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Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins

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Abstract

We studied the amino acid frequency and substitution patterns between homologues of prokaryotic species adapted to temperatures in the range 0–102°C, and found a significant temperature-dependent difference in frequency for many of the amino acids. This was particularly clear when we analysed the surface and core residues separately. The difference between the surface and the core is getting more pronounced in proteins adapted to warmer environments, with a more hydrophobic core, and more charged and long-chained amino acids on the surface of the proteins. We also see that mesophiles have a more similar amino acid composition to psychrophiles than to thermophiles, and that archea appears to have a slightly different pattern of substitutions than bacteria.

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Abbreviations

OGT:

Optimal growth temperature

SASA:

Solvent accessible surface area

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Acknowledgements

Thanks to William R. Taylor and Trond H. Bø for valuable input. This research was funded by the Norwegian functional genomics program (FUGE) of the Research Council of Norway, through the Envision project and through the technology platform for bioinformatics.

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Authors and Affiliations

  1. Computational Biology Unit (CBU), BCCS, University of Bergen, Bergen, Norway

    Gisle Sælensminde & Inge Jonassen

  2. Department of Biomedicine, University of Bergen, Bergen, Norway

    Øyvind Halskau Jr

  3. Department of Chemistry, University of Tromsø, Tromsø, Norway

    Ronny Helland

  4. Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway

    Ronny Helland & Nils-Peder Willassen

  5. Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Tromsø, Norway

    Nils-Peder Willassen

  6. Department of Informatics, University of Bergen, Bergen, Norway

    Gisle Sælensminde & Inge Jonassen

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  1. Gisle Sælensminde
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Correspondence to Gisle Sælensminde.

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Communicated by F. Robb.

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Sælensminde, G., Halskau, Ø., Helland, R. et al. Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. Extremophiles 11, 585–596 (2007). https://doi.org/10.1007/s00792-007-0072-3

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  • DOI: https://doi.org/10.1007/s00792-007-0072-3

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