virus Interactive Pathways.

    Barik, Sailen

    International journal of molecular sciences

    2023  Volume 24, Issue 22

    Abstract: The hepatitis C virus (HCV) is a major causative agent of hepatitis that may also lead to liver cancer and lymphomas. Chronic hepatitis C affects an estimated 2.4 million people in the USA alone. As the sole member of the ... ...

    Abstract The hepatitis C virus (HCV) is a major causative agent of hepatitis that may also lead to liver cancer and lymphomas. Chronic hepatitis C affects an estimated 2.4 million people in the USA alone. As the sole member of the genus
    MeSH term(s) Humans ; Hepacivirus/genetics ; Hepatitis C, Chronic ; Hepatitis C ; Immunity, Innate ; Host Microbial Interactions ; Virus Replication
    Language English
    Publishing date 2023-11-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242216100
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Special Issue: Structure, Function and Evolution of Protein Domains.

    Barik, Sailen

    International journal of molecular sciences

    2022  Volume 23, Issue 11

    Abstract: Essentially, all proteins perform their biological roles through the use of specific domains that number in the hundreds, if not thousands [ ... ]. ...

    Abstract Essentially, all proteins perform their biological roles through the use of specific domains that number in the hundreds, if not thousands [...].
    MeSH term(s) Evolution, Molecular ; Protein Domains ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2022-05-31
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23116201
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Special Issue

    Sailen Barik

    International Journal of Molecular Sciences, Vol 23, Iss 6201, p

    Structure, Function and Evolution of Protein Domains

    2022  Volume 6201

    Abstract: Essentially, all proteins perform their biological roles through the use of specific domains that number in the hundreds, if not thousands [.] ...

    Abstract Essentially, all proteins perform their biological roles through the use of specific domains that number in the hundreds, if not thousands [.]
    Keywords n/a ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book: RNai

    Barik, Sailen

    design and application

    (Methods in molecular biology ; 442)

    2008  

    Author's details ed. by Sailen Barik
    Series title Methods in molecular biology ; 442
    Collection
    Language English
    Size XIV, 270 S. : Ill., graph. Darst.
    Publisher Humana Press
    Publishing place Totowa, NJ
    Publishing country United States
    Document type Book
    HBZ-ID HT015446589
    ISBN 978-1-58829-874-4 ; 9781597451918 ; 1-58829-874-4 ; 1597451916
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2008 A 2903 order for loan Magazin

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  6. Article ; Online: Mechanisms of Viral Degradation of Cellular Signal Transducer and Activator of Transcription 2

    Sailen Barik

    International Journal of Molecular Sciences, Vol 23, Iss 489, p

    2022  Volume 489

    Abstract: Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and ... ...

    Abstract Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and activator of transcription 2 (STAT2) plays a key role, ultimately leading to an antiviral state of the cell. In retaliation, many viruses counteract the immune response, often by the destruction and/or inactivation of STAT2, promoted by specific viral proteins that do not possess protease activities of their own. This review offers a summary of viral mechanisms of STAT2 subversion with emphasis on degradation. Some viruses also destroy STAT1, another major member of the STAT family, but most viruses are selective in targeting either STAT2 or STAT1. Interestingly, degradation of STAT2 by a few viruses requires the presence of both STAT proteins. Available evidence suggests a mechanism in which multiple sites and domains of STAT2 are required for engagement and degradation by a multi-subunit degradative complex, comprising viral and cellular proteins, including the ubiquitin–proteasomal system. However, the exact molecular nature of this complex and the alternative degradation mechanisms remain largely unknown, as critically presented here with prospective directions of future study.
    Keywords RNA virus ; interferon ; STAT ; immunity ; proteasome ; ubiquitin ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Mechanisms of Viral Degradation of Cellular Signal Transducer and Activator of Transcription 2.

    Barik, Sailen

    International journal of molecular sciences

    2022  Volume 23, Issue 1

    Abstract: Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and ... ...

