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Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins

Authors

  • Anna V. Glyakina,

    1. Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    2. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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  • Ilya V. Likhachev,

    1. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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  • Nikolay K. Balabaev,

    1. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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  • Oxana V. Galzitskaya

    Corresponding author
    1. Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    • Correspondence to: Oxana V. Galzitskaya, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia. E-mail: ogalzit@vega.protres.ru

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ABSTRACT

Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the right-handed three-helix domains are more mechanically resistant than the left-handed domains. Such results are observed at different extension velocities studied (192 trajectories obtained at the following conditions: v = 0.1, 0.05, and 0.01 Å ps−1, T = 300 K) and under constant stretching force (64 trajectories, F = 800 pN, T = 300 K). We can explain this by the fact, at least in part, that the right-handed domains have a larger number of contacts per residue and the radius of cross section than the left-handed domains. Proteins 2014; 82:90–102. © 2013 Wiley Periodicals, Inc.

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