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- Title
Functional Loop Dynamics of the Streptavidin-Biotin Complex.
- Authors
Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.
- Abstract
Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.
- Subjects
STREPTAVIDIN; BIOTIN; MOLECULAR dynamics; CONFORMATIONAL analysis; BINDING sites; TETRAMERS (Oligomers)
- Publication
Scientific Reports, 2015, p7906
- ISSN
2045-2322
- Publication type
Article
- DOI
10.1038/srep07906