The fusion of different protein domains via peptide linkers is a powerful, modular approach to obtain proteins with new functions. A detailed understanding of the conformational behavior of peptide linkers is important for applications such as fluorescence resonance energy transfer (FRET)-based sensor proteins and multidomain proteins involved in multivalent interactions. To investigate the conformational behavior of flexible glycine- and serine-containing peptide linkers, we constructed a series of fusion proteins of enhanced cyan and yellow fluorescent proteins (ECFP-linker-EYFP) in which the linker length was systematically varied by incorporating between 1 and 9 GGSGGS repeats. As expected, both steady-state and time-resolved fluorescence measurements showed a decrease in energy transfer with increasing linker length. The amount of energy transfer observed in these fusion proteins can be quantitatively understood by simple models that describe the flexible linker as a worm-like chain with a persistence length of 4.5 A or a Gaussian chain with a characteristic ratio of 2.3. The implications of our results for understanding the properties of FRET-based sensors and other fusion proteins with Gly/Ser linkers are discussed.

The antigen-capturing activity of antibodycoated nanoparticles is very important for affinity-based bioanalytical tools. In this paper, a comprehensive study is reported of the antigen-capturing activity of antibodies that are nondirectionally immobilized on a nanoparticle surface. Superparamagnetic nanoparticles (500 nm) were covalently functionalized with different quantities of monoclonal antibodies against cardiac troponin I (cTnI). At a low antibody surface coverage, up to 4% of the immobilized antibodies could capture antigen molecules from solution. At high antibody coverage (≥50 × 10 2 antibodies per nanoparticle, i.e., ≥ 64 × 10 2 antibodies per μm 2 ), the fraction of antigen-capturing antibodies drops well below 4% and the number of active antibodies saturates at about 120 per nanoparticle. The fraction of active antibodies is small, yet surprisingly their dissociation constants (K d ) are low, between 10 and 200 pM. In addition, the surface-binding activity of the antibody-coated nanoparticles was analyzed in an optomagnetic sandwich immunoassay biosensor, measuring cTnI in undiluted blood plasma. The data show that the immunoassay response scales with the number of active antibodies, increasing initially and saturating at higher antibody densities. The observations are summarized in a molecular sketch of the attachment, ordering, and functionality of antibodies on the nanoparticle surface.

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Real-time imaging of molecular events in living cells is important for understanding the basis of physiological processes and diseases. [1][2][3] Genetically encoded sensors that use fluorescence resonance energy transfer (FRET) [4] between two fluorescent proteins are attractive in this respect because they do not require cell-invasive procedures, can be targeted to different locations in the cell, and are easily adapted through mutagenesis and directed evolution approaches. [5][6][7] Following the pioneering work of Roger Tsien and others, on genetically encoded protease and calcium sensors, FRET-based imaging probes have been developed for many other small molecules and cell signaling events. [8][9][10][11][12][13] In these probes, conformational changes in a sensor domain are translated into a change in energy-transfer efficiency between donor and acceptor fluorescent domains, which is detected by a change in the ratio of donor and acceptor emission. This ratiometric response is independent of the sensor concentration, which is an important advantage of FRET-based sensors. In practice, however, most FRET-based sensors display only a relatively small difference in emission ratio upon activation. Improvement of these ratiometric changes has been recognized as an important prerequisite for use of these sensor systems in high-throughput applications based on fluorescence plate readers and fluorescence assisted cell sorting (FACS). [14,15] Recently a pair of CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein) variants, CyPet and YPet, respectively, have been reported that were optimized for FRET through a process of directed evolution.[16] When incorporated in a protease sensor, a 20-fold change in emission ratio was observed upon cleavage of a flexible peptide that linked CyPet and YPet, compared to only a fourfold change for the same construct with enhanced CFP (ECFP) and enhanced YFP (EYFP) domains. However, the mechanism behind their remarkable FRET properties has remained unclear. A total of eighteen mutations were introduced in the course of their development, many of which were at the exterior of the protein, at a large distance from the fluorophore. Moreover, no large differences in quantum yield or extinction coefficient were reported; this suggests that the photophysical properties of the fluorescent proteins were not significantly altered. We therefore hypothesized that the increase in FRET observed for CyPet and YPet could be due to an enhanced tendency to interact when connected by a peptide linker. The parent green fluorescent protein (GFP) has a known tendency to dimerize, [17] and analysis of the mutations in YPet have identified two residues, S208F and V224L, that are present at the dimer interface, as shown by the X-ray structure of the GFP dimer. Here, we show that A C H T U N G T R E N N U N G introduction of just these two mutations in both fluorescent domains of ECFP-linker-EYFP constructs results in a fourfold increase in the EYFP-to-ECFP emission ratio, which yields a 16-fol...

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