Membrane-bound alpha-synuclein forms an extended helix: long-distance pulsed ESR measurements using vesicles, bicelles, and rodlike micelles

We apply pulsed dipolar ESR spectroscopy (Ku-band DEER) to elucidate the global conformation of the Parkinson's disease-associated protein, alpha-synuclein (alphaS) bound to small unilamellar phospholipid vesicles, rodlike SDS micelles, or lipid bicelles. By measuring distances as long as approximately 7 nm between introduced pairs of nitroxide spin labels, we show that distances are close to the expectations for a single continuous helix in all cases studied. In particular, we find distances of 7.5 nm between sites 24 and 72; 5.5 nm between sites 24 and 61; and 2 nm between sites 35 and 50. We conclude that alphaS does not retain a "hairpin" structure with two antiparallel helices, as is known to occur with spheroidal micelles, in agreement with our earlier finding that the protein's geometry is determined by the surface topology rather than being constrained by the interhelix linker. While the possibility of local helix discontinuities in the structure of membrane-bound alphaS remains, our data are more consistent with one intact helix. Importantly, we demonstrate that bicelles produce very similar results to liposomes, while offering a major improvement in experimentally accessible distance range and resolution, and thus are an excellent lipid membrane mimetic for the purpose of pulse dipolar ESR spectroscopy.     

Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors

We have constructed molecular models of octameric micelles formed by a recently developed lipopeptide detergent consisting of a single amphipathic alpha-helix coupled to two acyl chains at either end of the helix. The models explain the experimentally observed aggregation behavior of peptides with different acyl chain lengths. The octameric micelles form a unique coiled-coil structure, with the acyl chains in a nearly frozen conformation inside the cylindrical assemblies. Two extreme models with helices either all parallel or in an alternating orientation suggest that the alternating orientation is energetically more favorable. The models suggest several new directions for further diversifying this new class of detergents for the structural studies of membrane proteins.     

Effect of the peptide secondary structure on the peptide amphiphile supramolecular structure and interactions

Bottom-up fabrication of self-assembled nanomaterials requires control over forces and interactions between building blocks. We report here on the formation and architecture of supramolecular structures constructed from two different peptide amphiphiles. Inclusion of four alanines between a 16-mer peptide and a 16 carbon long aliphatic tail resulted in a secondary structure shift of the peptide headgroups from α helices to β sheets. A concomitant shift in self-assembled morphology from nanoribbons to core-shell worm-like micelles was observed by cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). In the presence of divalent magnesium ions, these a priori formed supramolecular structures interacted in distinct manners, highlighting the importance of peptide amphiphile design in self-assembly.     

Sexual attraction in the silkworm moth: structure of the pheromone-binding-protein-bombykol complex

BACKGROUND: Insects use volatile organic molecules to communicate messages with remarkable sensitivity and specificity. In one of the most studied systems, female silkworm moths (Bombyx mori) attract male mates with the pheromone bombykol, a volatile 16-carbon alcohol. In the male moth's antennae, a pheromone-binding protein conveys bombykol to a membrane-bound receptor on a nerve cell. The structure of the pheromone-binding protein, its binding and recognition of bombykol, and its full role in signal transduction are not known. RESULTS: The three-dimensional structure of the B. mori pheromone-binding protein with bound bombykol has been determined by X-ray diffraction at 1.8 A resolution. CONCLUSIONS: The pheromone binding protein of B. mori has six helices, and bombykol binds in a completely enclosed hydrophobic cavity formed by four antiparallel helices. Bombykol is bound in this cavity through numerous hydrophobic interactions, and sequence alignments suggest critical residues for specific pheromone binding.     

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.     

ABC三嵌段共聚物胶束从多间隔结构到多核结构转变的Monte Carlo模拟

采用Monte Carlo模拟方法研究了疏水-亲水-疏水(H-P-H)型ABC三嵌段共聚物在B嵌段的选择性溶剂中的自组装行为. 模拟结果表明, 通过调节A嵌段和C嵌段的疏水性和二者之间的不相容性, 体系中可以形成多种形貌各异的胶束. 根据胶束中疏水核结构的特点, 这些胶束大体上可以被分为多核型胶束和多间隔型胶束两种类型. 通过增强疏水嵌段的疏水性或降低A嵌段和C嵌段间的不相容性, H-P-H型ABC三嵌段共聚物胶束能够发生从多核型胶束向多间隔型胶束的转变. 进一步分析胶束中聚合物的链构象等微观结构信息发现, A嵌段和C嵌段间的排斥作用和疏水作用之间存在竞争关系, 而这种竞争关系是影响体系中形成多核型胶束还是多间隔型胶束的决定性因素.     

