Functional Loop Dynamics of the Streptavidin-Biotin Complex

Jianing Song, Yongle Li, Changge Ji, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop 3-4 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 loop 3-4 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 (Î "G) 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 loop 3-4 and biotin. (3) The closure of loop 3-4 is concerted to the stable binding of biotin to streptavidin. When the loop 3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop 3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop 3-4 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.

Original languageEnglish (US)
Article number7906
JournalScientific reports
StatePublished - Jan 20 2015

ASJC Scopus subject areas

  • General


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