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Protein Thermostabilizing Factors: High Relative Occurrence of Amino Acids, Residual Properties, and Secondary Structure Type in Different Residual State

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Abstract

The relative occurrences of amino acids, residual properties, and secondary structure type found in the residual structure states were compared between thermophilic and mesophilic proteins to find out the protein-thermostabilizing factors. The thermostabilizing patterns in each residual structure state are as follows: (1) in fully exposed state, higher relative occurrences of GLN, ILE, and PHE; (2) in exposed state, higher relative occurrences of ARG, GLU, salt bridges, the residue with low solvation energy, and the residues in 3/10 helix, and lower relative occurrences of ALA, SER, and VAL; (3) in partially exposed state, higher relative occurrence of flexible residue and lower relative occurrence of SER; (4) in buried state, higher relative occurrences of ARG and GLU, and lower relative occurrence of MET; and (5) in well-buried state, higher relative occurrences of ALA, cation–pi interaction, the residues in 3/10 helix, and lower relative occurrences of ASP, GLY, and the residues in the extended beta strand. These findings could be useful for developing protein thermostabilization strategies according to each residual structure state.

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Acknowledgments

This work was supported by the National Research Foundation (NRF) grant by the Korean Government (MEST; NRF-2011-C1AAA001-2011-0030345) and also supported by the Mid-career Researcher Program through NRF grant funded by the MEST (NRF-2010-0026498).

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Authors and Affiliations

  1. Department of Biotechnology and Bioinformatics, Korea University, Sejong, 339-700, South Korea

    Seung Pil Pack

  2. Department of Chemical and Biochemical Engineering, Dongguk University, Seoul, 100-715, South Korea

    Taek Jin Kang

  3. School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-742, South Korea

    Young Je Yoo

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  1. Seung Pil Pack
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  2. Taek Jin Kang
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  3. Young Je Yoo
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Correspondence to Seung Pil Pack or Young Je Yoo.

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Seung Pil Pack and Taek Jin Kang equally contributed to this paper.

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Pack, S.P., Kang, T.J. & Yoo, Y.J. Protein Thermostabilizing Factors: High Relative Occurrence of Amino Acids, Residual Properties, and Secondary Structure Type in Different Residual State. Appl Biochem Biotechnol 171, 1212–1226 (2013). https://doi.org/10.1007/s12010-013-0195-1

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