The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel

Protein folding is a dynamic process with continuous transitions among different conformations. In this work, the dynamics in the protein folding network of villin headpiece subdomain (HP35) has been investigated based on multiple reversible folding trajectories of HP35 and its ultrafast folding mutant where sub-angstrom folding was achieved. The four folding states were clearly separated on the network, validating the classification of the states. Examination of the eight conformers with different formation of the individual helices revealed high plasticity of the three helices in all the four states. A consistent feature between the wild type and mutant protein is the dominant conformer 111 (all three helices formed) in the folded state and conformers 111 and 011 (helices II and III formed) in the major intermediate state, indicating the critical role of helices II and III in the folding mechanism. When compared to the wild type, the folding landscape of the ultrafast folding mutant exhibited a deeper folding funnel towards the folded state. The very beginning of the folding (0-10 ns) was very similar for both protein variants but it soon diverged and displayed different folding pathways. Although going through the major intermediate state is the dominant pathway for both, it was also observed that some folding went through the minor intermediate state for the mutant. The intriguing difference resulting from the mutation at two residues in helix III has been carefully analyzed and discussed in details.     

Effect of temperature on self-assembly of bovine beta-casein above and below isoelectric pH. Structural analysis by cryogenic-transmission electron microscopy and small-angle X-ray scattering

beta-Casein is one of the main proteins in milk, recently classified as an intrinsically unstructured protein. At neutral pH, it is composed of a highly polar N-terminus domain and a hydrophobic C-terminus tail. This amphiphilic block-copolymer-like structure leads to self-organization of the protein monomers into defined micelles. Recently, it has been shown that at room temperature, beta-casein also self-organizes into micelles in an acidic environment, but the effect of temperature on the micelles' formation and properties at the low pH regime were not explored. In the present study, we used two complementary techniques, cryogenic-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS), to characterize at high-resolution the micelles' shape, dimensions, and aggregation numbers and to determine how these properties are affected by temperature between 1 and 40 degrees C. Two different regimes were studied: highly acidic pH where the protein is cationic, and neutral pH, where it is anionic. We found that flat disk-like micelles with low aggregation numbers formed at low temperature in the two pH regimes. Close to neutral pH increase in temperature involves a transition in the micelles' shape and dimensions from flat disks to bulky, almost spheroidal micelles, coupled with a sharp increase in the micelles' aggregation number. In contrast, no effects on the micelles' morphology or aggregation number were detected in the acidic environment within the entire temperature range studied. The self-organization into disk micelles and the lack of effect of temperature in the acidic environment are linked to the unstructured character of the protein and to the charge distribution map. The latter indicates that below the isoelectric pH (pI), beta-casein loses the distinct separation of hydrophobic and hydrophilic domains, thereby suggesting that it may no longer be considered as a classical head-tail block-copolymer amphiphile as in neutral pH.     

Binding of sodium dodecyl sulfate and hexaethylene glycol mono-n-dodecyl ether to the block copolymer L64: electromotive force, microcalorimetry, surface tension, and small angle neutron scattering investigations of mixed micelles and polymer/micellar surfactant complexes

The interactions of sodium dodecyl sulfate (SDS) with the triblock copolymer L64 (EO13-PO30-EO13) and hexaethylene glycol mono-n-dodecyl ether (C12EO6) were studied using electromotive force, isothermal titration microcalorimetry, differential scanning microcalorimetry, and surface tension measurements. In certain regions of binding, mixed micelles are formed, and here we could evaluate an interaction parameter using regular solution theory. The mixed micelles of L64 with both SDS and C12EO6 exhibit synergy. When L64 is present in its nonassociated state, it forms polymer/micellar SDS complexes at SDS concentrations above the critical aggregation concentration (cac). The cac is well below the critical micellar concentration (cmc) of pure SDS, and a model suggesting how bound micelles are formed at the cac in the presence of a polymer is described. The interaction of nonassociated L64 with C12EO6 is a very rare example of strong binding between a nonionic surfactant and a nonionic polymer, and C12EO6/L64 mixed micelles are formed. We also carried out small angle neutron scattering measurement to determine the structure of the monomeric polymer/micellar SDS complex, as well as the mixed L64/C12EO6 aggregates. In these experiments, contrast matching was achieved by using the h and d forms of SDS, as well as C12EO6. During the early stages of the formation of polymer-bound SDS micelles, SDS aggregates with aggregation numbers of approximately 20 were found and such complexes contain 4-6 bound L64 monomers. The L64/C12EO6 data confirmed the existence of mixed micelles, and structural information involving the composition of the mixed micelle and the aggregation numbers were evaluated.     

