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  • 1.
    Friedman, Ran
    et al.
    Tel Aviv University, Tel Aviv, Israel.
    Nachliel, E.
    Tel Aviv University, Tel Aviv, Israel.
    Gutman, M.
    Tel Aviv University, Tel Aviv, Israel.
    Protein Surface - the Dynamics of the Interactions between Protein, Water and Small Solutes2005In: Journal of biological physics (Print), ISSN 0092-0606, E-ISSN 1573-0689, Vol. 31, no 3-4, p. 433-452Article in journal (Refereed)
    Abstract [en]

    Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na+ and Cl ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na+ and Cl ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

  • 2.
    Friedman, Ran
    et al.
    Tel Aviv University, Israel.
    Nachliel, Esther
    Tel Aviv University, Israel.
    Gutman, Menachem
    Tel Aviv University, Israel.
    Protein surface dynamics: Interaction with water and small solutes2005In: Journal of biological physics (Print), ISSN 0092-0606, E-ISSN 1573-0689, Vol. 31, no 3, p. 433-452Article in journal (Refereed)
    Abstract [en]

    Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na+and Cl ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na+ and Cl ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

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