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Betaglycan (BG) is a membrane-bound co-receptor of the TGF-β family that selectively binds transforming growth factor-β (TGF-β) isoforms and inhibin A (InhA) to enable temporal-spatial patterns of signaling essential for their functions in vivo. Here, using NMR titrations of methyl-labeled TGF-β2 with BG's C-terminal binding domain, BG(ZP-C), and surface plasmon resonance binding measurements with TGF-β2 variants, we found that the BG(ZP-C)–binding site on TGF-β2 is located on the inner surface of its extended finger region. Included in this binding site are Ile-92, Lys-97, and Glu-99, which are entirely or mostly specific to the TGF-β isoforms and the InhA α-subunit, but they are unconserved in other TGF-β family growth factors (GFs). In accord with the proposed specificity-determining role of these residues, BG bound bone morphogenetic protein 2 (BMP-2) weakly or not at all, and TGF-β2 variants with the corresponding residues from BMP-2 bound BG(ZP-C) more weakly than corresponding alanine variants. The BG(ZP-C)–binding site on InhA previously was reported to be located on the outside of the extended finger region, yet at the same time to include Ser-112 and Lys-119, homologous to TGF-β2 Ile-92 and Lys-97, on the inside of the fingers. Therefore, it is likely that both TGF-β2 and InhA bind BG(ZP-C) through a site on the inside of their extended finger regions. Overall, these results identify the BG(ZP-C)–binding site on TGF-β2 and shed light on the specificity of BG for select TGF-β–type GFs and the mechanisms by which BG influences their signaling.

International audience; A pathological hallmark of Huntington's disease (HD) is the formation of neuronal protein deposits containing mutant huntingtin fragments with expanded polyglutamine (polyQ) domains. Prior studies have shown the strengths of solid-state NMR (ssNMR) to probe the atomic structure of such aggregates, but have required in vitro isotopic labeling. Herein, we present an approach for the structural fingerprinting of fibrils through ssNMR at natural isotopic abundance (NA). These methods will enable the spectroscopic fingerprinting of unlabeled (e.g., ex vivo) protein aggregates and the extraction of valuable new long-range 13 C− 13 C distance constraints

It has been long assumed that post-mitotic neurons only utilize the error-prone non-homologous end–joining pathway to repair double-strand breaks (DSBs) associated with oxidative damage to DNA, given the inability of non-replicating neuronal DNA to utilize a sister chromatid template in the less error-prone homologous recombination (HR) repair pathway. However, we and others have found recently that active transcription triggers a replication-independent recombinational repair mechanism in G0/G1 phase of the cell cycle. Here we observed that the HR repair protein RAD52 is recruited to sites of DNA DSBs in terminally differentiated, post-mitotic neurons. This recruitment is dependent on the presence of a nascent mRNA generated during active transcription, providing evidence that an RNA-templated HR repair mechanism exists in non-dividing, terminally differentiated neurons. This recruitment of RAD52 in neurons is decreased by transcription inhibition. Importantly, we found that high concentrations of amyloid β, a toxic protein associated with Alzheimer's disease, inhibits the expression and DNA damage response of RAD52, potentially leading to a defect in the error-free, RNA-templated HR repair mechanism. This study shows a novel RNA-dependent repair mechanism of DSBs in post-mitotic neurons and demonstrates that defects in this pathway may contribute to neuronal genomic instability and consequent neurodegenerative phenotypes such as those seen in Alzheimer's disease.

ATP-binding cassette transporter A1 (ABCA1) mediates cholesterol efflux to lipid-free apolipoproteins and regulates the generation of high density lipoproteins. Previously, we have shown that lack of Abca1 significantly increases amyloid deposition and cognitive deficits in Alzheimer's disease model mice expressing human amyloid-β protein precursor (APP). The goal of this study was to determine if ABCA1 plays a role in memory deficits caused by amyloid-β (Aβ) oligomers and examine neurite architecture of pyramidal hippocampal neurons. Our results confirm previous findings that Abca1 deficiency significantly impairs spatial memory acquisition and retention in the Morris water maze and long-term memory in novel object recognition of APP transgenic mice at a stage of early amyloid pathology. Neither test demonstrated a significant difference between Abca1ko and wild-type (WT) mice. We also examined the effect of intra-hippocampal infused Aβ oligomers on cognitive performance of Abca1ko mice, compared to control infusion of scrambled Aβ peptide. Age-matched WT mice undergoing the same infusions were also used as controls. In this model system, we found a statistically significant difference between WT and Abca1ko mice infused with scrambled Aβ, suggesting that Abca1ko mice are vulnerable to the effect of mild stresses. Moreover, examination of neurite architecture in the hippocampi revealed a significant decrease in neurite length, number of neurite segments, and branches in Abca1ko mice when compared to WT mice. We conclude that mice lacking ABCA1 have basal cognitive deficits that prevent them from coping with additional stressors, which is in part due to impairment of neurite morphology in the hippocampus.

