Long-Chain Lipids Facilitate Insertion of Large Nanoparticles into Membranes of Small Unilamellar Vesicles.

Insertion of hydrophobic nanoparticles into phospholipid bilayers is limited to small particles that can incorporate into a hydrophobic membrane core between two lipid leaflets. Incorporation of nanoparticles above this size limit requires the development of challenging surface engineering methodologies. In principle, increasing the long-chain lipid component in the lipid mixture should facilitate incorporation of larger nanoparticles. Here, we explore the effect of incorporating very long phospholipids (C24:1) into small unilamellar vesicles on the membrane insertion efficiency of hydrophobic nanoparticles that are 5-11 nm in diameter. To this end, we improve an existing vesicle preparation protocol and utilized cryogenic electron microscopy imaging to examine the mode of interaction and evaluate the insertion efficiency of membrane-inserted nanoparticles. We also perform classical coarse-grained molecular dynamics simulations to identify changes in lipid membrane structural properties that may increase insertion efficiency. Our results indicate that long-chain lipids increase the insertion efficiency by preferentially accumulating near membrane-inserted nanoparticles to reduce the thermodynamically unfavorable disruption of the membrane.

Interfacing the Cell with "Biomimetic Membrane Proteins".

Integral membrane proteins mediate a myriad of cellular processes and are the target of many therapeutic drugs. Enhancement and extension of the functional scope of membrane proteins can be realized by membrane incorporation of engineered nanoparticles designed for specific diagnostic and therapeutic applications. In contrast to hydrophobic insertion of small amphiphilic molecules, delivery and membrane incorporation of particles on the nanometric scale poses a crucial barrier for technological development. In this perspective, the transformative potential of biomimetic membrane proteins (BMPs), current state of the art, and the barriers that need to be overcome in order to advance the field are discussed.

Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.

Intramolecular protein diffusion, the motion of one part of the polypeptide chain relative to another part, is a fundamental aspect of protein folding and may modulate amyloidogenesis of disease-associated intrinsically disordered proteins. Much work has determined such diffusion coefficients using a variety of probes, but there has been an apparent discrepancy between measurements using long-range probes, such as fluorescence resonance energy transfer, and short-range probes, such as Trp-Cys quenching. In this work, we make both such measurements on the same protein, α-synuclein, and confirm that such discrepancy exists. Molecular dynamics simulations suggest that such differences result from a diffusion coefficient that depends on the spatial distance between probes. Diffusional estimates in good quantitative agreement with experiment are obtained by accounting for the distinct distance ranges probed by fluorescence resonance energy transfer and Trp-Cys quenching.

Transient Secondary and Tertiary Structure Formation Kinetics in the Intrinsically Disordered State of α-Synuclein from Atomistic Simulations.

In the absence of a stable fold, transient secondary structure kinetics define the native state of the prototypical and pharmacologically relevant intrinsically disordered protein (IDP) α-Synuclein (aS). Here, we investigate kinetics preventing ordering and possibly pathogenic ß-sheet aggregation. Interestingly, transient ß-sheets form frequently at sub µs time scales precisely at the positions observed in aS amyloid fibrils. The formation kinetics competes with rapid secondary structure dissociation rates, thus explaining the low secondary structure content. The fast secondary structure dissociation times are very similar to the dynamics of tertiary structure rearrangements. These findings suggest that the fast dissociation kinetics slows down conformational selection processes for aS aggregation, which may be a general mechanism controlling the aggregation kinetics of IDPs.

Self-Assembled Cyclic d,l-α-Peptides as Generic Conformational Inhibitors of the α-Synuclein Aggregation and Toxicity: In Vitro and Mechanistic Studies.

Many peptides and proteins with large sequences and structural differences self-assemble into disease-causing amyloids that share very similar biochemical and biophysical characteristics, which may contribute to their cross-interaction. Here, we demonstrate how the self-assembled, cyclic d,l-α-peptide CP-2, which has similar structural and functional properties to those of amyloids, acts as a generic inhibitor of the Parkinson's disease associated α-synuclein (α-syn) aggregation to toxic oligomers by an "off-pathway" mechanism. We show that CP-2 interacts with the N-terminal and the non-amyloid-ß component region of α-syn, which are responsible for α-syn's membrane intercalation and self-assembly, thus changing the overall conformation of α-syn. CP-2 also remodels α-syn fibrils to nontoxic amorphous species and permeates cells through endosomes/lysosomes to reduce the accumulation and toxicity of intracellular α-syn in neuronal cells overexpressing α-syn. Our studies suggest that targeting the common structural conformation of amyloids may be a promising approach for developing new therapeutics for amyloidogenic diseases.

Capillary viscometer for fully automated measurement of the concentration and shear dependence of the viscosity of macromolecular solutions.

