Colin D. Heyes

Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions

Proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. In the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. Here, we have studied the structure and dynamics of the small enzyme ribonuclease HI (RNase H) in the presence of the chemical denaturant guanidinium chloride (GdmCl) using single-molecule fluorescence microscopy, with a particular focus on the characterization of the unfolded-state ensemble. A dye pair was specifically attached to the enzyme to measure structural changes through Förster resonance energy transfer (FRET). Enzyme immobilization on star-polymer surfaces that were specially developed for negligible interaction with folded and unfolded proteins enabled us to monitor conformational changes of individual proteins for several hundred seconds. FRET efficiency histograms were calculated from confocal scan images. They showed an expansion of the unfolded proteins with increasing GdmCl concentration. Cross-correlation analysis of donor and acceptor fluorescence intensity time traces from single molecules revealed reconfiguration of the polypeptide chain on a timescale of ≈20 μs at 1.7 M GdmCl. Slow conformational dynamics gave rise to characteristic, stepwise FRET efficiency changes. Transitions between folded and unfolded enzyme molecules occurred on the 100-s timescale, in excellent agreement with bulk denaturation experiments. Transitions between unfolded conformations were more frequent, with characteristic times of ≈2 s. These data were analyzed to obtain information on the free energy landscape of RNase H in the presence of chemical denaturants.

Zwitterionic Biocompatible Quantum Dots for Wide pH Stability and Weak Nonspecific Binding to Cells

Applications of water-soluble quantum dots (QDs) in the life sciences are limited by their poor colloidal stability in physiological media and nonspecific interaction with biomatter, particularly cell membranes. We have studied colloidal stability and nonspecific interactions with living cells for zwitterionic d-penicillamine-coated QDs (DPA-QDs) and the traditionally used carboxylated 11-mercaptoundecanoic acid-coated QDs (MUA-QDs) and found clear advantages of DPA-QDs. In single molecule fluorescence experiments, DPA-QDs showed no aggregation over the physiologically relevant pH range of 5-9, whereas MUA-QDs showed significant aggregation below pH 9. Upon exposure to living Mono Mac 6 cells, DPA-QDs, which possess overall charge-neutral surfaces, exhibited weak interactions with the cell membrane and were easily removed by flushing with buffer. By contrast, the highly charged MUA-QDs strongly associated with the cells and could not be removed even by extensive rinsing with buffer solution. DPA-QDs exhibit a high chemical stability even in strongly oxidizing conditions, in contrast to cysteine-coated QDs reported earlier. This beneficial property may arise from reduced interactions between DPA ligands due to steric effects of the methyl groups on their beta-carbon atoms.

Synthesis, patterning and applications of star-shaped poly(ethylene glycol) biofunctionalized surfaces

Poly(ethylene) glycol (PEG) is an excellent material to modify surfaces to resist non-specific protein adsorption. Linear PEG has been extensively studied both theoretically and experimentally and it has been found that resistance of PEG-coated surfaces to protein adsorption depends mainly on the molecular weight of the polymer and the surface grafting density. End-functionalized star-shaped PEGs allow for interpolymer crosslinking to form a dense layer. An excellent example of such a system consists of a 6-arm PEG/PPG (4 : 1) star polymer functionalized with isocyanate using IPDI. The end functionalization may be further biofunctionalized to recognize specific biomolecules such as streptavidin, His-tagged proteins, amino-terminated oligonucleotides and cell receptors. This functionalization may be patterned into specific geometries using stamping techniques or randomly distributed by statistical reaction of the end group with the biofunctional molecule in solution. The surface preparation uses simple spin-, dip- or spray-coating and produces smooth layers with low background fluorescence. These properties, together with the advantageous chemical properties of PEG, render the surfaces ideal for immobilizing proteins on surfaces with detection limits down to the single molecule level. Proteins immobilized on such surfaces are able to maintain their folded, functional form and are able to completely refold if temporarily exposed to denaturing conditions. Immobilized enzyme molecules were able to perform their function with the same activity as the enzyme in solution. Future directions of using surfaces coated with such crosslinked star polymers in highly sensitive and robust biotechnology applications will be discussed.