The cellular process of intrinsic apoptosis relies on the peroxidation of mitochondrial lipids as a critical molecular signal. Lipid peroxidation is connected to increases in mitochondrial reactive oxygen species, but there is also a required role for mitochondrial cytochrome c (cyt-c). In apoptotic mitochondria, cyt-c gains a new function as a lipid peroxidase that catalyzes the reactive oxygen species-mediated chemical modification of the mitochondrial lipid cardiolipin (CL). This peroxidase activity is caused by a conformational change in the protein, resulting from interactions between cyt-c and CL. The nature of the conformational change and how it causes this gain-of-function remain uncertain. Via a combination of functional, structural, and biophysical experiments we investigate the structure and peroxidase activity of cyt-c in its membrane-bound state. We reconstituted cyt-c with CL-containing lipid vesicles, and determined the increase in peroxidase activity resulting from membrane binding. We combined these assays of CL-induced proapoptotic activity with structural and dynamic studies of the membrane-bound protein via solid-state NMR and optical spectroscopy. Multidimensional magic angle spinning (MAS) solid-state NMR of uniformly 13C,15N-labeled protein was used to detect site-specific conformational changes in oxidized and reduced horse heart cyt-c bound to CL-containing lipid bilayers. MAS NMR and Fourier transform infrared measurements show that the peripherally membrane-bound cyt-c experiences significant dynamics, but also retains most or all of its secondary structure. Moreover, in two-dimensional and three-dimensional MAS NMR spectra the CL-bound cyt-c displays a spectral resolution, and thus structural homogeneity, that is inconsistent with extensive membrane-induced unfolding. Cyt-c is found to interact primarily with the membrane interface, without significantly disrupting the lipid bilayer. Thus, membrane binding results in cyt-c gaining the increased peroxidase activity that represents its pivotal proapoptotic function, but we do not observe evidence for large-scale unfolding or penetration into the membrane core.

Passive amyloid-β (Aβ) vaccination has shown significant effects on amyloid pathology in pre-depositing amyloid-β protein precursor (AβPP) mice but the results in older mice are inconsistent. A therapeutic effect of LXR and RXR agonists consisting of improved memory deficits and Aβ pathology has been demonstrated in different Alzheimer's disease (AD) mouse models. Here, we report the effect of a combination of N-terminal Aβ antibody and synthetic LXR agonist T0901317 (T0) on AD-like phenotype of APP23 mice. To examine the therapeutic potential of this combination, the treatment of mice started at 11 months of age, when amyloid phenotype in this model is fully developed, and continued for 50 days. We show that Aβ immunization with or without LXR agonist restored the performance of APP23 transgenic mice in two behavior paradigms without affecting the existing amyloid plaques. Importantly, we did not observe an increase of brain microhemorrhage which is considered a significant side effect of Aβ vaccination. Target engagement was confirmed by increased Abca1 and ApoE protein level as well as increased ApoE lipidation in soluble brain extract. In interstitial fluid obtained by microdialysis, we demonstrate that immunization and T0 significantly reduced Aβ levels, indicating an increased Aβ clearance. We found no interaction between the immunotherapy and T0, suggesting no synergism, at least with these doses. The results of our study demonstrate that anti-Aβ treatments can ameliorate cognitive deficits in AβPP mice with advanced AD-like phenotype in conjunction with a decrease of Aβ in brain interstitium and increase of ApoE lipidation without affecting the existing amyloid plaques.

Many amyloidogenic peptides are highly hydrophobic, introducing significant challenges to obtaining high quality peptides by chemical synthesis. For example, while good yield and purity can be obtained in the solid phase synthesis of the Alzheimer’s plaque peptide Aβ40, addition of a C-terminal Ile-Ala sequence to generate the more toxic Aβ42 molecule creates a much more difficult synthesis resulting in low yields and purities. We describe here a new method that significantly improves the Fmoc solid phase synthesis of Aβ peptides. In our method, Lys residues are linked to the desired peptide’s C-terminus through standard peptide bonds during the synthesis. These Lys residues are then removed post-purification using immobilized carboxypeptidase B. With this method we obtained both Aβ42 and Aβ46 of superior quality that, for Aβ42, rivals that obtained by recombinant expression. Intriguingly, the method appears to provide independent beneficial effects on both the total synthetic yield and on purification yield and final purity. Reversible Lys addition with carboxypeptidase B removal should be a generally useful method for making hydrophobic peptides that is applicable to any sequence not ending in Arg or Lys. As expected from the additional hydrophobicity of Aβ46, which is extended from the sequence Aβ42 by a C-terminal Thr-Val-Ile-Val sequence, this peptide makes typical amyloid at rates significantly faster than for Aβ42 or Aβ40. The enhanced amyloidogenicity of Aβ46 suggests that, even though it is present in relatively low amounts in the human brain, it could play a significant role in helping to initiate Aβ amyloid formation.

