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Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach

Author

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  • Yutaka Maruyama

    (Quemix Inc., 2-11-2 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
    Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi 214-8571, Japan
    These authors contributed equally to this work.)

  • Ayori Mitsutake

    (Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi 214-8571, Japan
    These authors contributed equally to this work.)

Abstract

The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins.

Suggested Citation

  • Yutaka Maruyama & Ayori Mitsutake, 2022. "Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach," J, MDPI, vol. 5(1), pages 1-12, February.
    • Handle: RePEc:gam:jjopen:v:5:y:2022:i:1:p:9-125:d:749109
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    References listed on IDEAS

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    2. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
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