Mechanism Of Amyloid Formation Research Articles

SAXS Analysis on the Molecular Mechanism of Amyloid Formation

SAXS Analysis on the Molecular Mechanism of Amyloid Formation

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein.

Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.

Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscapes

Developing an understanding of protein misfolding processes presents a crucial challenge for unlocking the mysteries of human disease. In this article, we present our observations of β-sheet-rich misfolded states on a number of protein dynamical landscapes investigated through molecular dynamics simulation and Markov state models. We employ a nonequilibrium statistical mechanical theory to identify the glassy states in a protein’s dynamics, and we discuss the nonnative, β-sheet-rich states that play a distinct role in the slowest dynamics within seven protein folding systems. We highlight the fundamental similarity between these states and the amyloid structures responsible for many neurodegenerative diseases, and we discuss potential consequences for mechanisms of protein aggregation and intermolecular amyloid formation.

Guilt by Association: The Physical Chemistry and Biology of Protein Aggregation

The aggregation of proteins and polypeptides is a major problem in the laboratory and in biotechnology, and is a serious issue in biology and human health.1−4 Protein aggregation is a topic that is ripe for investigation by physical chemical and biophysical methods, as well as by molecular dynamics (MD) simulations, and by more coarse grained modeling and analytical theory. Much recent attention in the physical chemistry community has focused on the process of amyloid fibril formation, motivated in part by its role in human disease. More than 30 different diseases involve amyloid formation, including devastating neurodegenerative disorders, but the mechanism of amyloid formation is not well understood, and there are very few viable therapeutic approaches. Amyloids are partially ordered aggregates of proteins that contain significant β-sheet structure arrayed in a cross-β structure in which the individual peptide chains are oriented perpendicular to the long axis of the fibril (Figure ​(Figure1). The1). The formation of amyloid is a fascinating and challenging problem in molecular self-assembly. However, it is worthwhile reminding ourselves that the importance of amyloids is directly related to their role in human disease, and thus experiments and simulations conducted under simplified conditions need to connect to biology to remain relevant. Fortunately, recent developments in methodology and experimental design, as well as growing collaborations between biophysicists and biologists hold the promise of providing a more rigorous, biologically relevant description of amyloid formation. Several of these advances are highlighted in the Perspectives included in this issue. Protein aggregation is not limited to amyloid formation, and new methods and approaches are also needed to study nonamyloidogenic aggregation. For example, considerable resources are invested in optimizing protein solubility and preventing aggregation of potential therapeutic proteins. Aggregation and poor solubility have limited the development of many monoclonal antibodies and other protein-based drugs and can lead to problems with immunogenicity, as well as loss of active protein.4 Protein aggregation can take other guises in biology beyond just amyloid. A classical example, and still arguably the best understood case of pathological protein aggregation, is the polymerization of sickle cell hemoglobin to form polymeric fibers. Elegant spectroscopic measurements together with detailed modeling have defined the mechanism of sickle cell polymerization, illustrating the power of physical chemical approaches.5 There are numerous other examples of deleterious aggregation that does not involve amyloid, including interesting mechanisms by which certain viruses subvert host defenses.

The Ability of Insulin To Inhibit the Formation of Amyloid by Pro-Islet Amyloid Polypeptide Processing Intermediates Is Significantly Reduced in the Presence of Sulfated Glycosaminoglycans

Islet amyloid polypeptide (IAPP) is responsible for amyloid deposition in type 2 diabetes and plays an important role in the loss of β-cell mass associated with the disease and in the failure of islet transplants, but the mechanism of islet amyloid formation is not understood. The incorrect processing of proIAPP to produce partially processed forms of the peptide has been proposed to play a role in the initiation of islet amyloid in vivo by promoting interactions with proteoglycans of the extracellular matrix. Insulin is a potent inhibitor of the formation of amyloid by IAPP in vitro in a homogeneous solution; however, its ability to inhibit IAPP in the presence of proteoglycans has not been tested, nor has its effect on the formation of amyloid by proIAPP processing intermediates been examined. Here we show that insulin is a much less effective amyloid inhibitor of both IAPP and proIAPP processing intermediates in vitro in the presence of model glycosaminoglycans, but does inhibit the formation of amyloid by proIAPP processing intermediates in a homogeneous solution. This highlights another mechanism by which sulfated proteoglycans could enhance islet amyloid formation in vivo. Interactions with sulfated proteoglycans can directly promote amyloid formation and can also significantly reduce the effectiveness of natural inhibitors.