Protein aggregation and/or amyloid formation is an important intrinsic constraint on protein sequence evolution1–4, the focus of a variety of cellular housekeeping operations5, a significant challenge in biotechnology6–9 and a component of the molecular mechanisms of a number of important human neurodegenerative diseases10,11. Significant effort has been expended in developing an understanding of the molecular determinants of protein aggregation, and in particular in devising algorithms that might be predictive for the propensity of amino acid sequences to aggregate12–20. The fundamental approaches taken in both the development of these algorithms and their validation differ considerably. Empirical assessments of these algorithms have been limited, however, and, where attempted, have in some cases been restricted to amino acid compositions that are highly favorable in promoting aggregation. Recently, we defined several contributions of the short, 17-amino acid peptide segment called httNT, which is located at the N-terminus of the Huntington's disease protein huntingtin (htt), to spontaneous amyloid formation by N-terminal fragments of htt such as htt exon121–26. For example, we found that the httNT segment, as part of exon1-like fragments, greatly enhances nucleation of amyloid growth by the adjacent polyglutamine (polyQ) segment, without itself becoming incorporated into amyloid21–23. We also found that the httNT sequence alone, as a separate peptide, is an effective, if transient, inhibitor of amyloid nucleation by exon1-like fragments25. As part of an effort to determine the molecular basis for this inhibition, we generated a series of scrambled variants of the httNTQ sequence25. Most of these sequences were well-behaved under our experimental conditions and could be evaluated as inhibitors in our experiments. Some of them could not be evaluated, however, because they themselves undergo efficient spontaneous growth of β-aggregates under our experimental conditions. This was especially intriguing because the WT httNT sequence by itself aggregates very slowly and only at high concentrations, and then only to form α-helix rich oligomers22,23. It struck us that the behavior of this set of scrambled peptides might serve as a good test for how well previously described amyloid prediction algorithms can predict facile amyloid formation in a novel series of sequences not designed for that purpose. In this paper we report the spontaneous aggregation tendencies of the full set of scrambled sequences and evaluate how well a number of recently described predictive algorithms are able to distinguish aggregating peptides from peptides that remain soluble under physiological conditions. The results show that the available algorithms are only modestly successful at predicting amyloid propensity under conditions approaching physiological. In fact, it is not clear that any of these algorithms is capable of evaluating kinetics constraints on amyloid formation, even among sequences that might be capable of achieving snug steric zipper27, amyloid-like packing arrangements.

The transforming growth factor β isoforms, TGF-β1, -β2, and -β3, are small secreted homodimeric signaling proteins with essential roles in regulating the adaptive immune system and maintaining the extracellular matrix. However, dysregulation of the TGF-β pathway is responsible for promoting the progression of several human diseases, including cancer and fibrosis. Despite the known importance of TGF-βs in promoting disease progression, no inhibitors have been approved for use in humans. Herein, we describe an engineered TGF-β monomer, lacking the heel helix, a structural motif essential for binding the TGF-β type I receptor (TβRI) but dispensable for binding the other receptor required for TGF-β signaling, the TGF-β type II receptor (TβRII), as an alternative therapeutic modality for blocking TGF-β signaling in humans. As shown through binding studies and crystallography, the engineered monomer retained the same overall structure of native TGF-β monomers and bound TβRII in an identical manner. Cell-based luciferase assays showed that the engineered monomer functioned as a dominant negative to inhibit TGF-β signaling with a Ki of 20–70 nm. Investigation of the mechanism showed that the high affinity of the engineered monomer for TβRII, coupled with its reduced ability to non-covalently dimerize and its inability to bind and recruit TβRI, enabled it to bind endogenous TβRII but prevented it from binding and recruiting TβRI to form a signaling complex. Such engineered monomers provide a new avenue to probe and manipulate TGF-β signaling and may inform similar modifications of other TGF-β family members.

Since early oligomeric intermediates in amyloid assembly are often transient and difficult to distinguish, characterize and quantify, the mechanistic basis of the initiation of spontaneous amyloid growth is often opaque. We describe here an approach to the analysis of the Aβ aggregation mechanism that uses Aβ-polyglutamine hybrid peptides designed to retard amyloid maturation and an adjusted thioflavin intensity scale that reveals structural features of aggregation intermediates. The results support an aggregation initiation mechanism for Aβ-polyQ hybrids, and by extension for full-length Aβ peptides, in which a modular Aβ C-terminal segment mediates rapid, non-nucleated formation of α-helical oligomers. The resulting high local concentration of tethered amyloidogenic segments within these α-oligomers facilitates transition to a β-oligomer population that, via further remodelling and/or elongation steps, ultimately generates mature amyloid. Consistent with this mechanism, an engineered Aβ C-terminal fragment delays aggregation onset by Aβ-polyglutamine peptides and redirects assembly of Aβ42 fibrils., The elucidation of amyloid nucleation mechanisms remains challenging as early oligomeric intermediates are transient and difficult to distinguish. Here the authors use Aβ- polyglutamine hybrid peptides designed to slow and limit amyloid maturation to provide insights into the structures of Aβ self-assembly intermediates.

The 17-amino-acid N-terminal segment (htt(NT)) that leads into the polyglutamine (polyQ) segment in the Huntington's disease protein huntingtin (htt) dramatically increases aggregation rates and changes the aggregation mechanism, compared to a simple polyQ peptide of similar length. With polyQ segments near or above the pathological repeat length threshold of about 37, aggregation of htt N-terminal fragments is so rapid that it is difficult to tease out mechanistic details. We describe here the use of very short polyQ repeat lengths in htt N-terminal fragments to slow this disease-associated aggregation. Although all of these peptides, in addition to htt(NT) itself, form α-helix-rich oligomeric intermediates, only peptides with Q(N) of eight or longer mature into amyloid-like aggregates, doing so by a slow increase in β-structure. Concentration-dependent circular dichroism and analytical ultracentrifugation suggest that the htt(NT) sequence, with or without added glutamine residues, exists in solution as an equilibrium between disordered monomer and α-helical tetramer. Higher order, α-helix rich oligomers appear to be built up via these tetramers. However, only htt(NT)Q(N) peptides with N=8 or more undergo conversion into polyQ β-sheet aggregates. These final amyloid-like aggregates not only feature the expected high β-sheet content but also retain an element of solvent-exposed α-helix. The α-helix-rich oligomeric intermediates appear to be both on- and off-pathway, with some oligomers serving as the pool from within which nuclei emerge, while those that fail to undergo amyloid nucleation serve as a reservoir for release of monomers to support fibril elongation. Based on a regular pattern of multimers observed in analytical ultracentrifugation, and a concentration dependence of α-helix formation in CD spectroscopy, it is likely that these oligomers assemble via a four-helix assembly unit. PolyQ expansion in these peptides appears to enhance the rates of both oligomer formation and nucleation from within the oligomer population, by structural mechanisms that remain unclear.

