Conformation of receptor adopted upon interaction with virus revealed by site-specific fluorescence quenchers and FRET analysis.

Human rhinovirus serotype 2 (HRV2) specifically binds to very-low-density lipoprotein receptor (VLDLR). Among the eight extracellular repeats of VLDLR, the third module (V3) has the highest affinity for the virus, and 12 copies of the genetically engineered concatamer V33333-His(6) were found to bind per virus particle. In the present study, ring formation of V33333-His(6) about each of the 12 5-fold symmetry axes on HRV2 was demonstrated by fluorescence resonance energy transfer (FRET) between donor and acceptor on N- and C-terminus, respectively. In particular, the N-terminus of V33333-His(6) was labeled with fluorescein, and the C-terminus with a new quencher which was bound to the His(6) tag with nanomolar affinity (K(d) approximately 10(-8) M) in the presence of 2 microM NiCl(2).

Receptor arrays for the selective and efficient capturing of viral particles.

We describe microarrays of receptors on gold/glass substrates for the selective capturing of viral particles at high density. Microscale gold squares were surface-modified with alkanethiol derivatives which enabled the immobilization of the His(6)-tagged virus-binding domain from the very-low density lipoprotein (VLDL) receptor. The free glass areas surrounding the gold squares were passivated with a dense film of poly(ethylene glycol) (PEG). As assessed by atomic force microscopy, human rhinovirus particles were captured onto the VLDL-receptor patches with a high surface coverage but were effectively repelled by the PEG layer, resulting in a 330 000-fold higher density of the particles on the gold as compared to the glass surfaces. The metal chelate-based coupling strategy was found to be superior to two alternative routes, which used the covalent coupling of viral particles or viral receptors to the substrate surface. The high-density receptor arrays were employed for sensing and characterizing viral particles with so far unprecedented selectivity.

Single-molecule force spectroscopy and imaging of the vancomycin/D-Ala-D-Ala interaction.

The clinically important vancomycin antibiotic inhibits the growth of pathogens such as Staphylococcus aureus by blocking cell wall synthesis through specific recognition of nascent peptidoglycan terminating in D-Ala-D-Ala. Here, we demonstrate the ability of single-molecule atomic force microscopy with antibiotic-modified tips to measure the specific binding forces of vancomycin and to map individual ligands on living bacteria. The single-molecule approach presented here provides new opportunities for understanding the binding mechanisms of antibiotics and for exploring the architecture of bacterial cell walls.

Antibody linking to atomic force microscope tips via disulfide bond formation.

Covalent binding of bioligands to atomic force microscope (AFM) tips converts them into monomolecular biosensors by which cognate receptors can be localized on the sample surface and fine details of ligand-receptor interaction can be studied. Tethering of the bioligand to the AFM tip via a approximately 6 nm long, flexible poly(ethylene glycol) linker (PEG) allows the bioligand to freely reorient and to rapidly "scan" a large surface area while the tip is at or near the sample surface. In the standard coupling scheme, amino groups are first generated on the AFM tip. In the second step, these amino groups react with the amino-reactive ends of heterobifunctional PEG linkers. In the third step, the 2-pyridyl-S-S groups on the free ends of the PEG chains react with protein thiol groups to give stable disulfide bonds. In the present study, this standard coupling scheme has been critically examined, using biotinylated IgG with free thiols as the bioligand. AFM tips with PEG-tethered biotin-IgG were specifically recognized by avidin molecules that had been adsorbed to mica surfaces. The unbinding force distribution showed three maxima that reflected simultaneous unbinding of 1, 2, or 3 IgG-linked biotin residues from the avidin monolayer. The coupling scheme was well-reproduced on amino-functionalized silicon nitride chips, and the number of covalently bound biotin-IgG per microm2 was estimated by the amount of specifically bound ExtrAvidin-peroxidase conjugate. Coupling was evidently via disulfide bonds, since only biotin-IgG with free thiol groups was bound to the chips. The mechanism of protein thiol coupling to 2-pyridyl-S-S-PEG linkers on AFM tips was further examined by staging the coupling step in bulk solution and monitoring turnover by release of 2-pyridyl-SH which tautomerizes to 2-thiopyridone and absorbs light at 343 nm. These experiments predicted 10(3)-fold slower rates for the disulfide coupling step than actually observed on AFM tips and silicon nitride chips. The discrepancy was reconciled by assuming 10(3)-fold enrichment of protein on AFM tips via preadsorption, as is known to occur on comparable inorganic surfaces.