Site-specific copper-catalyzed oxidation of α-synuclein: tightening the link between metal binding and protein oxidative damage in Parkinson's disease.

Amyloid aggregation of α-synuclein (AS) has been linked to the pathological effects associated with Parkinson's disease (PD). Cu(II) binds specifically at the N-terminus of AS and triggers its aggregation. Site-specific Cu(I)-catalyzed oxidation of AS has been proposed as a plausible mechanism for metal-enhanced AS amyloid formation. In this study, Cu(I) binding to AS was probed by NMR spectroscopy, in combination with synthetic peptide models, site-directed mutagenesis, and C-terminal-truncated protein variants. Our results demonstrate that both Met residues in the motif (1)MDVFM(5) constitute key structural determinants for the high-affinity binding of Cu(I) to the N-terminal region of AS. The replacement of one Met residue by Ile causes a dramatic decrease in the binding affinity for Cu(I), whereas the removal of both Met residues results in a complete lack of binding. Moreover, these Met residues can be oxidized rapidly after air exposure of the AS-Cu(I) complex, whereas Met-116 and Met-127 in the C-terminal region remain unaffected. Met-1 displays higher susceptibility to oxidative damage compared to Met-5 because it is directly involved in both Cu(II) and Cu(I) coordination, resulting in closer exposure to the reactive oxygen species that may be generated by the redox cycling of copper. Our findings support a mechanism where the interaction of AS with copper ions leads to site-specific metal-catalyzed oxidation in the protein under physiologically relevant conditions. In light of recent biological findings, these results support a role for AS-copper interactions in neurodegeneration in PD.

Amyloid Fibrils: the Eighth Wonder of the World in Protein Folding and Aggregation

Protein folding, misfolding, and aggregation are among the central topics of molecular biology in the postgenome era. Increasing evidence indicates that protein aggregation plays a vital role in a variety of biological processes. Specifically, fibrillar aggregates, i.e., filamentous assemblies of peptides and proteins that possess a common cross-β sheet structure, have been found in a wide range of organisms, from bacteria to mammals, and have been shown to possess different physiological functions.

Inhibition of Amyloid-β Aggregation in Alzheimer's Disease

The assembly of naturally occurring amyloid peptides into cytotoxic oligomeric and fibrillar aggregates is believed to be a major pathologic event in over 25 human diseases. Blocking of or interfering with the aggregation of amyloid peptides such as amyloid-β (Aβ) using small organic molecules, peptides and peptidomimetics, and nanoparticles that selectively bind or inhibit Aβ aggregates is a promising strategy for the development of novel pharmaceutical approaches and agents to treat Alzheimer's disease (AD). In a broad sense, considering many common features in structure, kinetics, and biological activity of amyloid peptides, potent inhibitors and associated inhibition strategies that are developed for targeting Aβ aggregation could also be generally applied to other amyloid-forming peptides in "protein-aggregation diseases". Due to the complex nature of Aβ self-assembly process, increasing knowledge in high-resolution structures of Aβ oligomers, atomic-level Aβ-inhibitor binding information, and cost-effective high-throughput screening method will improve our fundamental understanding of amyloid formation and inhibition mechanisms, as well as practical design of pharmaceutical strategies and drugs to treat AD. This review summarizes major findings, recent advances, and future challenges for the development of new Aβ-aggregation inhibitors, mainly focusing on three major classes of Aβ inhibitors with associated inhibition mechanisms and practical. examples.