TGF-β1, TGF- β2, and TGF-β3 are 26 kDa disulfide-linked homodimeric signaling proteins. They all signal through the TGF-β type I and type II receptors, yet TGF-β2, which is well known to bind TβRII several-hundred fold more weakly than TGF-β1 and TGF-β3, has an additional requirement for the TGF-β type III receptor (TβRIII), a membrane-anchored non-signaling receptor that potentiates the binding of TβRII. Though it is known that TβRIII has two component domains that bind TGF-β2 non-cooperatively at independent sites, the structure of these domains bound to TGF-β2 and residues responsible for specific binding are not yet known.

The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domain-swapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in “domain-swapping” fibrils. We discuss these observations in light of recent work on related amyloid-forming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.

The aggregation of polyglutamine containing protein sequences is implicated in a family of familial neurodegenerative diseases, the expanded CAG repeat diseases. While the cellular aggregation process undoubtedly depends on the flux and local environment of these proteins, their intrinsic physical properties and folding/aggregation propensities must also contribute to their cellular behavior. Here we describe a series of methods for determining mechanistic details of the spontaneous aggregation of polyQ-containing sequences, including the identification and structural examination of aggregation intermediates.

A hallmark of Alzheimer disease (AD) is the deposition of amyloid β (Aβ) in brain parenchyma and cerebral blood vessels, accompanied by cognitive decline. Previously, we showed that human apolipoprotein A-I (apoA-I) decreases Aβ(40) aggregation and toxicity. Here we demonstrate that apoA-I in lipidated or non-lipidated form prevents the formation of high molecular weight aggregates of Aβ(42) and decreases Aβ(42) toxicity in primary brain cells. To determine the effects of apoA-I on AD phenotype in vivo, we crossed APP/PS1ΔE9 to apoA-I(KO) mice. Using a Morris water maze, we demonstrate that the deletion of mouse Apoa-I exacerbates memory deficits in APP/PS1ΔE9 mice. Further characterization of APP/PS1ΔE9/apoA-I(KO) mice showed that apoA-I deficiency did not affect amyloid precursor protein processing, soluble Aβ oligomer levels, Aβ plaque load, or levels of insoluble Aβ in brain parenchyma. To examine the effect of Apoa-I deletion on cerebral amyloid angiopathy, we measured insoluble Aβ isolated from cerebral blood vessels. Our data show that in APP/PS1ΔE9/apoA-I(KO) mice, insoluble Aβ(40) is increased more than 10-fold, and Aβ(42) is increased 1.5-fold. The increased levels of deposited amyloid in the vessels of cortices and hippocampi of APP/PS1ΔE9/apoA-I(KO) mice, measured by X-34 staining, confirmed the results. Finally, we demonstrate that lipidated and non-lipidated apoA-I significantly decreased Aβ toxicity against brain vascular smooth muscle cells. We conclude that lack of apoA-I aggravates the memory deficits in APP/PS1ΔE9 mice in parallel to significantly increased cerebral amyloid angiopathy.

The aggregated, β-sheet rich amyloid structure represents a stable, alternatively folded state of polypeptides. Amyloid fibrils are associated with several important neurodegenerative diseases, such as Alzheimer’s and Huntington’s diseases 1, as well as a number of peripheral diseases of organ failure 2. Amyloid fibrils can be produced in vitro from many proteins, consistent with the polymeric structure of proteins and the relationship of amyloid fibrils to synthetic polymers 3. The fundamental unit of amyloid fibrils is the cross-β structure, in which β-sheet extended chains and sheet-sheet stacking interactions are perpendicular to the fibril axis and β-sheet H-bonds are parallel to the fibril axis 4. Details of the three-dimensional structures of amyloid fibrils are still being elucidated 5; 6; 7; 8; 9; 10; 11; 12 One striking feature of amyloid fibrils that sets them apart from most globular proteins is the ability of a single polypeptide chain to grow into more than one stable structure 13. The existence of multiple protein aggregate conformations, each of which can propagate with retention of structure, has long been speculated to be the basis for strain and species barrier effects in mammalian and yeast prion biology 14; 15. Polymorphism at the electron microscopy level, for example in Aβ amyloid fibrils 16; 17, has been known for some time, but it has not been clear whether these shape differences were due merely to different modes of super-assembly of a common protofilament structure, or to more substantial internal structural differences, such as β-sheet formation and side-chain packing. Previous solid state NMR and electron microscopy analyses suggest that the folded structures of Aβ(1–40) in two polymorphic amyloid fibrils are only modestly different, while the major structural differences are in how the folded peptides pack within the fibril cross-section 9; 18. Analysis of amyloid polymorphs of other protein sequences, however, suggests the possibility of polymorphic structures differing more extensively in the details of segmental folding, H-bonding and packing within the fibril 13; 19, and this is further suggested by the different manners in which sequence-related fragments from amyloid proteins pack within “β-spine” crystal structures 6. Polymorphism in amyloid fibrils may have profound biological consequences. It has been demonstrated that different polymorphic yeast prion fibrils generated in vitro produce different prion strain behavior when these are introduced into yeast 20; 21. Two structurally and functionally different polymorphic fibrils have been generated by exposing Aβ(1–40) to different growth conditions in vitro 22, and the identification of a third polymorphic form produced by elongation of Aβ peptides in vitro using fibrils extracted from AD brain 23 supports the idea that fibril polymorphism may contribute to variations within human diseases. In this paper we describe the creation of five self-propagating amyloid fibril structures by subjecting wild type Aβ(1–40) to different trial growth conditions. These Aβ(1–40) polymorphic fibrils vary considerably in structural properties. In particular, we find that amyloid polymorphs exhibit significant differences in the extent and locations of stable β-sheet, as probed by the number of backbone amides highly protected from hydrogen-deuterium exchange. We find that fibril stabilities assessed by their free energies of elongation 24 correlate extremely well with these β-sheet contents, consistent with the central role of β-sheet in fibril structure. The results illustrate the facility with which some peptides produce fibril polymorphs and suggest that β-sheet content contributes significantly to fibril properties.

Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. The combination of deep UV resonance Raman (DUVRR) spectroscopy and post mortem hydrogen-deuterium exchange (HX) was utilized for probing parallel vs antiparallel beta-sheets in fibrils prepared from full-length Abeta(1-40) and Abeta(34-42) peptides, respectively. Using previously published structural data based on solid-state NMR analysis, we verified the applicability of Asher's approach for the quantitative characterization of peptide conformation in the Abeta(1-40) fibril core. We found that the conformation of the parallel beta-sheet in the Abeta(1-40) fibril core is atypical for globular proteins, while in contrast, the antiparallel beta-sheet in Abeta(32-42) fibrils is a common structure in globular proteins. In contrast to the case for globular proteins, the conformations of parallel and antiparallel beta-sheets in Abeta fibril cores are substantially different, and their differences can be distinguished by DUVRR spectroscopy.

Spinocerebellar ataxia type 1 (SCA1) is one of a group of nine expanded CAG repeat diseases, in which polyglutamine (polyQ) expansion above a threshold is associated with increased disease risk and aggregation. SCA1 is unique in which the polyQ in the disease protein, ataxin1, often contains a few His residues that appear to block toxicity. Here, we ask how His insertions affect aggregation by comparing a Q(30) peptide with and without a centrally inserted His-Gln-His sequence. We found that at pH 7.5-8.5, His interruptions decrease polyQ aggregation rates but do not change the spontaneous growth mechanism: nucleated growth polymerization with a critical nucleus of one without non-fibrillar intermediates. The decreased aggregation rates are because of reductions in nucleation equilibrium constants. At pH 6, however, the His-interrupted peptide aggregates by a different mechanism that involves a low ThT-binding intermediate and produces a polymorphic amyloid product. In aggregates grown at pH 7.5, the His residues are solvent-accessible. Aggregates of His-inserted polyQ are good seeds for Q(30) elongation, suggesting the potential to recruit polyQ proteins in the cell. Our data are therefore most consistent with His insertions blocking toxicity by suppressing rates and/or altering pathways of spontaneous aggregation.

Simple polyglutamine (polyQ) peptides aggregate in vitro via a nucleated growth pathway directly yielding amyloid-like aggregates. We show here that the 17-amino-acid flanking sequence (HTT(NT)) N-terminal to the polyQ in the toxic huntingtin exon 1 fragment imparts onto this peptide a complex alternative aggregation mechanism. In isolation, the HTT(NT) peptide is a compact coil that resists aggregation. When polyQ is fused to this sequence, it induces in HTT(NT), in a repeat-length dependent fashion, a more extended conformation that greatly enhances its aggregation into globular oligomers with HTT(NT) cores and exposed polyQ. In a second step, a new, amyloid-like aggregate is formed with a core composed of both HTT(NT) and polyQ. The results indicate unprecedented complexity in how primary sequence controls aggregation within a substantially disordered peptide and have implications for the molecular mechanism of Huntington's disease.

Amyloid formation reactions exhibit two classes of polymorphisms: the metastable intermediates commonly observed during amyloid formation and the range of conformationally distinct mature fibrils often seen at the reaction endpoint. Although recent data suggest that spherical oligomers and protofibrils in most cases are not obligate intermediates of amyloid assembly, oligomeric states might sometimes serve as on-pathway intermediates. Mature amyloid polymorphs self-propagate as a result of the normally very high fidelity of amyloid elongation, giving rise to strain behavior and species barriers in prion phenomena. Oligomers, protofibrils and various polymorphic forms of mature amyloid fibrils seem to be distinguished by differences in atomic structure that give rise to differences in observed morphologies.

