Towards Multiparametric Fluorescent Imaging of Amyloid Formation: Studies of a YFP Model of α-Synuclein Aggregation

Misfolding and aggregation of proteins are characteristics of a range of increasingly prevalent neurodegenerative disorders including Alzheimer's and Parkinson's diseases. In Parkinson's disease and several closely related syndromes, the protein α-synuclein (AS) aggregates and forms amyloid-like deposits in specific regions of the brain. Fluorescence microscopy using fluorescent proteins, for instance the yellow fluorescent protein (YFP), is the method of choice to image molecular events such as protein aggregation in living organisms. The presence of a bulky fluorescent protein tag, however, may potentially affect significantly the properties of the protein of interest; for AS in particular, its relative small size and, as an intrinsically unfolded protein, its lack of defined secondary structure could challenge the usefulness of fluorescent-protein-based derivatives. Here, we subject a YFP fusion of AS to exhaustive studies in vitro designed to determine its potential as a means of probing amyloid formation in vivo. By employing a combination of biophysical and biochemical studies, we demonstrate that the conjugation of YFP does not significantly perturb the structure of AS in solution and find that the AS-YFP protein forms amyloid deposits in vitro that are essentially identical with those observed for wild-type AS, except that they are fluorescent. Of the several fluorescent properties of the YFP chimera that were assayed, we find that fluorescence anisotropy is a particularly useful parameter to follow the aggregation of AS-YFP, because of energy migration Förster resonance energy transfer (emFRET or homoFRET) between closely positioned YFP moieties occurring as a result of the high density of the fluorophore within the amyloid species. Fluorescence anisotropy imaging microscopy further demonstrates the ability of homoFRET to distinguish between soluble, pre-fibrillar aggregates and amyloid fibrils of AS-YFP. Our results validate the use of fluorescent protein chimeras of AS as representative models for studying protein aggregation and offer new opportunities for the investigation of amyloid aggregation in vivo using YFP-tagged proteins.     

Intramolecular Movements in EF-G, Trapped at Different Stages in Its GTP Hydrolytic Cycle, Probed by FRET

Elongation factor G (EF-G) is one of several GTP hydrolytic proteins (GTPases) that cycles repeatedly on and off the ribosome during protein synthesis in bacterial cells. In the functional cycle of EF-G, hydrolysis of guanosine 5′-triphosphate (GTP) is coupled to tRNA-mRNA translocation in ribosomes. GTP hydrolysis induces conformational rearrangements in two switch elements in the G domain of EF-G and other GTPases. These switch elements are thought to initiate the cascade of events that lead to translocation and EF-G cycling between ribosomes. To further define the coupling mechanism, we developed a new fluorescent approach that can detect intramolecular movements in EF-G. We attached a fluorescent probe to the switch I element (sw1) of Escherichia coli EF-G. We monitored the position of the sw1 probe, relative to another fluorescent probe anchored to the GTP substrate or product, by measuring the distance-dependent, Förster resonance energy transfer between the two probes. By analyzing EF-G trapped at five different functional states in its cycle, we could infer the cyclical movements of sw1 within EF-G. Our results provide evidence for conformational changes in sw1, which help to drive the unidirectional EF-G cycle during protein synthesis. More generally, our approach might also serve to define the conformational dynamics of other GTPases with their cellular receptors.     

Molecular Mechanism of Polypeptide Translocation Catalyzed by the Escherichia coli ClpA Protein Translocase