How to Determine the Size of Folding Nuclei of Protofibrils from the Concentration Dependence of the Rate and Lag-Time of Aggregation. I. Modeling the Amyloid Protofibril Formation

The question about the size of nuclei of formation of protofibrils (which constitute mature amyloid fibrils) formed by different proteins and peptides is yet open and debatable because of the absence of solid knowledge of underlying mechanisms of amyloid formation. In this work, a kinetic model of the process of formation of amyloid protofibrils is suggested, which allows calculation of the size of the nuclei using only kinetic data. In addition to the stage of primary nucleation, which is believed to be present in many protein aggregation processes, the given model includes both linear growth of protofibrils (proceeding only at the cost of attaching of monomers to the ends) and exponential growth of protofibrils at the cost of growth from the surface, branching, and fragmentation with the secondary nuclei. Theoretically, only the exponential growth is compatible with the existence of a pronounced lag-period (which can take much more time then the growth of aggregates themselves). The obtained analytical solution allows us to determine the size of the primary and secondary nuclei from the experimentally obtained concentration dependences of the time of growth and the new parameter-the ratio Lrel of the lag-time duration to the time of growth of amyloid protofibrils.

1P057 カルシトニンアミロイド凝集機構の解明と抑制法の考案(01C. 蛋白質 : 物性,ポスター,第52回日本生物物理学会年会(2014年度))

1P057 カルシトニンアミロイド凝集機構の解明と抑制法の考案(01C. 蛋白質 : 物性,ポスター,第52回日本生物物理学会年会(2014年度))

Ion Mobility Spectrometry Reveals the Mechanism of Amyloid Formation of Aβ(25–35) and Its Modulation by Inhibitors at the Molecular Level: Epigallocatechin Gallate andScyllo-inositol

Amyloid cascades leading to peptide β-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with the cellular machinery. The relationship between the transformation from natively unstructured assembly to the β-sheet oligomers to disease is important in understanding disease onset and the development of therapeutic agents. Research on this early oligomeric region has largely been unsuccessful since traditional techniques measure only ensemble average oligomer properties. Here, ion mobility methods are utilized to deduce the modulation of peptide self-assembly pathways in the amyloid-β protein fragment Aβ(25-35) by two amyloid inhibitors (epigallocatechin gallate and scyllo-inositol) that are currently in clinical trials for Alzheimer's Disease. We provide evidence that suppression of β-extended oligomers from the onset of the conversion into β-oligomer conformations is essential for effective attenuation of β-structured amyloid oligomeric species often associated with oligomer toxicity. Furthermore, we demonstrate the ease with which ion mobility spectrometry-mass spectrometry can guide the development of therapeutic agents and drug evaluation by providing molecular level insight into the amyloid formation process and its modulation by small molecule assembly modulators.

Soluble oligomers are sufficient for transmission of a yeast prion but do not confer phenotype

Amyloidogenic proteins aggregate through a self-templating mechanism that likely involves oligomeric or prefibrillar intermediates. For disease-associated amyloidogenic proteins, such intermediates have been suggested to be the primary cause of cellular toxicity. However, isolation and characterization of these oligomeric intermediates has proven difficult, sparking controversy over their biological relevance in disease pathology. Here, we describe an oligomeric species of a yeast prion protein in cells that is sufficient for prion transmission and infectivity. These oligomers differ from the classic prion aggregates in that they are soluble and less resistant to SDS. We found that large, SDS-resistant aggregates were required for the prion phenotype but that soluble, more SDS-sensitive oligomers contained all the information necessary to transmit the prion conformation. Thus, we identified distinct functional requirements of two types of prion species for this endogenous epigenetic element. Furthermore, the nontoxic, self-replicating amyloid conformers of yeast prion proteins have again provided valuable insight into the mechanisms of amyloid formation and propagation in cells.

