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ORIENTATION OF WATER MOLECULES NEAR A GLOBULAR PROTEIN

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Abstract

Orientation of water molecules in the vicinity of the globular protein SNase is studied. It is shown that two types of characteristic orientations can be distinguished among molecules in direct contact with the protein. Approximately 44% of these molecules are oriented by their OH vector towards the nearest protein atom forming a donor hydrogen bond; 20% of them are directed by their oxygen towards the nearest atom while their protons are directed mainly away from the protein. By forming a network of hydrogen bonds with other water molecules, these molecules initiate orientation correlations in the protein environment within a region of 0.45 nm. More distant water molecules are arranged randomly with respect to the protein. The orientation is described by the angle between vector N directed from the water molecule to the nearest protein atom and characteristic vectors of the water molecule (directions OH, OL, and dipole moment D). A more detailed information about orientations is retrieved from a two-dimensional distribution diagram P(cos(θ), φ) representing direction N in a spherical coordinate system associated with the water molecule. The diagram provides an unambiguous description for the orientation of water molecules and allows a quantitative calculation of the fraction of molecules with a specified orientation.

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Funding

The reported study was funded by RFBR, project number 18-03-00045.

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Authors and Affiliations

  1. Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia

    V. P. Voloshin & N. N. Medvedev

  2. Novosibirsk State University, Novosibirsk, Russia

    N. N. Medvedev

Authors
  1. V. P. Voloshin
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  2. N. N. Medvedev
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Correspondence to N. N. Medvedev.

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Russian Text © The Author(s), 2021, published in Zhurnal Strukturnoi Khimii, 2021, Vol. 62, No. 5, pp. 745-757.https://doi.org/10.26902/JSC_id72868

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Voloshin, V.P., Medvedev, N.N. ORIENTATION OF WATER MOLECULES NEAR A GLOBULAR PROTEIN. J Struct Chem 62, 692–703 (2021). https://doi.org/10.1134/S002247662105005X

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  • DOI: https://doi.org/10.1134/S002247662105005X

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