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    Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea

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    Type
    Article
    Authors
    Takahashi, Masateru
    Takahashi, Etsuko
    Joudeh, Luay cc
    Marini, Monica cc
    Das, Gobind cc
    Elshenawy, Mohamed cc
    Gespers (Akal), Anastassja cc
    Sakashita, Kosuke cc
    Alam, Intikhab
    Tehseen, Muhammad cc
    Sobhy, Mohamed Abdelmaboud
    Stingl, Ulrich cc
    Merzaban, Jasmeen cc
    Di Fabrizio, Enzo M. cc
    Hamdan, Samir cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Chemical Engineering Program
    Computational Bioscience Research Center (CBRC)
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    KAUST Catalysis Center (KCC)
    Laboratory of DNA Replication and Recombination
    Marine Microbial Ecology Research Group
    Marine Science Program
    Material Science and Engineering Program
    Office of the VP
    Physical Science and Engineering (PSE) Division
    Proteomics and Protein Expression
    Red Sea Research Center (RSRC)
    Date
    2018-01-24
    Online Publication Date
    2018-01-24
    Print Publication Date
    2018-06
    Permanent link to this record
    http://hdl.handle.net/10754/626952
    
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    Abstract
    The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein’s surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of KOD DNA polymerase.—Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.
    Citation
    Takahashi M, Takahashi E, Joudeh LI, Marini M, Das G, et al. (2018) Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea. The FASEB Journal: fj.201700862RR. Available: http://dx.doi.org/10.1096/fj.201700862rr.
    Sponsors
    The authors thank the King Abdullah University of Science and Technology (KAUST) BioScience Core Laboratory for providing Pfu polymerase. This research was funded by the Saudi Economic and Development Company (SEDCO) Research Excellence Project and baseline funding from KAUST to S.M.H. The authors declare no conflicts of interest.
    Publisher
    FASEB
    Journal
    The FASEB Journal
    DOI
    10.1096/fj.201700862rr
    PubMed ID
    29401622
    Additional Links
    http://www.fasebj.org/doi/10.1096/fj.201700862RR
    ae974a485f413a2113503eed53cd6c53
    10.1096/fj.201700862rr
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC); Bioscience Program; Marine Science Program; Physical Science and Engineering (PSE) Division; Chemical Engineering Program; Material Science and Engineering Program; KAUST Catalysis Center (KCC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

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