Effect of age and sex differences on wild-type transthyretin amyloid formation in familial amyloidotic polyneuropathy: A proteomic approach

BackgroundAge and sex differences are closely related to the onset of senile systemic amyloidosis (SSA) caused by wild-type (WT) transthyretin (TTR). However, the effects of these differences on the amyloid formation mechanism in familial amyloid polyneuropathy (FAP) caused by variant TTR, have remained unclear. To elucidate age and sex differences in FAP, we investigated biochemical characteristics of amyloid deposits in different tissue sites of FAP by proteomic analysis. MethodsWe used shotgun liquid chromatography/tandem mass spectrometry to analyze the proportions of variant and WT TTR in amyloid deposits in different tissues, such as cardiac, kidney, peripheral nerves, and gastrointestinal tissues, from 23 autopsied FAP cases. Results and conclusionsThe analysis revealed a highly significant correlation between the proportion of WT TTR and age at autopsy in cardiac tissues, whereas the analysis indicated no correlation in kidney, peripheral nerves, and gastrointestinal tissues. In addition, we demonstrated age-related significantly increased WT TTR deposits, but not variant TTR deposits, in cardiac tissues of male patients. Taken together, these data suggest that both age and sex differences affect cardiac amyloid formation, mainly derived from WT TTR, in FAP.

Understanding the Mechanism of Somatostatin-14 Amyloid Formation In Vitro

Somatostatin-14 (SST-14) is a small cyclic peptide hormone secreted by hypothalamus, one of the well-known functions of which in the body is growth hormone inhibition. SST-14 has previously been reported to spontaneously self-assemble in water containing 150 mM NaCl into amyloid-like nanofibrils. Recently, it was shown that SST-14 forms amyloid in presence of glycosaminoglycan heparin at secretory granule relevant conditions. However, the pathway of its amyloid formation in not understood yet. In the present work, we studied the mechanism of SST-14 amyloid formation in vitro as well as in silico, in the presence and absence of heparin. Our in vitro data suggests that SST-14 in presence of heparin, transforms from its monomeric ‘random coil’ conformation to a secondary structure representing amyloid, via a ‘helix-rich intermediate. It was observed in this study that SST-14 adopts a ‘nucleation-dependent polymerization’ mechanism of amyloid formation. We also studied the disulphide bond reduced ‘non-cyclic’ SST-14 (ncSST) form for amyloid formation, and observed that ncSST formed amyloid fibrils instantaneously in presence of heparin compared to the cyclic form. Furthermore, the ncSST fibrils were observed to possess higher conformational and thermal stability relative to the cyclic SST-14 fibrils.Using all-atom molecular dynamics simulations, we studied molecular interactions among SST-14 peptides in the presence and absence of heparin. Our in silico results suggest that heparin induces aggregation of SST-14 by increasing local concentration of the peptides and promotes interpeptide contacts and secondary structure transformation in the peptides. Overall, this study offers the mechanism of somatostatin-14 oligomerization and amyloid formation, which has substantial value in understanding its storage within secretory granules.

Design and Characterization of Peptide Modulators of IAPP-Membrane Binding

Type II Diabetes (T2D) is characterized by the formation of pancreatic amyloid deposits of the peptide hormone islet amyloid polypeptide (IAPP). Recent evidence suggests that α-helical oligomeric species of IAPP formed en route to, or independently of, amyloid formation may be cytotoxic to β-islet cells of the pancreas and play a role in the pathogenesis of T2D. These α-helical oligomers interact with anionic lipid bilayers, and may cooperatively and transiently convert to leakage-competent oligomers that disrupt the bilayer [Last, Rhoades & Miranker (2011) PNAS 108:9460]. We used Rosetta modeling software and Monte Carlo simulations to rationally design short peptides to selectively bind one of two early intermediate dimer structures of IAPP proposed from single-molecule fluorescence experiments: one hypothesized to lead to the formation of leakage-competent oligomers, and one hypothesized to inhibit such formation. Here we describe the computational design as well as the in vitro characterization of six candidate peptides. Half of the peptides were predicted to preferentially bind a dimer of IAPP believed to lead to leakage-competent oligomers, and half were targeted to a dimer not believed to lead to leakage-competent oligomers. We characterized the short peptides by measuring their effects on IAPP-induced leakage across DOPG liposomes at various concentrations. As another metric for interactions between IAPP and these short peptides, we also performed isothermal titration calorimetry on the binding of the short peptides with IAPP. The methods utilized here could serve useful in studying the mechanism of amyloid formation, and in the development of specific peptide binding partners targeting other proteins.

