User:Noam Gonen/Avidin

Structure

The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD ≈ 10−15M, making it one of the strongest known non-covalent bonds[2].The overall fold of the avidin monomer is constructed of eight antiparallel β-strands which form classical β-barrel.

Monomer- monomer interaction

Interaction 1-2

Monomers are linked by hydrogen bond interactions between the respective N-terminal portions of β8-strands of each monomer. The β8-strands form a short antiparallel β-sheet. Each monomer contributes Trp-110 to its partner as an	 additional and very significant component of the biotin-binding site. When biotin is bound, interaction 1-2 is enhanced greatly, owing to the Trp-110-biotin interaction. The buried surface area of interaction is〖729Å〗^2.

Interaction 1-3

Monomers interaction is relatively weak, involving only three equivalent hydrophobic residues from each monomer, Met-96, Val-115, and Ile-11. Resultant van der Waals interactions have the least contribution to the overall stability of the tetrameric structure of avidin. The buried surface area of interaction is〖120Å〗^2 .

Interaction 1-4

Intricate interaction, which is decisive to the observed structural stability of the avidin tetramer.The cohesion of the two monomers, is so intimate that it is difficult to distinguish between them in the resultant dimer. Sections of four β -strands (β4, β5, β6, and β7) from each monomer take part in this extensive interaction.The buried surface area of interaction is〖1951Å〗^2 .

Biotin binding

Hydrophobic residues in the binding site of avidin

These include Trp-70, Phe-72, Phe-79, and Trp-97 from one monomer, and Trp-110 (dashed lines), which is provided by the adjacent symmetry-related monomer.

Hydrophilic interactions in the binding site of avidin

Ureido oxygen of the biotin molecule forms three hydrogen bonds with the side chains of Asn-12, Ser-16, and Tyr-33 of avidin forming a tetrahedral oxyanion. In addition, each of the two ureido nitrogens participates in a single hydrogen-bond interaction with Thr-35 and Asn-118. The biotin sulfur may interact with Thr-77.

References