The removal of damaged or unneeded proteins by ATP-dependent proteases is crucial for cell survival in all organisms. Integral components of ATP-dependent proteases are motor proteins that unfold stably folded proteins that have been targeted for removal. These protein unfoldases/polypeptide translocases use ATP to unfold the target proteins and translocate them into a proteolytic component. Despite the central role of these motor proteins in cell homeostasis, a number of important questions regarding the molecular mechanisms of enzyme catalyzed protein unfolding and translocation remain unanswered. Here, we demonstrate that Escherichia coli ClpA, in the absence of the proteolytic component ClpP, processively and directionally steps along the polypeptide backbone with a kinetic step size of ∼ 14 amino acids, independent of the concentration of ATP with a rate of ∼ 19 amino acids s⁻¹ at saturating concentrations of ATP. In contrast to earlier studies by others, we have developed single-turnover fluorescence stopped-flow methods that allow us to quantitatively examine the molecular mechanism of the motor component ClpA decoupled from the proteolytic component ClpP. For the first time, we reveal that in the absence of ClpP ClpA translocates polypeptides directionally, processively and in discrete steps similar to other motor proteins that translocate vectorially on a linear lattice, such as nucleic acid helicases and kinesin. We believe that the methods employed here will be generally applicable to the examination of other AAA?+ protein translocases involved in a variety of important biological functions where the substrate is not covalently modified; for example, membrane fusion, membrane transport, protein disaggregation, and protein refolding.     

Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study

Protein kinase Cα (PKCα) possesses a conserved C2 domain (PKCα C2 domain) that acts as a Ca²⁺-regulated membrane targeting element. Upon activation by Ca²⁺, the PKCα C2 domain directs the kinase protein to the plasma membrane, thereby stimulating an array of cellular pathways. At sufficiently high Ca²⁺ concentrations, binding of the C2 domain to the target lipid phosphatidylserine (PS) is sufficient to drive membrane association; however, at typical physiological Ca²⁺ concentrations, binding to both PS and phosphoinositidyl-4,5-bisphosphate (PIP₂) is required for specific plasma membrane targeting. Recent EPR studies have revealed the membrane docking geometries of the PKCα C2 domain docked to (i) PS alone and (ii) both PS and PIP₂ simultaneously. These two EPR docking geometries exhibit significantly different tilt angles relative to the plane of the membrane, presumably induced by the large size of the PIP₂ headgroup. The present study utilizes the two EPR docking geometries as starting points for molecular dynamics simulations that investigate atomic features of the protein-membrane interaction. The simulations yield approximately the same PIP₂-triggered change in tilt angle observed by EPR. Moreover, the simulations predict a PIP₂:C2 stoichiometry approaching 2:1 at a high PIP₂ mole density. Direct binding measurements titrating the C2 domain with PIP₂ in lipid bilayers yield a 1:1 stoichiometry at moderate mole densities and a saturating 2:1 stoichiometry at high PIP₂ mole densities. Thus, the experiment confirms the target lipid stoichiometry predicted by EPR-guided molecular dynamics simulations. Potential biological implications of the observed docking geometries and PIP₂ stoichiometries are discussed.     

Relative Affinity of Calcium Pump Isoforms for Phospholamban Quantified by Fluorescence Resonance Energy Transfer

To investigate the regulation of SERCA1a [sarco(endo)plasmic reticulum calcium ATPase] and SERCA2a calcium pump isoforms by phospholamban (PLB), we quantified PLB-SERCA interactions by fluorescence resonance energy transfer (FRET) in live cells. For both SERCA1a and SERCA2a, FRET to PLB increased with increasing protein expression level to a maximum value corresponding to a probe separation distance of 64 Å. The data indicate that the respective regulatory complexes assume the same overall quaternary conformation. However, FRET measurements also revealed that PLB has a 50% higher apparent affinity for SERCA1a relative to SERCA2a. The results suggest that despite the structural similarities of the respective regulatory complexes, there is preferential binding of PLB to SERCA1a over SERCA2a. This apparent selectivity may have implications for biochemical studies in which SERCA1a is used as a substitute for SERCA2a. It may also be an important strategic consideration for therapeutic overexpression of SERCA isoforms in cardiac muscle.     

The influence of nest attendance and provisioning on nestling stress physiology in the Florida scrub-jay

Stressful conditions during development may have lasting consequences for an animal's lifetime fitness. We investigated the degree to which parental provisioning and nest attendance influenced baseline levels of the stress hormone corticosterone in nestling Florida scrub-jays. Provisioning rates of male and female breeders and nest attendance of female breeders were recorded during focal watches conducted between days 3 and 5 post-hatch. A small blood sample was taken from each nestling on day 11 post-hatch and used to quantify levels of baseline corticosterone. The proportion of time spent by female breeders at a considerable distance from the nest was positively related to nestling corticosterone levels. Nestling corticosterone was also negatively related to parental provisioning rate, although this effect seemed to be secondary to the effect of the female's time away from the nest. These results indicate that parental behavior contributes to nestling stress physiology, which may in turn direct the formation of the adult phenotype and influence an individual's chances of survival.     