Cytochrome c (cyt-c) plays a key role in activating intrinsic apoptosis, a closely regulated cell death mechanism. Complete understanding of this process has implications for treatment of neurodegenerative diseases like Huntington's disease, as well as cancer. A pivotal signaling event in this apoptotic pathway is the peroxidation of the mitochondrial lipid cardiolipin (CL) by cyt-c. Cyt-c gains CL-specific lipid peroxidase activity by binding to CL during apoptosis, but exactly what structural changes lead to its proapoptotic activity have remained elusive. We have performed both structural and functional measurements to determine changes in structure and dynamics of cyt-c that accompany the activation of its peroxidase function upon binding to CL. Specifically, we used FTIR and multidimensional magic-angle-spinning (MAS) solid-state NMR (ssNMR) on samples mimicking proapoptotic conditions that trigger cyt-c's peroxidase activity. Comparison to FTIR and solution NMR data for the soluble protein revealed that cyt-c did not experience major unfolding upon membrane binding. We probed the protein-lipid interactions via ssNMR on both the protein and the lipids, and additionally used fluorescence quenching measurements of resonance energy transfer between the cyt-c heme and fluorescently labeled lipids. We conclude that increases in peroxidase activity of peripherally CL-bound cyt-c do not result from extensive unfolding of cyt-c. We instead propose an alternative mechanism in which localized structural changes, rather than global unfolding, in the CL-bound protein may be enough to allow for significant lipid peroxidation function to arise.

Repeat length disease thresholds vary among the 10 expanded polyglutamine (polyQ) repeat diseases, from about 20 to about 50 glutamine residues. The unique amino acid sequences flanking the polyQ segment are thought to contribute to these repeat length thresholds. The specific portions of the flanking sequences that modulate polyQ properties are not always clear, however. This ambiguity may be important in Huntington’s disease (HD), for example, where in vitro studies of aggregation mechanisms have led to distinctly different mechanistic models. Most in vitro studies of the aggregation of the huntingtin (HTT) exon1 fragment implicated in the HD mechanism have been conducted on inexact molecules that are imprecise either on the N-terminus (recombinantly produced peptides) or on the C-terminus (chemically synthesized peptides). In this paper, we investigate the aggregation properties of chemically synthesized HTT exon1 peptides that are full-length and complete, containing both normal and expanded polyQ repeat lengths, and compare the results directly to previously investigated molecules containing truncated C-termini. The results on the full-length peptides are consistent with a two-step aggregation mechanism originally developed based on studies of the C-terminally truncated analogues. Thus, we observe relatively rapid formation of spherical oligomers containing from 100 to 600 HTT exon1 molecules and intermediate formation of short protofibril-like structures containing from 500 to 2600 molecules. In contrast to this relatively rapid assembly, mature HTT exon1 amyloid requires about one month to dissociate in vitro, which is similar to the time required for neuronal HTT exon1 aggregates to disappear in vivo after HTT production is discontinued.

More than 20 human diseases are associated with amyloid fibril formation, one of which is Huntington's Disease (HD). HD, which poses a risk for ∼200,000 Americans, is a neurodegenerative disease that degrades cognitive and motor functions and is one of ten disorders to feature polyglutamine (polyQ) domain expansion. The self-aggregation of expanded polyQ segments in the huntingtin protein (htt) leads to fibril formation. Flanking regions of the polyQ domain affect the kinetics of this aggregation. As protein aggregation appears to correlate to disease onset, we aim to understand the structure of the mature fibrils, a critical step toward resolving structural changes along the fibril formation pathway.Fibrils of site-specific isotopically labeled peptides mimicking polyQ-containing N-terminal fragments of the htt protein were studied by magic-angle-spinning (MAS) solid-state NMR (ssNMR). We probed the conformation of both the polyQ amyloid core and its flanking regions by multidimensional MAS ssNMR, finding an a-helical conformation for residues in the very N-terminus (httNT), which is known to initiate the aggregation process. Structural models of the aggregation pathway and fibril were assessed based on structural data, relaxation times, and order parameters from MAS ssNMR measurements. Fibrils featuring mutations in the linker region connecting the httNT helix to the amyloid core were also investigated. Earlier animal studies have shown these mutations to reduce toxicity, and EM shows significant changes in fibril morphology. The site-specific effects of these and other mutations, on both the httNT and the polyQ core, were explored through structural and dynamics measurements. The characterization of the mutants, which mimic post-translational Ser phosphorylation, suggests biophysical connections between the stability and molecular structure of species along the aggregation pathway and the observed changes in toxicity.

The recognition and binding of specific lipid species is critical for the cellular targeting, folding and activity of various membrane-associated or peripherally bound proteins. These interactions facilitate localization of the protein in question in the proper membrane in the cell. In certain cases, binding to cholesterol is thought to play a key role in the targeting of membrane-associated proteins to cholesterol-rich membranes, and to laterally-segregated cholesterol-enriched domains within the plasma membrane. Previous studies have identified a cholesterol-binding motif that may be found in numerous proteins. This relatively short cholesterol recognition/interaction amino acid consensus (CRAC) is thought to enable tight cholesterol binding, both in a protein-context and in isolation. Experimental challenges have limited the availability of structural data on the molecular or biophysical nature of this interaction. Using solid-state NMR (ssNMR), we explore the structural features of this domain as found in the cholesterol-binding protein caveolin 1. The use of ssNMR permits the study of this cholesterol-binding domain in cholesterol-rich lipid bilayers designed to emulate native caveolar membranes. Site-specific structural constraints were obtained for the bound protein fragment, revealing a transition from an extended, β-stranded conformation to an α-helical structure near the central Tyr residue characteristic of CRAC motifs – consistent with certain pre-existing models of CRAC motif structure. Furthermore, complementary static and magic-angle-spinning (MAS) NMR measurements reveal the effects on lipid dynamics and indicate immersion of the polypeptide into the membrane hydrophobic core. These structural and motional data on both partners in this polypeptide-membrane interaction provide an unprecedented site-specific perspective on a cholesterol-binding CRAC motif.

