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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
Abstract
Single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of diffusion coefficients (translational and rotational) of water adjacent to specific patches on the protein surface seem not to be correlated to the orientational ordering of hydration water, but instead they depend on spatial roughness and degree of exposure of the patch to the solvent. Finally, a relationship between the mobility of various surface atoms of the protein and the mean values of diffusion coefficient of the adjacent water molecules has been observed. The latter finding suggests a close relationship between the dynamics of the inner kinesin movements and the behavior of solvation water which is in turn determined by the topography of contact surface between the protein and the surrounding water molecules.
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- Category:
- Articles
- Type:
- artykuł w czasopiśmie wyróżnionym w JCR
- Published in:
-
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
no. 14,
pages 5561 - 5569,
ISSN: 1463-9076 - Language:
- English
- Publication year:
- 2012
- Bibliographic description:
- Kuffel A., Zielkiewicz J.: The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein// PHYSICAL CHEMISTRY CHEMICAL PHYSICS. -Vol. 14, nr. iss. 16 (2012), s.5561-5569
- Verified by:
- Gdańsk University of Technology
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