Journal article
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
Journal of chemical theory and computation, Vol.5(2), pp.242-256
02/01/2009
DOI: 10.1021/ct800499p
PMID: 26610102
Abstract
Successful modeling of the processes of protein folding and aggregation may ultimately require accurate descriptions of proteins' diffusive characteristics, which are expected to be influenced by hydrodynamic effects; a comprehensive study of the diffusion and folding of 11 model proteins with an established simulation model extended to include hydrodynamic interactions between residues has therefore been carried out. Molecular simulations that neglect hydrodynamic interactions are incapable of simultaneously reproducing the expected experimental translational and rotational diffusion coefficients of folded proteins, drastically underestimating both when reasonable hydrodynamic radii are employed. In contrast, simulations that include hydrodynamic interactions produce diffusion coefficients that match very well with the expected experimental values for translation and rotation and also correctly capture the significant decrease in translational diffusion coefficient that accompanies protein unfolding. These effects are reflected in folding simulations of the same proteins: the inclusion of hydrodynamic interactions accelerates folding by 2-3-fold with the rate enhancement for the association of secondary structure elements exhibiting a strong sensitivity on the sequence-distance between the associating elements.
Details
- Title: Subtitle
- Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
- Creators
- Tamara Frembgen-Kesner - University of IowaAdrian H. Elcock - University of Iowa
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.5(2), pp.242-256
- Publisher
- Amer Chemical Soc
- DOI
- 10.1021/ct800499p
- PMID
- 26610102
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Number of pages
- 15
- Grant note
- Carver Trust Iowa Presidential Fellowship
- Language
- English
- Date published
- 02/01/2009
- Academic Unit
- Physics and Astronomy; Biochemistry and Molecular Biology
- Record Identifier
- 9984293086602771
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