The conformational preferences of polyglutamine (polyQ) sequences are of major interest because of their central importance in the expanded CAG repeat diseases that include Huntington's disease. Here, we explore the response of various biophysical parameters to the introduction of β-hairpin motifs within polyQ sequences. These motifs (tryptophan zipper, disulfide, d-Pro-Gly, Coulombic attraction, l-Pro-Gly) enhance formation rates and stabilities of amyloid fibrils with degrees of effectiveness well correlated with their known abilities to enhance β-hairpin formation in other peptides. These changes led to decreases in the critical nucleus for amyloid formation from a value of n=4 for a simple, unbroken Q23 sequence to approximate unitary n values for similar length polyQs containing β-hairpin motifs. At the same time, the morphologies, secondary structures, and bioactivities of the resulting fibrils were essentially unchanged from simple polyQ aggregates. In particular, the signature pattern of solid-state NMR (13)C Gln resonances that appears to be unique to polyQ amyloid is replicated exactly in fibrils from a β-hairpin polyQ. Importantly, while β-hairpin motifs do produce enhancements in the equilibrium constant for nucleation in aggregation reactions, these Kn values remain quite low (~10(-)(10)) and there is no evidence for significant enhancement of β-structure within the monomer ensemble. The results indicate an important role for β-turns in the nucleation mechanism and structure of polyQ amyloid and have implications for the nature of the toxic species in expanded CAG repeat diseases.

Mammalian prions are thought to consist of misfolded aggregates (protease-resistant isoform of the prion protein [PrP res ]) of the cellular prion protein (PrP C ). Transmissible spongiform encephalopathy (TSE) can be induced in animals inoculated with recombinant PrP (rPrP) amyloid fibrils lacking mammalian posttranslational modifications, but this induction is inefficient in hamsters or transgenic mice overexpressing glycosylphosphatidylinositol (GPI)-anchored PrP C . Here we show that TSE can be initiated by inoculation of misfolded rPrP into mice that express wild-type (wt) levels of PrP C and that synthetic prion strain propagation and selection can be affected by GPI anchoring of the host's PrP C . To create prions de novo , we fibrillized mouse rPrP in the absence of molecular cofactors, generating fibrils with a PrP res -like protease-resistant banding profile. These fibrils induced the formation of PrP res deposits in transgenic mice coexpressing wt and GPI-anchorless PrP C (wt/GPI − ) at a combined level comparable to that of PrP C expression in wt mice. Secondary passage into mice expressing wt, GPI − , or wt plus GPI − PrP C induced TSE disease with novel clinical, histopathological, and biochemical phenotypes. Contrary to laboratory-adapted mouse scrapie strains, the synthetic prion agents exhibited a preference for conversion of GPI − PrP C and, in one case, caused disease only in GPI − mice. Our data show that novel TSE agents can be generated de novo solely from purified mouse rPrP after amplification in mice coexpressing normal levels of wt and anchorless PrP C . These observations provide insight into the minimal elements required to create prions in vitro and suggest that the PrP C GPI anchor can modulate the propagation of synthetic TSE strains.

Aggregation of expanded polyglutamine repeat-containing fragments of the huntingtin (htt) protein may play a key role in Huntington's disease. Consistent with this hypothesis, two Ser-to-Asp mutations in the 17-amino-acid N-terminal htt(NT) segment abrogate both visible brain aggregates and disease symptoms in a full-length Q(97) htt mouse model while compromising aggregation kinetics and aggregate morphology in an htt fragment in vitro [Gu et al. (2009). Serines 13 and 16 are critical determinants of full-length human mutant huntingtin induced disease pathogenesis in HD mice. Neuron64, 828-840]. The htt(NT) segment has been shown to play a critical role in facilitating nucleation of amyloid formation in htt N-terminal exon1 fragments. We show here how these Ser-to-Asp mutations dramatically affect aggregation kinetics and aggregate structural integrity. First, these negatively charged Ser replacements impair the assembly of the α-helical oligomers that play a critical role in htt amyloid nucleation, thus providing an explanation for reduced amyloid formation rates. Second, these sequence modifications alter aggregate morphology, decrease aggregate stability, and enhance the steric accessibility of the htt(NT) segment within the aggregates. Together, these changes make the sequence-modified peptides kinetically and thermodynamically less likely to aggregate and more susceptible, if they do, to posttranslational modifications and degradation. These effects also show how phosphorylation of a protein might achieve cellular effects via direct impacts on the protein's aggregation properties. In fact, preliminary studies on exon1-like molecules containing phosphoryl-Ser residues at positions 13 and 16 show that they reduce aggregation rates and generate atypical aggregate morphologies similar to the effects of the Ser-to-Asp mutants.