The construction and operation of a novel viscometer/rheometer are described. The instrument is designed to measure the viscosity of a macromolecular solution while automatically varying both solute concentration and shear rate. Viscosity is calculated directly from Poiseuille's law, given the measured difference in pressure between two ends of a capillary tube through which the solution is flowing at a known rate. The instrument requires as little as 0.75 mL of a solution to provide a full profile of viscosity as a function of concentration and shear rate, and it can measure viscosities as high as 500 cP and as low as 1 cP, at shear rates between 10 and 2 × 10(3) s(-1). The results of control experiments are presented to document the accuracy and precision of measurement at both low and high concentration of synthetic polymers and proteins.

Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion.

The effect of an inert small molecule osmolyte, trimethyl amine N-oxide (TMAO), upon the conformational equilibria of Escherichia coli adenylate kinase was studied using time-resolved FRET. The relative populations of open and closed clefts between the LID and the CORE domains were measured as functions of the concentrations of the substrate ATP over the concentration range 0-18 mM and TMAO over the concentration range 0-4 M. A model was constructed according to which the enzyme exists in equilibrium among four conformational states, corresponding to combinations of open and closed conformations of the LID-CORE and AMP-CORE clefts. ATP is assumed to bind only to those conformations with the closed LID-CORE cleft, and TMAO is assumed to be differentially excluded as a hard spherical particle from each of the four conformations in accordance with calculations based upon x-ray crystallographic structures. This model was found to describe quantitatively the dependence of the fraction of the closed LID-CORE cleft upon the concentrations of both ATP and TMAO over the entire range of concentrations with just five undetermined parameters.

Point-localized, site-specific membrane potential optical recording by single fluorescent nanodiscs.

Nanodisc technology was implemented as a platform for voltage nanosensors. A fluorescence (Förster) resonance energy transfer (FRET)- based voltage-sensing scheme employing fluorescent nanodiscs and the hydrophobic ion dipicrylamine was developed and utilized to optically record membrane potentials on the single-nanodisc level. Ensemble and single-nanosensor recordings were demonstrated for HEK293 cells and primary cortical neuron cells. Conjugation of nanodiscs to anti-GABAA antibodies allowed for site-specific membrane potential measurements from postsynaptic sites.

Optical probing of local membrane potential with fluorescent polystyrene beads.

The study of electrical activity in single cells and local circuits of excitable cells, such as neurons, requires an easy-to-use, high-throughput methodology that allows for the measurement of membrane potential. Investigating the electrical properties in specific subcompartments of neurons, or in a specific type of neurons, introduces additional complexity. An optical voltage-imaging technique that allows high spatial and temporal resolution could be an ideal solution. However, most valid voltage-imaging techniques are nonspecific. Those that are more site-directed require a lot of preliminary work and specific adaptations, among other drawbacks. Here, we explore a new method for membrane voltage imaging, based on Förster resonance energy transfer between fluorescent polystyrene (FPS) beads and dipicrylamine. Not only has it been shown that fluorescence intensity correlates with membrane potential, but more importantly, the membrane potential from individual particles can be detected. Among other advantages, FPS beads can be synthesized with surface functional groups and can be targeted to specific proteins by conjugation of recognition molecules. Therefore, in the presence of dipicrylamine, FPS beads represent single-particle detectors of membrane potential that can be localized to specific membrane compartments. This new and easily accessible platform for targeted optical voltage imaging can further elucidate the mechanisms of neuronal electrical activity.

The obese phenotype-inducing N82K mutation in human leptin disrupts receptor-binding and biological activity.

A novel homozygous mutation of the leptin gene was recently reported in an Egyptian child and his sister with severe early onset obesity. This mutation results from the substitution of asparagine (AAC) by lysine (AAA) at codon 103 of a non-mature (signal peptide-containing) leptin and corresponds to the N82K mutation in the mature protein. The patient had very low serum leptin levels, raising the question of whether the obese phenotype resulted from low leptin levels or from its lower intrinsic activity. To answer this question, we characterized the functional consequences of the N82K mutation. Wild-type (WT) human leptin was mutated accordingly, expressed in Escherichia coli at high yield, purified to homogeneity as a monomer and compared to WT human leptin prepared by the same methodology. Circular dichroism analysis of the mutated leptin indicated proper refolding and a secondary structure identical to that of the WT human leptin. In contrast to WT human leptin, the N82K mutant did not form a detectable complex with human leptin-binding domain (hLBD) and its binding capacity to hLBD assessed in a nonradioactive receptor-binding assay was at least 500-fold lower than that of WT human leptin. The biological activity of the N82K mutant, tested in two cell bioassays, was reduced by more than three orders of magnitude relative to WT human leptin. Therefore, though the present report does not explain the reason for the low circulating leptin levels it definitely documents that the reported obese phenotype originates not only from low serum leptin levels but also from the N82K mutant's almost total lack of intrinsic leptin activity.