Glycopeptides related to beta-endorphin adopt helical amphipathic conformations in the presence of lipid bilayers

A series of glycosylated endorphin analogues designed to penetrate the blood-brain barrier (BBB) have been studied by circular dichroism and by 2D-NMR in the presence of water; TFE/water; SDS micelles; and in the presence of both neutral and anionic bicelles. In water, the glycopeptides showed only nascent helix behavior and random coil conformations. Chemical shift indices and nuclear Overhauser effects (NOE) confirmed helices in the presence of membrane mimics. NOE volumes provided distance constraints for molecular dynamics calculations used to provide detailed backbone conformations. In all cases, the glycopeptides were largely helical in the presence of membrane bilayer models (micelles or bicelles). Plasmon waveguide resonance (PWR) studies showed hen egg phosphatidyl choline (PC) bilayers produce amphipathic helices laying parallel to the membrane surface, with dissociation constants (K(D)) in the low nanomolar to micromolar concentration range. Two low-energy states are suggested for the glycosylated endorphin analogues, a flexible aqueous state and a restricted membrane bound state. Strong interactions between the glycopeptide amphipaths and membranes are crucial for penetration of the BBB via an endocytotic mechanism (transcytosis).     

Effect of particle surface selectivity on composite nanostructures in nanoparticle/diblock copolymer mixture dilute solution

In this study the phase behavior of nanoparticle/diblock copolymer composites in dilute solution has been investigated by the hybrid particle-field (HPF) method. We focus on the influence of particle surface selectivity (i.e. hydrophobic and hydrophilic) on the distribution of nanoparticles in the micelles formed by the diblock copolymers. These two types of particle surface selectivity are simulated systematically. The different competition between the energy from enthalpy and the energy from entropy has been observed in the two kinds of composite systems. Our simulation results show that the particle surface selectivity is a crucial factor for determining the thermodynamic properties in the complex dilute solution, and the morphologies of micelles are controlled by the volume fraction of the nanoparticles. The change of particle distribution in various micelles enriches the composite microstructures that can be formed by nanoparticle and diblock copolymer.     

THE EFFECT OF POLYMER ON THE CLOUD POINT OF A SERIES OF TRIBLOCK NONIONIC SURFACTANTS IN AQUEOUS SOLUTION

A series of triblock nonionic surfactants with different Propylene oxide and ethylene oxide chain lengths were synthesized. The triblock nonionic surfactants and poly(ethylene glycols) with different molecular weight were used, to find the effects of polymer chain length and size of the micelles on the cloud point of the surfactants. Two possible models are considered on the basis of cloud point changes of the solutions, to describe the polymer- surfactant interactions. One model suggests that flocculation depletion for the polymer chains exist between two regular micelles. This provides the driving force for the neighboring micelles to approach each other and destabilize the colloidal system. The flocculation effect is more important for polymers with a shorter chain block the approach of the micelles, since there is no typical polymer-surfactant association formed but just simple small molecule associations in which the steric and solvation effects of the polymer chains make the inter-micelles interactions repulsive. The other model considers that intra-chain micelles of polysoap are formed among the surfactant monomers and long polymer chains. The bridging attraction between two intra-chain micelles in such structures can enhance the collisions among the micelles, due to the exchange of amphiphilic monomers among the neighboring micelles.     

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.     

Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor

G‐protein‐coupled receptor (GPCR) ligands impart differing degrees of signaling in the G‐protein and arrestin pathways, in phenomena called “biased signaling”. However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ‐opioid receptor (μOR) in the balanced‐ and biased‐ligand‐bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G‐protein‐ and arrestin‐mediated signaling levels in each ligand‐bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.     

Self-assembly of mixed anionic and nonionic surfactants in aqueous solution

We present the phase diagram and the microstructure of the binary surfactant mixture of AOT and C(12)E(4) in D(2)O as characterized by surface tension and small angle neutron scattering. The micellar region is considerably extended in composition and concentration compared to that observed for the pure surfactant systems, and two types of aggregates are formed. Spherical micelles are present for AOT-rich composition, whereas cylindrical micelles with a mean length between 80 and 300 ? are present in the nonionic-rich region. The size of the micelles depends on both concentration and molar ratio of the surfactant mixtures. At higher concentration, a swollen lamellar phase is formed, where electrostatic repulsions dominate over the Helfrich interaction in the mixed bilayers. At intermediate concentrations, a mixed micellar/lamellar phase exists.     