Aggregation of islet amyloid polypeptide: from physical chemistry to cell biology

Amyloid formation in the pancreas by islet amyloid polypeptide (IAPP) leads to β-cell death and dysfunction, contributing to islet transplant failure and to type-2 diabetes. IAPP is stored in the β-cell insulin secretory granules and cosecreted with insulin in response to β-cell secretagogues. IAPP is believed to play a role in the control of food intake, in controlling gastric emptying and in glucose homeostasis. The polypeptide is natively unfolded in its monomeric state, but is one of the most amyloidogenic sequences known. The mechanisms of IAPP amyloid formation in vivo and in vitro are not understood; the mechanisms of IAPP induced cell death are unclear; and the nature of the toxic species is not completely defined. Recent work is shedding light on these important issues.

Prion Domain of Yeast Ure2 Protein Adopts a Completely Disordered Structure: A Solid-Support EPR Study

Amyloid fibril formation is associated with a range of neurodegenerative diseases in humans, including Alzheimer’s, Parkinson’s, and prion diseases. In yeast, amyloid underlies several non-Mendelian phenotypes referred to as yeast prions. Mechanism of amyloid formation is critical for a complete understanding of the yeast prion phenomenon and human amyloid-related diseases. Ure2 protein is the basis of yeast prion [URE3]. The Ure2p prion domain is largely disordered. Residual structures, if any, in the disordered region may play an important role in the aggregation process. Studies of Ure2p prion domain are complicated by its high aggregation propensity, which results in a mixture of monomer and aggregates in solution. Previously we have developed a solid-support electron paramagnetic resonance (EPR) approach to address this problem and have identified a structured state for the Alzheimer’s amyloid-β monomer. Here we use solid-support EPR to study the structure of Ure2p prion domain. EPR spectra of Ure2p prion domain with spin labels at every fifth residue from position 10 to position 75 show similar residue mobility profile for denaturing and native buffers after accounting for the effect of solution viscosity. These results suggest that Ure2p prion domain adopts a completely disordered structure in the native buffer. A completely disordered Ure2p prion domain implies that the amyloid formation of Ure2p, and likely other Q/N-rich yeast prion proteins, is primarily driven by inter-molecular interactions.

Role of Prion Protein Aggregation in Neurotoxicity

In several neurodegenerative diseases, such as Parkinson, Alzheimer’s, Huntington, and prion diseases, the deposition of aggregated misfolded proteins is believed to be responsible for the neurotoxicity that characterizes these diseases. Prion protein (PrP), the protein responsible of prion diseases, has been deeply studied for the peculiar feature of its misfolded oligomers that are able to propagate within affected brains, inducing the conversion of the natively folded PrP into the pathological conformation. In this review, we summarize the available experimental evidence concerning the relationship between aggregation status of misfolded PrP and neuronal death in the course of prion diseases. In particular, we describe the main findings resulting from the use of different synthetic (mainly PrP106-126) and recombinant PrP-derived peptides, as far as mechanisms of aggregation and amyloid formation, and how these different spatial conformations can affect neuronal death. In particular, most data support the involvement of non-fibrillar oligomers rather than actual amyloid fibers as the determinant of neuronal death.

Insights into the Mechanisms of Amyloid Formation of ZnII-Ab11-28: pH-Dependent Zinc Coordination and Overall Charge as Key Parameters for Kinetics and the Structure of ZnII-Ab11-28 Aggregates

Self-assembly of amyloidogenic peptides and their metal complexes are of multiple interest including their association with several neurological diseases. Therefore, a better understanding of the role of metal ions in the aggregation process is of broad interest. We report pH-dependent structural and aggregation studies on Zn(II) binding to the amyloidogenic peptide Ab11-28. The results suggest that coordination of the N-terminal amine to Zn(II) is responsible for the inhibition of amyloid formation and the overall charge for amorphous aggregates.

Co-localisation of advanced glycation end products and d-β-aspartic acid-containing proteins in gelatinous drop-like corneal dystrophy

PurposeGelatinous drop-like corneal dystrophy (GDLD), also known as familial subepithelial corneal amyloidosis, is an autosomal recessive disorder that causes progressive corneal opacity due to accumulation of amyloid fibrils in the...