Stoichiometry of the Human Glycine Receptor Revealed by Direct Subunit counting

The subunit stoichiometry of heteromeric glycine-gated channels determines fundamental properties of these key inhibitory neurotransmitter receptors; however, the ratio of α1- to β-subunits per receptor remains controversial. We used single-molecule imaging and stepwise photobleaching in Xenopus oocytes to directly determine the subunit stoichiometry of a glycine receptor to be 3α1:2β. This approach allowed us to determine the receptor stoichiometry in mixed populations consisting of both heteromeric and homomeric channels, additionally revealing the quantitative proportions for the two populations.

Probing the “Dark” Fraction of Core–Shell Quantum Dots by Ensemble and Single Particle pH-Dependent Spectroscopy

The optical properties of core-shell CdSe-ZnS quantum dots (QDs) are characterized by complex photophysics leading to difficulties in interpreting quantitative measurements based on QD emission. By comparing the pH dependence of fluorescence of single QDs to that of an ensemble, we have been able to propose a molecular scale model of how QD surface chemical and physical processes are affected by protons and oxygen. We show that the connection between the ensemble fluorescence intensity and the single QD fluorescence properties such as dark fraction, blinking, particle brightness, and a multiexponential fluorescence lifetime decay is not trivial. The ensemble fluorescence intensity is more weakly dependent on pH than the single particle fluorescence which, together with fluorescence lifetime analysis, provided evidence that the dark fraction of QDs emits photons with low quantum efficiency and long lifetime. We uncovered two surface-dependent mechanisms that affected the fluorescence emission: an immediate physical effect of charges surrounding the QD and an irreversible chemical effect from reaction of the H(+) and O(2) with the QD shell surface. These results will have important implications for those using QD-based fluorescence lifetime imaging as well as for proper implementation of these probes for quantitative cellular imaging applications.

Fluorescence intensity and intermittency as tools for following dopamine bioconjugate processing in living cells.

CdSe/ZnS quantum dots (QDs) conjugated to biomolecules that quench their fluorescence, particularly dopamine, have particular spectral properties that allow determination of the number of conjugates per particle, namely, photoenhancement and photobleaching. In this work, we quantify these properties on a single-particle and ensemble basis in order to evaluate their usefulness as a tool for indicating QD uptake, breakdown, and processing in living cells. This creates a general framework for the use of fluorescence quenching and intermittency to better understand nanoparticle-cell interactions.

Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates

Background: Targeting of proteins requires a signal recognition particle (SRP) and multiple protein interactions. Results: We observed a decrease in the structural dynamics of cpSRP43 and an increase in substrate affinity upon its binding to cpSRP54. Conclusion: Changes in domain dynamics induced by cpSRP subunit interactions mediate substrate affinity. Significance: Relating structure and dynamics of SRP proteins allows for a better understanding of vectorial targeting within cells. Protein targeting is critical in all living organisms and involves a signal recognition particle (SRP), an SRP receptor, and a translocase. In co-translational targeting, interactions among these proteins are mediated by the ribosome. In chloroplasts, the light-harvesting chlorophyll-binding protein (LHCP) in the thylakoid membrane is targeted post-translationally without a ribosome. A multidomain chloroplast-specific subunit of the SRP, cpSRP43, is proposed to take on the role of coordinating the sequence of targeting events. Here, we demonstrate that cpSRP43 exhibits significant interdomain dynamics that are reduced upon binding its SRP binding partner, cpSRP54. We showed that the affinity of cpSRP43 for the binding motif of LHCP (L18) increases when cpSRP43 is complexed to the binding motif of cpSRP54 (cpSRP54pep). These results support the conclusion that substrate binding to the chloroplast SRP is modulated by protein structural dynamics in which a major role of cpSRP54 is to improve substrate binding efficiency to the cpSRP.

