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  1. AU="Chandra, Soumyanetra"
  2. AU="Wang, Jinguang"
  3. AU="Jogai, Sanjay"
  4. AU="Singh, Kuljit"
  5. AU="Tran, Phuoc Tien"
  6. AU="Alban Jonchère"
  7. AU="Ravi Varma Aithabathula"
  8. AU="Suter, Martin"
  9. AU="Chugunov, Konstantin V"
  10. AU="Moshkdanian, Ghazale"
  11. AU="Phuangthong, Chelsea"
  12. AU="Schiro, B J"
  13. AU="Chu, Dan"
  14. AU="Muhanna, Adel"
  15. AU="Ankit Mittal"
  16. AU="Dos Santos Costa Maldonado, Izabel Regina"
  17. AU="Mohamed El-Hadidi"
  18. AU="Crespo, Raquel"
  19. AU="Cozzolino, Marica"
  20. AU="Bao, Hongwei"
  21. AU="Golling, T."
  22. AU="Young, Jonathan R"
  23. AU="Lee, Jae Young"
  24. AU="Deng, Xing-Wang"
  25. AU="Wiarda, Grant"
  26. AU="Pereira, Naveen"
  27. AU="Garriga, Anna"
  28. AU="PLK. Priyadarsini"
  29. AU="Nicole E. Edgar"
  30. AU=Fredrick Kurt
  31. AU="Rowe, Mike"
  32. AU="Imannezhad, Shima"
  33. AU="DiTullio, Giacomo R"
  34. AU="Padrick, Shae B"
  35. AU="Vachiraarunwong, Arpamas"
  36. AU="Mohammad-Najar, Narges"
  37. AU="Sarica, Kemal"
  38. AU="Lescure, Alain"
  39. AU="Darawan Rinchai"
  40. AU="Sarah K McKenzie"
  41. AU="Joseph Edgar Blais"
  42. AU="Garate, Jose Antonio"

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  1. Artikel ; Online: Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA.

    Chandra, Soumyanetra / Manjunath, Kavyashree / Asok, Aparna / Varadarajan, Raghavan

    Protein science : a publication of the Protein Society

    2023  Band 32, Heft 3, Seite(n) e4580

    Abstract: Unlike globular proteins, mutational effects on the function of Intrinsically Disordered Proteins (IDPs) are not well-studied. Deep Mutational Scanning of a yeast surface displayed mutant library yields insights into sequence-function relationships in ... ...

    Abstract Unlike globular proteins, mutational effects on the function of Intrinsically Disordered Proteins (IDPs) are not well-studied. Deep Mutational Scanning of a yeast surface displayed mutant library yields insights into sequence-function relationships in the CcdA IDP. The approach enables facile prediction of interface residues and local structural signatures of the bound conformation. In contrast to previous titration-based approaches which use a number of ligand concentrations, we show that use of a single rationally chosen ligand concentration can provide quantitative estimates of relative binding constants for large numbers of protein variants. This is because the extended interface of IDP ensures that energetic effects of point mutations are spread over a much smaller range than for globular proteins. Our data also provides insights into the much-debated role of helicity and disorder in partner binding of IDPs. Based on this exhaustive mutational sensitivity dataset, a rudimentary model was developed in an attempt to predict mutational effects on binding affinity of IDPs that form alpha-helical structures upon binding.
    Mesh-Begriff(e) Intrinsically Disordered Proteins/chemistry ; Ligands ; Mutation ; Protein Conformation, alpha-Helical ; Protein Conformation ; Protein Binding
    Chemische Substanzen Intrinsically Disordered Proteins ; Ligands
    Sprache Englisch
    Erscheinungsdatum 2023-01-10
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4580
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Rapid Identification of Secondary Structure and Binding Site Residues in an Intrinsically Disordered Protein Segment.

    Chandra, Soumyanetra / Chattopadhyay, Gopinath / Varadarajan, Raghavan

    Frontiers in genetics

    2021  Band 12, Seite(n) 755292

    Abstract: Mycobacterium ... ...

    Abstract Mycobacterium tuberculosis
    Sprache Englisch
    Erscheinungsdatum 2021-11-02
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.755292
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality.

    Chandra, Soumyanetra / Gupta, Kritika / Khare, Shruti / Kohli, Pehu / Asok, Aparna / Mohan, Sonali Vishwa / Gowda, Harsha / Varadarajan, Raghavan

    Molecular biology and evolution

    2022  Band 39, Heft 10

    Abstract: Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin- ... ...

    Abstract Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
    Mesh-Begriff(e) Bacterial Proteins ; Bacterial Toxins/genetics ; Codon/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Mutation ; Toxin-Antitoxin Systems
    Chemische Substanzen Bacterial Proteins ; Bacterial Toxins ; CcdA protein, Bacteria ; Codon ; Escherichia coli Proteins
    Sprache Englisch
    Erscheinungsdatum 2022-09-07
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msac187
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 2137: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

  4. Artikel ; Online: Discovery and pharmacophoric characterization of chemokine network inhibitors using phage-display, saturation mutagenesis and computational modelling.

    Vales, Serena / Kryukova, Jhanna / Chandra, Soumyanetra / Smagurauskaite, Gintare / Payne, Megan / Clark, Charlie J / Hafner, Katrin / Mburu, Philomena / Denisov, Stepan / Davies, Graham / Outeiral, Carlos / Deane, Charlotte M / Morris, Garrett M / Bhattacharya, Shoumo

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 5763

    Abstract: CC and CXC-chemokines are the primary drivers of chemotaxis in inflammation, but chemokine network redundancy thwarts pharmacological intervention. Tick evasins promiscuously bind CC and CXC-chemokines, overcoming redundancy. Here we show that short ... ...

    Abstract CC and CXC-chemokines are the primary drivers of chemotaxis in inflammation, but chemokine network redundancy thwarts pharmacological intervention. Tick evasins promiscuously bind CC and CXC-chemokines, overcoming redundancy. Here we show that short peptides that promiscuously bind both chemokine classes can be identified from evasins by phage-display screening performed with multiple chemokines in parallel. We identify two conserved motifs within these peptides and show using saturation-mutagenesis phage-display and chemotaxis studies of an exemplar peptide that an anionic patch in the first motif and hydrophobic, aromatic and cysteine residues in the second are functionally necessary. AlphaFold2-Multimer modelling suggests that the peptide occludes distinct receptor-binding regions in CC and in CXC-chemokines, with the first and second motifs contributing ionic and hydrophobic interactions respectively. Our results indicate that peptides with broad-spectrum anti-chemokine activity and therapeutic potential may be identified from evasins, and the pharmacophore characterised by phage display, saturation mutagenesis and computational modelling.
    Mesh-Begriff(e) Chemokines ; Chemical Phenomena ; Computer Simulation ; Mutagenesis ; Bacteriophages
    Chemische Substanzen Chemokines
    Sprache Englisch
    Erscheinungsdatum 2023-09-16
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-41488-z
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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