Cyclometalated ruthenium(II) complexes of benzo[h]quinoline (bzqH)[Ru(bzq)(NCMe)4], [Ru(bzq)(LL)(NCMe)2], and [Ru(bzq)(LL)2] (LL = bpy, phen)

Cyclometalation of benzo[h]quinoline (bzqH) by [RuCl(μ-Cl)(η⁶-C₆H₆)]₂ in acetonitrile occurs in a similar way to that of 2-phenylpyridine (phpyH) to afford [Ru(bzq)(MeCN)₄]PF₆ (3) in 52% yield. The properties of 3 containing ‘non-flexible’ benzo[h]quinoline were compared with the corresponding [Ru(phpy)(MeCN)₄]PF₆ (1) complex with ‘flexible’ 2-phenylpyridine. The [Ru(phpy)(MeCN)₄]PF₆ complex is known to react in MeCN solvent with ‘non-flexible’ diimine 1,10-phenanthroline to form [Ru(phpy)(phen)(MeCN)₂]PF₆, being unreactive toward ‘flexible’ 2,2′-bipyridine under the same conditions. In contrast, complex 3 reacts both with phen and bpy in MeCN to form [Ru(bzq)(LL)(MeCN)₂]PF₆ {LL = bpy (4) and phen (5)}. Similar reaction of 3 in methanol results in the substitution of all four MeCN ligands to form [Ru(bzq)(LL)₂]PF₆ {LL = bpy (6) and phen (7)}. Photosolvolysis of 4 and 5 in MeOH occurs similarly to afford [Ru(bzq)(LL)(MeCN)(MeOH)]PF₆ as a major product. This contrasts with the behavior of [Ru(phpy)(LL)(MeCN)₂]PF₆, which lose one and two MeCN ligands for LL = bpy and phen, respectively. The results reported demonstrate a profound sensitivity of properties of octahedral compounds to the flexibility of cyclometalated ligand. Analogous to the 2-phenylpyridine counterparts, compounds 4-7 are involved in the electron exchange with reduced active site of glucose oxidase from Aspergillus niger. Structure of complexes 4 and 6 was confirmed by X-ray crystallography.     

Reactivity difference between protolytic forms of some macrocyclic chromium(III) complexes in ligand substitution and electron transfer processes

The review provides insight into the mechanism of ligand substitution and electron transfer (from chromium(III) to iron(III)) by comparison of the reactivity of some tetraazamacrocyclic chromium(III) complexes in the conjugate acid-base forms. Use of two geometrical isomers made possible to estimate the influence of geometry and protolytic reactions in trans and cis position towards the leaving group on the rate enhancement. Studies on the reaction rates in different media demonstrated the role played by outer sphere interactions in a monodentate ligand substitution.     

Synchronous intra-Golgi transport induces the release of Ca from the Golgi apparatus

The mechanisms of secretory transport through the Golgi apparatus remain an issue of debate. The precise functional importance of calcium ions (Ca²⁺) for intra-Golgi transport has also been poorly studied. Here, using different approaches to measure free Ca²⁺ concentrations in the cell cytosol ([Ca²⁺]_cyt) and inside the lumen of the Golgi apparatus ([Ca²⁺]_GA), we have revealed transient increases in [Ca²⁺]_cyt during the late phase of intra-Golgi transport that are concomitant with a decline in the maximal [Ca²⁺]_GA restoration ability. Thus, this redistribution of Ca²⁺ from the Golgi apparatus into the cytosol during the movement of cargo through the Golgi apparatus appears to have a role in intra-Golgi transport, and mainly in the late Ca²⁺-dependent phase of SNARE-regulated fusion of Golgi compartments.