Principles governing oligomer formation in amyloidogenic peptides

Elucidating the Oligomerization and Cellular Interactions of a Trimer Derived from Aβ through Fluorescence and Mass Spectrometric Studies

Aβ oligomers play a central role in the neurodegeneration observed with Alzheimer's disease. Our laboratory has developed covalently stabilized trimers derived from residues 17-36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells. 2AT-L and fluorescently labeled 2AT-L analogues assemble in the membrane-like environment of SDS-PAGE, showing diffuse bands of oligomers in equilibrium. Native ion mobility-mass spectrometry (native IM-MS) of 2AT-L allows for the identification of discrete oligomers in solution and shows similar patterns of oligomer formation between 2AT-L and fluorescently labeled analogues. Fluorescence microscopy with SH-SY5Y cells reveals that fluorescently labeled 2AT-L analogues colocalize within lysosomes. FLIM studies with phasor analysis further elucidate the assembly of 2AT-L within cells and establish the occurrence of FRET, indicating the presence of oligomers within cells. Collectively, these multiple complementary techniques help better understand the complex behavior of the 2AT-L model system.

Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

We focus on the concentration dependency of fibril-forming peptides, which have the potential of aggregation by themselves. In this study, we performed replica-exchange molecular dynamics simulations of Lys-Phe-Phe-Glu (KFFE) fragments, which are known to form fibrils in experiments under different concentration environments. The analysis by static structure factors suggested that the density fluctuation of the KFFE fragments becomes large as the concentration increases. It was also found that the number of β-structures and oligomers also increases under a high concentration environment. Hence, a high concentration environment of fibril-forming peptides is likely to cause protein aggregation.

Synthesis and study of macrocyclic β-hairpin peptides for investigating amyloid oligomers

Chemically constrained peptides that self-assemble can be used to better understand the molecular basis of amyloid diseases. The formation of small assemblies of the amyloidogenic peptides and proteins, termed oligomers, is central to amyloid diseases. The use of chemical model systems can help provide insights into the structures and interactions of amyloid oligomers, which are otherwise difficult to study. This chapter describes the use of macrocyclic β-hairpin peptides as model systems to study amyloid oligomers. The first part of the chapter describes the chemical synthesis of the macrocyclic β-hairpin peptides and covalent assemblies thereof. The second part of the chapter describes the characterization of the oligomers formed by the macrocyclic β-hairpin peptides, focusing on SDS-PAGE, size-exclusion chromatography (SEC), and X-ray crystallography. The procedures provided focus on the β-amyloid peptide, but these strategies are applicable to a broad range of amyloid-derived peptides and proteins.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.

A theoretical study of polymorphism in VQIVYK fibrils

The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY "face" sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK "back" sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.

High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease

In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.

Structural Basis for Lipid Binding and Function by an Evolutionarily Conserved Protein, Serum Amyloid A

Serum amyloid A (SAA) is a plasma protein that transports lipids during inflammation. To explore SAA solution conformations and lipid-binding mechanism, we used hydrogen-deuterium exchange mass spectrometry, lipoprotein reconstitution, amino acid sequence analysis, and molecular dynamics simulations. Solution conformations of lipid-bound and lipid-free mSAA1 at pH~7.4 agreed in details with the crystal structures but also showed important differences. The results revealed that amphipathic α-helices h1 and h3 comprise a lipid-binding site that is partially pre-formed in solution, is stabilized upon binding lipids, and shows lipid-induced folding of h3. This site sequesters apolar ligands via a concave hydrophobic surface in SAA oligomers. The largely disordered/dynamic C-terminal region is conjectured to mediate the promiscuous binding of other ligands. The h1-h2 linker region is predicted to form an unexpected β-hairpin that may represent an early amyloidogenic intermediate. The results help establish structural underpinnings for understanding SAA interactions with its key functional ligands, its evolutional conservation, and its transition to amyloid.