Ratiometric widefield imaging with spectrally balanced detection.

Ratiometric imaging is an invaluable tool for quantitative microscopy, allowing for robust detection of FRET, anisotropy, and spectral shifts of nano-scale optical probes in response to local physical and chemical variations such as local pH, ion composition, and electric potential. In this paper, we propose and demonstrate a scheme for widefield ratiometric imaging that allows for continuous tuning of the cutoff wavelength between its two spectral channels. This scheme is based on angle-tuning the image splitting dichroic beamsplitter, similar to previous works on tunable interference filters. This configuration allows for ratiometric imaging of spectrally heterogeneous samples, which require spectral tunability of the detection path in order to achieve good spectrally balanced ratiometric detection.

Concentration-dependent viscosity of binary and ternary mixtures of nonassociating proteins: measurement and analysis.

Using a recently developed automated viscometer (Grupi, A.; Minton, A. P. Anal. Chem. 2012, 84, 10732-10736), the dependence of solution viscosity upon the concentrations of bovine serum albumin, hen egg ovomucoid, and human fibrinogen have been measured individually and in binary and ternary mixtures over a wide range of compositions and at total concentrations of up to 300 g/L. The concentration dependence of viscosity of all solutions is quantitatively described over the entire range of concentrations and compositions by a semiempirical equation requiring specification of only two composition-independent global parameters per protein.

Segmental conformational disorder and dynamics in the intrinsically disordered protein α-synuclein and its chain length dependence.

Conformational ensembles of fully disordered natural polypeptides represent the starting point of protein refolding initiated by transfer to folding conditions. Thus, understanding the transient properties and dimensions of such peptides under folding conditions is a necessary step in the understanding of their subsequent folding behavior. Such ensembles can also undergo alternative folding and form amyloid structures, which are involved in many neurological degenerative diseases. Here, we performed a structural study of this initial state using time-resolved fluorescence resonance energy transfer analysis of a series of eight partially overlapping double-labeled chain segments of the N-terminal and NAC domains of the α-synuclein molecule. The distributions of end-to-end distance and segmental intramolecular diffusion coefficients were simultaneously determined for eight labeled chain segments. We used the coefficient of variation, C(v), as a measure of the conformational heterogeneity (i.e., structural disorder). With the exception of two segments, the C(v)s were characteristic of a fully disordered state of the chain. Subtle deviations from this behavior at the segment labeled in the NAC domain and the segment at the N termini reflected subtle conformational bias that might be related to the initiation of transition to amyloid aggregates. The chain length dependence of the mean segmental end-to-end distance followed a power law as predicted by Flory, but the dependence was steeper than previously predicted, probably due to the contribution of the excluded volume effect, which is more dominant for shorter-chain segments. The observed intramolecular diffusion coefficients (<10 to ∼25 Çº(2)/ns) are only an order of magnitude lower than the common diffusion coefficients of low molecular weight probes. This diffusion coefficient increased with chain length, probably due to the cumulative contributions of minor bond rotations along the chain. These results gave us a reference both for characteristics of a natural unfolded polypeptide at the moment of initiation of folding and for detection of possible initiation sites of the amyloid transition.

Time-resolved FRET detection of subtle temperature-induced conformational biases in ensembles of α-synuclein molecules.

The α-synuclein (αS) molecule, a polypeptide of 140 residues, is an intrinsically disordered protein that is involved in the onset of Parkinson's disease. We applied time-resolved excitation energy transfer measurements in search of specific deviations from the disordered state in segments of the αS backbone that might be involved in the initiation of aggregation. Since at higher temperatures, the αS molecule undergoes accelerated aggregation, we studied the temperature dependence of the distributions of intramolecular segmental end-to-end distances and their fast fluctuations in eight labeled chain segments of the αS molecule. Over the temperature range of 5-40 °C, no temperature-induced unfolding or folding was detected at the N-terminal domain (residues 1-66) of the αS molecule. The intramolecular diffusion coefficient of the segments' ends relative to each other increased monotonously with temperature. A common very high upper limiting value of ∼25 A²/ns was reached at 40 °C, another indication of a fully disordered state. Three exceptions were two segments with reduced values of the diffusion coefficients (the shortest segment where the excluded volume effect is dominant and the segment labeled in the NAC domain) and a nonlinear cooperative transition in the N-terminal segment. These specific subtle deviations from the common pattern of temperature dependence reflect specific structural constraints that could be critical in controlling the stability of the soluble monomer, or for its aggregation. Such very weak effects might be dominant in determination of the fate of ensembles of disordered polypeptides either to folding or to misfolding.