Broad distribution of energetically important contacts across an extended protein interface

Infection of cells by HIV depends upon profound structural rearrangements within the trimeric viral protein gp41. Critical to this process is the formation of a six-helix bundle in which a set of three N-terminal heptad repeat (NHR) helices assemble to form a core displaying long grooves that provide docking sites for three C-terminal heptad repeat (CHR) helices. We report experiments designed to discriminate between two alternative hypotheses regarding the source of affinity between individual CHR helices and the complementary groove: (1) affinity is dominated by interactions of a small cluster of side chains at one end of the CHR helix; or (2) affinity depends upon interactions distributed across the long CHR helix. We have employed two complementary experimental designs, and results from both favor the latter hypothesis.     

Surfactant/nonionic copolymer interaction: a SLS, DLS, ITC, and NMR investigation

The interactions between an oxyphenylethylene-oxyethylene nonionic diblock copolymer with the anionic surfactant sodium dodecyl sulfate (SDS) have been studied in dilute aqueous solutions by static and dynamic light scattering (SLS and DLS, respectively), isothermal titration calorimetry (ITC), and 13C and self-diffusion nuclear magnetic resonance techniques. The studied copolymer, S20E67, where S denotes the hydrophobic styrene oxide unit and E the hydrophilic oxyethylene unit, forms micelles of 15.6 nm at 25 degrees C, whose core is formed by the styrene oxide chains surrounded by a water swollen polyoxyethylene corona. The S20E67/SDS system has been investigated at a copolymer concentration of 2.5 g dm(-3), for which the copolymer is fully micellized, and with varying surfactant concentration up to approximately 0.15 M. When SDS is added to the solution, two different types of complexes are observed at various surfactant concentrations. From SLS and DLS it can be seen that, at low SDS concentrations, a copolymer-rich surfactant mixed micelle or complex is formed after association of SDS molecules to block copolymer micelles. These interactions give rise to a strong decrease in both light scattering intensity and hydrodynamic radius of the mixed micelles, which has been ascribed to an effective reduction of the complex size, and also an effect arising from the increasing electrostatic repulsion of charged surfactant-copolymer micelles. At higher surfactant concentrations, the copolymer-rich surfactant micelles progressively are destroyed to give surfactant-rich-copolymer micelles, which would be formed by a surfactant micelle bound to one or very few copolymer unimers. ITC data seem to confirm the results of light scattering, showing the dehydration and rehydration processes accompanying the formation and subsequent destruction of the copolymer-rich surfactant mixed micelles. The extent of interaction between the copolymer and the surfactant is seen to involve as much as carbon 3 (C3) of the SDS molecule. Self-diffusion coefficients corroborated light scattering data.     

The interaction between triton X series surfactants and poly (ethylene glycol) in aqueous solutions

 A series of Triton X surfactants with different ethylene oxide chain length and poly(ethylene glycols) with different molecular weight were used, to find the effects of polymer chain length and size of the micelles on the cloud point of the surfactants. Two possible models are considered on the basis of cloud point changes of the solutions, to describe the polymer–surfactant interactions. One model considers that intra-chain micelles of polysoap are formed among the surfactant monomers and long polymer chains. The bridging attraction between two intra-chain micelles in such structures can enhance the collisions among the micelles, due to the exchange of amphiphilic monomers among the neighboring micelles. The other model suggests that flocculation depletion for the polymer chains exists between two regular micelles. This provides the driving force for the neighboring micelles to approach each other and destabilize the colloidal system. The flocculation effect is more significant for polymer with a long chain. Polymers with a shorter chain block the approach of the micelles, since there is no typical polymer–surfactant association formed but just simple small molecule associations in which the steric and solvation effects of the polymer chains make the inter-micelle interactions repulsive. Received: 19 August 1997 Accepted: 11 December 1997     

Interaction between casein and sodium dodecyl sulfate

The interaction of the anionic surfactant sodium dodecyl sulfate (SDS) with 2.0 mg/ml casein was first investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), and fluorescence spectra. ITC results show that individual SDS molecules first bind to casein micelles by the hydrophobic interaction. The micelle-like SDS aggregate is formed on the casein chains when SDS concentration reaches the critical aggregation concentration (c1), which is far below the critical micellar concentration (cmc) of SDS in the absence of casein. With the further increase of SDS concentration to the saturate binding concentration c2, SDS molecules no longer bind to the casein chains, and free SDS micelles coexist with casein micelles bound with SDS aggregates in the system. DLS results show that the addition of SDS leads to an increase in the hydrodynamic radius of casein micelles with bound surfactant at SDS concentration higher than 4 mM, and also an increase in the casein monomer molecule (or submicelles) at SDS concentration higher than 10 mM. Fluorometric results suggest the addition of SDS leads to some changes in the binding process of hydrophobic probes to casein micelles.