Members of the caveolin protein family are implicated in the formation of caveolae and play important roles in a number of signaling pathways and in the regulation of various proteins. We employ complementary spectroscopic methods to study the structure of the caveolin scaffolding domain (CSD) in caveolin-1 fragments, while bound to cholesterol-rich membranes. This key domain is thought to be involved in multiple critical functions that include protein recognition, oligomerization, and cholesterol binding. In our membrane-bound peptides, residues within the flanking intramembrane domain (IMD) are found to adopt an α-helical structure, consistent with its commonly believed helical hairpin conformation. Intriguingly, in these same peptides, we observe a β-stranded conformation for residues in the CSD, contrasting with earlier reports, which commonly do not reflect β-structure. Our experimental data based on solid-state NMR, CD, and FTIR are found to be consistent with computational analyses of the secondary structure preference of the primary sequence. We discuss how our structural data of membrane binding Cav fragments may match certain general features of cholesterol-binding domains and could be consistent with the role for CSD in protein recognition and homo-oligomerization.

Huntington's disease (HD) is one of ten neurodegenerative diseases caused by expanded CAG repeats. A characteristic feature of postmortem HD brains is the presence of intra-nuclear inclusions comprising N terminal mutant Huntingtin (htt) fragments. Based on these and other results, it was posited that protein aggregation might play a crucial role in mediating disease pathologies. Using exon-1 peptide models, we have been able to delineate a clear link between polyglutamine expansion and aggregation propensities as modulated by the first 17 residues adjacent to polyglutamine in the N terminus (httNT). Here we investigate the effect of httNT amino acid modifications - in particular mutations designed to block or mimic putative post-translational modification (PMTs) - on the aggregation of these exon-1 peptides. A particularly striking result was that exon-1 peptides in which both httNT serine residues are mutated to the phospho-Ser mimic aspartate aggregate more slowly and form irregular/immature aggregates, compared to peptides with WT httNT sequence. These results nicely correlate with results in a tg mouse model of HD, in which the Ser->Asp double mutant produces no aggregates and does not develop HD symptoms (X. W. Yang, personal communication). Analysis of single Ser to Asp mutants suggests that these mutations act in concert to produce these effects. Over the PMT mutations studied, we observed a correlation between net hydrophobicity and aggregation propensity. This observation was further corroborated in two multiple mutants containing mutations not associated with PMTs that are designed to either increase or suppress net hydrophobicity. We believe our data to date support our hypothesis that one to a few mutations or PMTs in the N terminal segment can have significant effects on the development of HD pathology, possibly mediated largely by biophysical effects.

The infectious agent of transmissible spongiform encephalopathies (TSE) is believed to comprise, at least in part, the prion protein (PrP). Other molecules can modulate the conversion of the normal PrP(C) into the pathological conformer (PrP(Sc)), but the identity and mechanisms of action of the key physiological factors remain unclear. PrP can bind to nucleic acids with relatively high affinity. Here, we report small-angle X-ray scattering (SAXS) and nuclear magnetic resonance spectroscopy measurements of the tight complex of PrP with an 18 bp DNA sequence. This double-stranded DNA sequence (E2DBS) binds with nanomolar affinity to the full-length recombinant mouse PrP. The SAXS data show that formation of the rPrP-DNA complex leads to larger values of the maximum dimension and radius of gyration. In addition, the SAXS studies reveal that the globular domain of PrP participates importantly in the formation of the complex. The changes in NMR HSQC spectra were clustered in two major regions: one in the disordered portion of the PrP and the other in the globular domain. Although interaction is mediated mainly through the PrP globular domain, the unstructured region is also recruited to the complex. This visualization of the complex provides insight into how oligonucleotides bind to PrP and opens new avenues to the design of compounds against prion diseases.

The N-terminal 17 amino acid sequence in huntingtin (httNT) plays a crucial role in the aggregation of htt N-terminal fragment peptides (htt NTFs). In the current mechanistic model, httNT segments pack into α-helical bundles to form oligomers that create high local concentrations of appended polyglutamine (polyQ) segments, favoring nucleation of polyQ amyloid. Consistent with this model, we found previously that isolated httNT peptide added in trans inhibits the aggregation of htt NTF peptides, presumably by co-assembling with htt NTFs into mixed oligomers with decreased local polyQ concentrations. In a further test of this model, we found that the aggregation inhibitory activities of a set of ten scrambled httNT sequences correlate with their α-helical potential. We have now selected three of these scrambled sequences - (a) one that inhibits htt NTF aggregation (schttNTASSQ), (b) one that does not inhibit (schttNTFAKF), and (c) one that readily forms amyloid fibrils itself (unlike httNT or the other sequences) but does not inhibit (schttNTSAFM) - and used them in place of httNT to make synthetic analogs of htt NTF by adding a Q37P10K2 sequence. Consistent with expectations, we found that the peptide with the inhibitory, high α-helical potential, leader sequence (schttNTASSQ) exhibits an aggregation profile similar to that of the httNT-containing control peptide. In contrast, despite their identical amino acid compositions, htt NTF analogs containing the other two scrambled sequences (low aggregation inhibition, low α-helix) exhibit aggregation behavior more typical of simple polyQ sequences, hence deriving no kinetic benefit from their N-terminal sequences. Our results support a strong role for α-helix formation within httNT in greatly enhancing the kinetics of formation of the polyQ core of htt NTF amyloid.