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Establishing knowledge on the sequence arrangement pattern of nucleated protein folding

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Listed:
  • Fei Leng
  • Chao Xu
  • Xia-Yu Xia
  • Xian-Ming Pan

Abstract

The heat-tolerance mechanisms of (hyper)thermophilic proteins provide a unique opportunity to investigate the unsolved protein folding problem. In an attempt to determine whether the interval between residues in sequence might play a role in determining thermostability, we constructed a sequence interval-dependent value function to calculate the residue pair frequency. Additionally, we identified a new sequence arrangement pattern, where like-charged residues tend to be adjacently assembled, while unlike-charged residues are distributed over longer intervals, using statistical analysis of a large sequence database. This finding indicated that increasing the intervals between unlike-charged residues can increase protein thermostability, with the arrangement patterns of these charged residues serving as thermodynamically favorable nucleation points for protein folding. Additionally, we identified that the residue pairs K-E, R-E, L-V and V-V involving long sequence intervals play important roles involving increased protein thermostability. This work demonstrated a novel approach for considering sequence intervals as keys to understanding protein folding. Our findings of novel relationships between residue arrangement and protein thermostability can be used in industry and academia to aid the design of thermostable proteins.

Suggested Citation

  • Fei Leng & Chao Xu & Xia-Yu Xia & Xian-Ming Pan, 2017. "Establishing knowledge on the sequence arrangement pattern of nucleated protein folding," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-12, March.
  • Handle: RePEc:plo:pone00:0173583
    DOI: 10.1371/journal.pone.0173583
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    References listed on IDEAS

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    1. Thomas Hamelryck & Mikael Borg & Martin Paluszewski & Jonas Paulsen & Jes Frellsen & Christian Andreetta & Wouter Boomsma & Sandro Bottaro & Jesper Ferkinghoff-Borg, 2010. "Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-11, November.
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