Are Bidentate Ligands Really Better than Monodentate Ligands For Nanoparticles

Coordinating ligands are widely used to vary the solubility and reactivity of nanoparticles for subsequent bioconjugation. Although long-term colloidal stability is enhanced by using bidentate coordinating ligands over monodentate ones, other properties such as nonspecific adsorption of target molecules and ligand exchange have not been quantified. In this study, we modified a near-infrared dye to serve as a highly sensitive reporter for nonspecific binding of thiolated target molecules to nanoparticle surfaces that are functionalized with monodentate or bidentate coordinated ligands. Specifically, we analyzed nonspecific binding mechanisms to quantum dots (QDs) by fitting the adsorption profiles to the Hill equation and the parameters are used to provide a microscopic picture of how ligand density and lability control nonspecific adsorption. Surprisingly, bidentate ligands are worse at inhibiting adsorption to QD surfaces at low target/QD ratios, although they become better as the ratio increases, but only if the nanoparticle surface area is large enough to overcome steric effects. This result highlights that a balance between ligand density and lability depends on the dentate nature of the ligands and controls how molecules in solution can coordinate to the nanoparticle surface. These results will have major implications for a range of applications in nanobiomedicine, bioconjugation, single molecule spectroscopy, self-assembly, and nano(photo)catalysis where both nonspecific and specific surface interactions play important roles. As an example, we tested the ability of monodentate and bidentate functionalized nanoparticles to resist nonspecific adsorption of IgG antibodies that contained free thiol groups at a 1:1 QD/IgG ratio and found that QDs with monodentate ligands did indeed result in lower nonspecific adsorption.

3D imaging of flow patterns in an internally-pumped microfluidic device: redox magnetohydrodynamics and electrochemically-generated density gradients.

Redox magnetohydrodynamics (MHD) is a promising technique for developing new electrochemical-based microfluidic flow devices with unique capabilities, such as easily switching flow direction and adjusting flow speeds and flow patterns as well as avoiding bubble formation. However, a detailed description of all the forces involved and predicting flow patterns in confined geometries is lacking. In addition to redox-MHD, density gradients caused by the redox reactions also play important roles. Flow in these devices with small fluid volumes has mainly been characterized by following microbead motion by optical microscopy either by particle tracking velocimetry (PTV) or by processing the microbead images by particle image velocimetry (PIV) software. This approach has limitations in spatial resolution and dimensionality. Here we use fluorescence correlation spectroscopy (FCS) to quantitatively and accurately measure flow speeds and patterns in the ~5-50 μm/s range in redox-MHD-based microfluidic devices, from which 3D flow maps are obtained with a spatial resolution down to 2 μm. The 2 μm spatial resolution flow speeds map revealed detailed flow profiles during redox-MHD in which the velocity increases linearly from above the electrode and reaches a plateau across the center of the cell. By combining FCS and video-microscopy (with PTV and PIV processing approaches), we are able to quantify a vertical flow of ~10 μm/s above the electrodes as a result of density gradients caused by the redox reactions and follow convection flow patterns. Overall, combining FCS, PIV, and PTV analysis of redox-MHD is a powerful combination to more thoroughly characterize the underlying forces in these promising microfluidic devices.

Intrinsic GTP hydrolysis is observed for a switch 1 variant of Cdc42 in the presence of a specific GTPase inhibitor

ABSTRACT The Ras-related protein Cell division cycle 42 (Cdc42) is important in cell-signaling processes. Protein interactions involving Cdc42 occur primarily in flexible “Switch” regions that help regulate effector binding. We studied the kinetics of intrinsic GTP hydrolysis reaction in the absence and presence of a biologically active peptide derivative of a p21-activated kinase effector (PBD46) for wt Cdc42 and compared it to the Switch 1 variant Cdc42(T35A). While the binding of PBD46 to wt Cdc42 results in complete inhibition of GTP hydrolysis, this interaction in Cdc42(T35A) does not. Comparison of the crystal structure of wt Cdc42 in the absence of effector (1AN0.pdb), as well as the NMR structure of wt Cdc42 bound to an effector in the Switch 1 region (1CF4.pdb) (www.rcsb.org) suggests that the orientation of T35 with bound Mg2+ changes in the presence of effector, resulting in movement of GTP away from the catalytic box leading to the inhibition of GTP hydrolysis. For Cdc42(T35A), molecular dynamics simulations and structural analyses suggest that the nucleotide does not undergo the conformational shift observed for the wt Cdc42-effector interaction. Our data suggest that change in dynamics in the Switch 1 region of Cdc42 caused by the T35A mutation (Chandrashekar, et al. 2011, Biochemistry, 50, p. 6196) fosters a conformation for this Cdc42 variant that allows hydrolysis of GTP in the presence of PBD46, and that alteration of the conformational dynamics could potentially modulate Ras-related over-activity.