ArticleScientific reports2015
Functional loop dynamics of the streptavidin-biotin complex.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature.Communications biology · 2022Article
- Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study.Frontiers in molecular biosciences · 2022Article
- Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools.Glycobiology · 2020Article
- Direction Matters: Monovalent Streptavidin/Biotin Complex under Load.Nano letters · 2019Article
- Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water.Frontiers in chemistry · 2019Article
- Synthetic mimics of biotin/(strept)avidin.Chemical Society reviews · 2017Review
- Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide.PLoS computational biology · 2017Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 (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 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.
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