Adsorption of Amyloidogenic Peptides to Functionalized Surfaces Is Biased by Charge and Hydrophilicity

Surfaces are abundant in living systems, such as in the form of cellular membranes, and govern many biological processes. In this study, the adsorption of the amyloidogenic model peptides GNNQQNY, NNFGAIL, and VQIVYK as well as the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5) were studied at low concentrations (100 μM) to different surfaces. The technique of a quartz crystal microbalance with dissipation monitoring (QCM-D) was applied as it enables the monitoring of mass binding to sensors at nanogram sensitivity. Gold-coated quartz sensors were used as unmodified gold surfaces or functionalized with self-assembled monolayers (SAMs) of alkanethiols (terminated as methyl, amino, carboxyl, and hydroxyl) resulting in different adsorption affinities of the peptides. Our objective was to evaluate the underlying role of the nature and feature of interfaces in biological systems which could concentrate peptides and impact or trigger peptide aggregation processes. In overall, the largely hydrophobic peptides adsorbed with preference to hydrophobic or countercharged surfaces. Further, the glycoprotein lubricin (LUB) was tested as an antiadhesive coating. Despite its hydrophilicity, the adsorption of peptides to LUB coated sensors was similar to the adsorption to unmodified gold surfaces, which indicates that some peptides diffused through the LUB layer to reach the underlying gold sensor surface. The LUB protein-antiadhesive is thus more effective as a biomaterial coating against larger biomolecules than small peptides under the conditions used here. This study provides directions toward a better understanding of amyloid peptide adsorption to biologically relevant interfaces, such as cellular membranes.

Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.

Nonproductive Binding Modes as a Prominent Feature of Aβ40 Fiber Elongation: Insights from Molecular Dynamics Simulation

The formation of amyloid fibers has been implicated in a number of neurodegenerative diseases. The growth of amyloid fibers is strongly thermodynamically favorable, but kinetic traps exist where the incoming monomer binds in an incompatible conformation that blocks further elongation. Unfortunately, this process is difficult to follow experimentally at the atomic level. It is also too complex to simulate in full detail and to date has been explored either through coarse-grained simulations, which may miss many important interactions, or full atomic simulations, in which the incoming peptide is constrained to be near the ideal fiber geometry. Here we use an alternate approach starting from a docked complex in which the monomer is from an experimental NMR structure of one of the major conformations in the unbound ensemble, a largely unstructured peptide with the central hydrophobic region in a 3₁₀ helix. A 1000 ns full atomic simulation in explicit solvent shows the formation of a metastable intermediate by sequential, concerted movements of both the fiber and the monomer. A Markov state model shows that the unfolded monomer is trapped at the end of the fiber in a set of interconverting antiparallel β-hairpin conformations. The simulation here may serve as a model for the binding of other non-β-sheet conformations to amyloid fibers.

Radial distribution function of semiflexible oligomers with stretching flexibility

The radial distribution of the end-to-end distance R_ee is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of R_ee ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of R_ee. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of R_ee for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of R_ee becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.

Alzheimer's disease amyloid beta peptides in vitro electrochemical oxidation

The oxidative behaviour of the human amyloid beta (Aβ_1-40 and Aβ_1-42) peptides and a group of similar peptides: control inverse (Aβ_40-1 and Aβ_42-1), mutants (Aβ_1-40Phe¹⁰ and Aβ_1-40Nle³⁵), rat Aβ_1-40Rat, and fragments (Aβ_1-28, Aβ_1-16, Aβ_10-20, Aβ_12-28, and Aβ_17-42), in solution or adsorbed, at a glassy carbon electrode, by cyclic and differential pulse voltammetry, were investigated and compared. Structurally the Aβ_1-40 and Aβ_1-42 sequences contain five electroactive amino acid residues, one tyrosine (Tyr¹⁰), three histidines (His⁶, His¹³ and His¹⁴) and one methionine (Met³⁵). The Aβ peptide 3D structure influenced the exposure of the redox residues to the electrode surface and their oxidation peak currents. Depending on the amino acid sequence length and content, the Aβ peptides gave one or two oxidation peaks. The first electron transfer reaction corresponded to the tyrosine amino acid residue oxidation, and the second to both histidines and methionine amino acid residues. The highest contribution to the second oxidation peak current was from His¹³, followed by His¹⁴ and His⁶ residues, and Met³⁵ residue had the lowest contribution. The Aβ peptides electron transfer depended on peptide hydrophobicity and 3D structure, the redox residues position in the sequence, the redox residues close to N-termini giving the highest oxidation peak currents.

