Research ArticleBIOPHYSICS

Quantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions

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Science Advances  13 Dec 2019:
Vol. 5, no. 12, eaax0024
DOI: 10.1126/sciadv.aax0024
  • Fig. 1 Intraprotein vdW interaction energy along the folding trajectory of Fip35-WW in solvated geometry.

    Top: vdW energetics as obtained with MBD and the pairwise approaches vdW(TS) and vdW(TS)@SCS, i.e., vdW(TS) with self-consistent screening. RMSD from native state shown in grey. Bottom: Beyond-pairwise contributions, as given by the difference between many-body and pairwise treatment. For a more comprehensive version, see Supplementary Materials.

  • Fig. 2 Relative vdW solvation energy, Erel(sol), during the folding process of the Fip35-WW.

    Top: Backbone RMSD from final conformation illustrating the hydrophobic collapse around 35 μs (gray). The vdW contribution to the relative solvation energy is shown for the pairwise vdW(TS) model (red) and MBD (blue). Bottom: Difference in the relative stabilization by the solvent between MBD and the pairwise vdW(TS) and D3 referenced to the unfolded state.

  • Fig. 3 Characteristics of correlated electronic fluctuations.

    (A) Illustration of low-frequency plasmon-like fluctuations in solvated Fip35-WW, which show the largest contribution to the protein-water interaction (solvent shown in atomistic detail: oxygen, red; hydrogen, white). The arrows (blue) depict the direction of simultaneous electron density deformations (eigenmode of the electron density). If no arrow is shown, the given atom does not contribute notably to the eigenmode. (B) Contributions to the vdW solvation energy within the pairwise vdW(TS) approach and the MBD formalism as radial distribution functions.

  • Fig. 4 Characteristics of protein-water dispersion interactions.

    Independent of the secondary structure, the vdW solvation energy captures the hydrophobic collapse in the form of a 20–30 kcal/mol jump (“ΔEsol at collapse”), and many-body protein-water vdW interactions consistently stabilize native states in solvation. Low-frequency, collective electronic fluctuations contribute substantially to the relative solvation energy [ΔEsol(low ω)] in all cases.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/12/eaax0024/DC1

    Section S1. Computational details and vdW models

    Section S2. Summary of gas-phase energetics for Fip35-WW

    Section S3. vdW energetics in detail

    Section S4. Correlation and rescaling of vdW solvation energies

    Section S5. Total electronic energy of solvation

    Section S6. Effect of overcompaction of unfolded states

    Fig. S1. vdW interaction energy of Fip35-WW in gas phase.

    Fig. S2. vdW energetics of Fip35-WW in solvation.

    Fig. S3. Relative vdW solvation energy of cln025.

    Fig. S4. Relative vdW energetics of cln025 in absence of solvent.

    Fig. S5. Correlation of rescaled relative vdW solvation energies as obtained from pairwise models in comparison to the results obtained from many-body treatment.

    Fig. S6. Total electronic energy of solvation of the Fip35-WW as obtained with DFTB in conjunction with the MBD model.

    Fig. S7. Total electronic energy of solvation of the chignolin variant cln025 as obtained with DFTB in conjunction with the MBD model.

    Fig. S8. Intraprotein vdW interaction energy of cln025 based on improved structural sampling.

    Fig. S9. Relative vdW solvation energy of cln025 based on improved structural sampling.

    References (6170)

  • Supplementary Materials

    This PDF file includes:

    • Section S1. Computational details and vdW models
    • Section S2. Summary of gas-phase energetics for Fip35-WW
    • Section S3. vdW energetics in detail
    • Section S4. Correlation and rescaling of vdW solvation energies
    • Section S5. Total electronic energy of solvation
    • Section S6. Effect of overcompaction of unfolded states
    • Fig. S1. vdW interaction energy of Fip35-WW in gas phase.
    • Fig. S2. vdW energetics of Fip35-WW in solvation.
    • Fig. S3. Relative vdW solvation energy of cln025.
    • Fig. S4. Relative vdW energetics of cln025 in absence of solvent.
    • Fig. S5. Correlation of rescaled relative vdW solvation energies as obtained from pairwise models in comparison to the results obtained from many-body treatment.
    • Fig. S6. Total electronic energy of solvation of the Fip35-WW as obtained with DFTB in conjunction with the MBD model.
    • Fig. S7. Total electronic energy of solvation of the chignolin variant cln025 as obtained with DFTB in conjunction with the MBD model.
    • Fig. S8. Intraprotein vdW interaction energy of cln025 based on improved structural sampling.
    • Fig. S9. Relative vdW solvation energy of cln025 based on improved structural sampling.
    • References (6170)

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