    Abstract Virus infection of eukaryotes triggers cellular innate immune response, a major arm of which is the type I interferon (IFN) family of cytokines. Binding of IFN to cell surface receptors triggers a signaling cascade in which the signal transducer and activator of transcription 2 (STAT2) plays a key role, ultimately leading to an antiviral state of the cell. In retaliation, many viruses counteract the immune response, often by the destruction and/or inactivation of STAT2, promoted by specific viral proteins that do not possess protease activities of their own. This review offers a summary of viral mechanisms of STAT2 subversion with emphasis on degradation. Some viruses also destroy STAT1, another major member of the STAT family, but most viruses are selective in targeting either STAT2 or STAT1. Interestingly, degradation of STAT2 by a few viruses requires the presence of both STAT proteins. Available evidence suggests a mechanism in which multiple sites and domains of STAT2 are required for engagement and degradation by a multi-subunit degradative complex, comprising viral and cellular proteins, including the ubiquitin-proteasomal system. However, the exact molecular nature of this complex and the alternative degradation mechanisms remain largely unknown, as critically presented here with prospective directions of future study.
    MeSH term(s) Amino Acid Sequence ; Animals ; Humans ; Models, Biological ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; STAT2 Transcription Factor/chemistry ; STAT2 Transcription Factor/metabolism ; STAT2 Transcription Factor/ultrastructure ; Ubiquitin/metabolism ; Viruses/metabolism
    Chemical Substances STAT2 Transcription Factor ; Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2022-01-01
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23010489
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms.

    Barik, Sailen

    International journal of molecular sciences

    2022  Volume 23, Issue 20

    Abstract: RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. ...

    Abstract RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
    MeSH term(s) Humans ; Animals ; RNA-Dependent RNA Polymerase ; Nucleosides/pharmacology ; SARS-CoV-2 ; Antiviral Agents/therapeutic use ; RNA ; RNA, Viral/chemistry
    Chemical Substances RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Nucleosides ; Antiviral Agents ; RNA (63231-63-0) ; RNA, Viral
    Language English
    Publishing date 2022-10-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232012649
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: An Analytical Review of the Structural Features of Pentatricopeptide Repeats

    Sailen Barik

    International Journal of Molecular Sciences, Vol 22, Iss 5407, p

    Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture

    2021  Volume 5407

    Abstract: Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel ... ...

    Abstract Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. The focus of the present work was on PPR, but TPR, its better-studied cousin, is often included for comparison. The analyses revealed that critical amino acids, namely Gly, Pro, Ala and Trp, were placed at distinct locations in the higher order structure of PPR domains. While most TPRs occur in repeats of three, the PPRs exhibited a much greater diversity in repeat numbers, from 1 to 30 or more, separated by spacers of various sequences and lengths. Studies of PPR strings in proteins showed that the majority of PPR units are single, and that the longer tandems (i.e., without space in between) occurred in decreasing order. The multi-PPR domains also formed superhelical vortices, likely governed by interhelical angles rather than the spacers. These findings should be useful in designing and understanding the PPR domains.
    Keywords protein structure ; tricopeptide repeats ; PPR ; helix ; protein-RNA interaction ; solvation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 572 ; 612
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture.

    Barik, Sailen

    International journal of molecular sciences

    2021  Volume 22, Issue 10

    Abstract: Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel ... ...

    Abstract Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. The focus of the present work was on PPR, but TPR, its better-studied cousin, is often included for comparison. The analyses revealed that critical amino acids, namely Gly, Pro, Ala and Trp, were placed at distinct locations in the higher order structure of PPR domains. While most TPRs occur in repeats of three, the PPRs exhibited a much greater diversity in repeat numbers, from 1 to 30 or more, separated by spacers of various sequences and lengths. Studies of PPR strings in proteins showed that the majority of PPR units are single, and that the longer tandems (i.e., without space in between) occurred in decreasing order. The multi-PPR domains also formed superhelical vortices, likely governed by interhelical angles rather than the spacers. These findings should be useful in designing and understanding the PPR domains.
    MeSH term(s) Amino Acid Sequence ; Amino Acids/genetics ; Animals ; Chloroplasts/genetics ; Humans ; Peptides/genetics ; Plant Proteins/genetics ; Plants/genetics ; Protein Domains/genetics ; Tetratricopeptide Repeat/genetics
    Chemical Substances Amino Acids ; Peptides ; Plant Proteins
    Language English
    Publishing date 2021-05-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22105407
    Database MEDical Literature Analysis and Retrieval System OnLINE

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