Thermodynamics of amyloid formation and the role of intersheet interactions

The self-assembly of proteins into β-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to explore the thermodynamic forces driving amyloid formation in a finite canonical (NVT) system. By means of generalized-ensemble Monte Carlo techniques and a semi-analytical method, the thermodynamic properties of this model are investigated for different sets of intersheet interaction parameters. When the interactions support lateral growth into multi-layered fibrillar structures, an evaporation/condensation transition is observed, between a supersaturated solution state and a thermodynamically distinct state where small and large fibril-like species exist in equilibrium. Intermediate-size aggregates are statistically suppressed. These properties do not hold if aggregate growth is one-dimensional.

Fe(2+) binding on amyloid β-peptide promotes aggregation

The metal ions Zn(2+) , Cu(2+) , and Fe(2+) play a significant role in the aggregation mechanism of Aβ peptides. However, the nature of binding between metal and peptide has remained elusive; the detailed information on this from the experimental study is very difficult. Density functional theory (dft) (M06-2X/6-311++G (2df,2pd) +LANL2DZ) has employed to determine the force field resulting due to metal and histidine interaction. We performed 200 ns molecular dynamics (MD) simulation on Aβ1-42 -Zn(2+) , Aβ1-42 -Cu(2+) , and Aβ1-42 -Fe(2+) systems in explicit water with different combination of coordinating residues including the three Histidine residues in the N-terminal. The present investigation, the Aβ1-42 -Zn(2+) system possess three turn conformations separated by coil structure. Zn(2+) binding caused the loss of the helical structure of N-terminal residues which transformed into the S-shaped conformation. Zn(2+) has reduced the coil and increases the turn content of the peptide compared with experimental study. On the other hand, the Cu(2+) binds with peptide, β sheet formation is observed at the N-terminal residues of the peptide. Fe(2+) binding is to promote the formation of Glu22-Lys28 salt-bridge which stabilized the turn conformation in the Phe19-Gly25 residues, subsequently β sheets were observed at His13-Lys18 and Gly29-Gly37 residues. The turn conformation facilitates the β sheets are arranged in parallel by enhancing the hydrophobic contact between Gly25 and Met35, Lys16 and Met35, Leu17 and Leu34, Val18 and Leu34 residues. The Fe(2+) binding reduced the helix structure and increases the β sheet content in the peptide, which suggested, Fe(2+) promotes the oligomerization by enhancing the peptide-peptide interaction. Proteins 2016; 84:1257-1274. © 2016 Wiley Periodicals, Inc.

Amyloid-β peptides time-dependent structural modifications: AFM and voltammetric characterization

