This study examines the binding of wild-type streptavidin and streptavidin mutants to biotinterminated self-assembled monolayers (SAMs) as a model of biomolecular recognition at solid-liquid interfaces. The types of streptavidin proteins employed in this work were wild-type, Tyr43Ala (Y43A), and Trp120Ala (W120A), which have biotin-binding affinities that span several orders of magnitude (K a varies from ∼10 13 M -1 for wild-type to 10 7 M -1 for W120A). Two types of biotin-terminated monolayers were examined: those formed by chemisorption of 11-mercaptoundecanoic-(8-biotinoylamido-3,6-dioxaoctyl) amide (1) and those formed from mixtures of 12-mercaptododecanoic-(8-biotinoylamido-3,6-dioxaoctyl) amide ( 2) and 11-mercapto undecanol (3). Our findings support two previously published studies that found that 1 forms monolayers on gold that are disordered, while 2 and mixtures of 2 and 3 form closely packed, well-organized SAMs. The kinetics of binding and desorption of wild-type streptavidin and the mutants to and from these monolayers were measured using surface plasmon resonance spectroscopy. Adsorption of the proteins was found to occur at a diffusion-limited rate and to saturate at different surface coverages depending on their biotin-binding affinity. On disordered monolayers formed from 1, only a fraction of the bound mutants could be dissociated by exposure to free biotin. The fraction of undissociated mutants correlated with the biotin-binding affinity, suggesting that the formation of nonspecific interactions depends on the residence time of the protein on the surface. On mixed SAMs formed from 2 and 3, complete dissociation of the proteins occurred upon exposure to free biotin in solution. The kinetics of desorption of streptavidin from mixed SAMs was analyzed using a model that included the possibility of bivalent protein binding to the SAM at high surface concentrations of biotin. It was found that rate constants of dissociation were larger for the dissociation of a streptavidin-biotin bond on the surface than in solution. On biotinylated SAMs, the kinetic constants of dissociation were dependent on the surface concentration of biotin. Slow dissociation rates at higher surface coverage result from attractive protein-protein interactions. The results demonstrate the importance of the preparation and the structure of the solid surface and the complexity of biomolecular recognition at solid-liquid interfaces. Molecular recognition is affected by interactions between the adsorbed proteins and the surface and also by interactions among adsorbed proteins. These conclusions have important implications for the development of reversible biosensors.

The high-affinity streptavidin-biotin complex is characterized by an extensive hydrogen-bonding network. A study of hydrogen-bonding energetics at the ureido oxygen of biotin has been conducted with site-directed mutations at Asn 23, Ser 27, and Tyr 43. A new competitive biotin binding assay was developed to provide direct equilibrium measurements of the alterations in Kd. S27A, Y43F, Y43A, N23A, and N23E mutants display DeltaDeltaG degrees at 37 degrees C relative to wild-type streptavidin of 2.9, 1.2, 2.6, 3.5, and 2.6 kcal/mol, respectively. The equilibrium-binding enthalpies for all of the mutants were measured by isothermal titration calorimetry, and the Y43A and N23A mutants display large decreases in the equilibrium binding enthalpy at 25 degrees C of 8.9 and 6.9 kcal/mol, respectively. The S27A and N23E mutants displayed small decreases in binding enthalpy of 1.6 and 0.9 kcal/mol relative to wild-type, while the Y43F mutant displayed a -2.6 kcal/mol increase in the binding enthalpy at 25 degrees C. At 37 degrees C, the Y43A and N23A mutants display decreases of 7.8 and 7.9 kcal/mol, respectively, while the S27A, N23E, and Y43F mutants displayed decreases of 4.9, 3.7, and 1.2 kcal/mol relative to wild-type. Kinetic analyses were also conducted to probe the contributions of the hydrogen bonds to the activation barrier. Wild-type streptavidin at 37 degrees C displays a koff of (4.1 +/- 0.3) x 10(-5) s-1, and the conservative Y43F, S27A, and N23A mutants displayed increases in koff to (20 +/- 1) x 10(-5) s-1, (660 +/- 40) x 10(-5) s-1, and (1030 +/- 220) x 10(-)5 s-1, respectively. The Y43A and N23E mutants displayed 93-fold and 188-fold increases in koff, respectively. Activation energies and enthalpies for each of the mutants were determined by transition-state analysis of the dissociation rate temperature dependence. All of the mutants except Y43F display large reductions in the activation enthalpy. The Y43F mutant has a more positive activation enthalpy, and thus a more favorable activation entropy that underlies the overall reduction in the activation barrier. For the most conservative mutant at each ureido oxygen hydrogen-bonding position, bound-state alterations account for most of the energetic changes in a single transition-state model, suggesting that the ureido oxygen hydrogen-bonding interactions are broken in the dissociation transition state.

It is currently unclear whether small molecules dissociate from a protein binding site along a defined pathway or through a collection of dissociation pathways. We report herein a joint crystallographic, computational, and biophysical study that suggests the Asp-128 3 Ala (

The streptavidin-biotin complex provides the basis for many important biotechnological applications and is an interesting model system for studying high-affinity protein-ligand interactions. We report here crystallographic studies elucidating the conformation of the flexible binding loop of streptavidin (residues 45 to 52) in the unbound and bound forms. The crystal structures of unbound streptavidin have been determined in two monoclinic crystal forms. The binding loop generally adopts an open conformation in the unbound species. In one subunit of one crystal form, the flexible loop adopts the closed conformation and an analysis of packing interactions suggests that protein-protein contacts stabilize the closed loop conformation. In the other crystal form all loops adopt an open conformation. Co-crystallization of streptavidin and biotin resulted in two additional, different crystal forms, with ligand bound in all four binding sites of the first crystal form and biotin bound in only two subunits in a second. The major change associated with binding of biotin is the closure of the surface loop incorporating residues 45 to 52. Residues 49 to 52 display a 310 helical conformation in unbound subunits of our structures as opposed to the disordered loops observed in other structure determinations of streptavidin. In addition, the open conformation is stabilized by a &sheet hydrogen bond between residues 45 and 52, which cannot occur in the closed conformation. The 310 helix is observed in nearly all unbound subunits of both the co-crystallized and ligand-free structures. An analysis of the temperature factors of the binding loop regions suggests that the mobility of the closed loops in the complexed structures is lower than in the open loops of the ligand-free structures. The two biotin bound subunits in the tetramer found in the MONO-bl crystal form are those that contribute Trp 120 across their respective binding pockets, suggesting a structural link between these binding sites in the tetramer. However, there are no obvious signatures of binding site communication observed upon ligand binding, such as quaternary structure changes or shifts in the region of Trp 120. These studies demonstrate that while crystallographic packing interactions can stabilize both the open and closed forms of the flexible loop, in their absence the loop is open in the unbound state and closed in the presence of biotin. If present in solution, the helical structure in the open loop conformation could moderate the entropic penalty associated with biotin binding by contributing an order-to-disorder component to the loop closure.

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