The human amyloid beta (Aβ) peptides, Aβ1-40 and Aβ1-42, structural modifications, from soluble monomers to fully formed fibrils through intermediate structures, were investigated, and the results were compared with those obtained for the inverse Aβ40-1 and Aβ42-1, mutant Aβ1-40Phe(10) and Aβ1-40Nle(35), and rat Aβ1-40Rat peptide sequences. The aggregation was followed at a slow rate, in chloride free media and room temperature, and revealed to be a sequence-structure process, dependent on the physicochemical properties of each Aβ peptide isoforms, and occurring at different rates and by different pathways. The fibrilization process was investigated by atomic force microscopy (AFM), via changes in the adsorption morphology from: (i) initially random coiled structures of ∼0.6 nm height, corresponding to the Aβ peptide monomers in random coil or in α-helix conformations, to (ii) aggregates and protofibrils of 1.5-6.0 nm height and (iii) two types of fibrils, corresponding to the Aβ peptide in a β-sheet configuration. The reactivity of the carbon electrode surface was considered. The hydrophobic surface induced rapid changes of the Aβ peptide conformations, and differences between the adsorbed fibrils, formed at the carbon surface (beaded, thin, <2.0 nm height) or in solution (long, smooth, thick, >2.0 nm height), were detected. Differential pulse voltammetry showed that, according to their primary structure, the Aβ peptides undergo oxidation in one or two steps, the first step corresponding to the tyrosine amino acids oxidation, and the second one to the histidine and methionine amino acids oxidation. The fibrilization process was electrochemically detected via the decrease of the Aβ peptide oxidation peak currents that occurred in a time dependent manner.

An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations

The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.

Advances in the Simulation of Protein Aggregation at the Atomistic Scale

Protein aggregation into highly structured amyloid fibrils is associated with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biological functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochemical forces that drive protein aggregation is still lacking. Such understanding is crucial for the development of drugs that can effectively inhibit aberrant amyloid aggregation and for the directed design of functional amyloids. Atomistic simulations can help understand protein aggregation. In particular, atomistic simulations can be used to study the initial formation of toxic oligomers which are hard to characterize experimentally and to understand the difference in aggregation behavior between different amyloidogenic peptides. Here, we review the latest atomistic simulations of protein aggregation, concentrating on amyloidogenic protein fragments, and provide an outlook for the future in this field.

Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering

The nucleation event of amyloid fibrils is one of the most crucial processes that dictate the timing and rate of the pathology of diseases; however, information regarding how protein molecules associate to produce fibril nuclei is currently limited. In order to explore this issue in more detail, we performed time-resolved small angle X-ray scattering (SAXS) measurements on insulin fibrillation, in combination with additional multidirectional analyses of thioflavin T fluorescence, FTIR spectroscopy, light scattering, and light transmittance, during the fibrillation process of bovine insulin. SAXS monitoring revealed that insulin molecules associated into rod-like prefibrillar aggregates in the very early stage of the reaction. After the formation of these early aggregates, they appeared to further coalesce mutually to form larger clusters, and the SAXS profiles subsequently showed the further time evolution of conformational development towards mature amyloid fibrils. Distinct types of structural units in terms of shape in a nano-scale order, cross-β content, and thioflavin T fluorescence intensity were observed in a manner that was dependent on the fibrillation pathways. These results suggest the presence of diverse substructures that characterize various fibrillation pathways, and eventually, manifest polymorphisms in mature amyloid fibrils.

Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles

Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations

Amyloids are associated with diseases, including Alzheimer's, as well as functional roles such as storage of peptide hormones. It is still unclear what differences exist between aberrant and functional amyloids. However, it is known that soluble oligomers formed during amyloid aggregation are more toxic than the final fibrils. Here, we perform molecular dynamics simulations to study the aggregation of the amyloid-β peptide Aβ25-35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Although the three peptides have similar primary sequences, tachykinin peptides, in contrast to Aβ25-35, form nontoxic amyloids. Our simulations reveal that the charge of the C-terminus is essential to controlling the aggregation process. In particular, when the kassinin C-terminus is not amidated, the aggregation kinetics decreases considerably. In addition, we observe that the monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations.

Amyloid misfolding, aggregation, and the early onset of protein deposition diseases: insights from AFM experiments and computational analyses

The development of Alzheimer's disease is believed to be caused by the assembly of amyloid β proteins into aggregates and the formation of extracellular senile plaques. Similar models suggest that structural misfolding and aggregation of proteins are associated with the early onset of diseases such as Parkinson's, Huntington's, and other protein deposition diseases. Initially, the aggregates were structurally characterized by traditional techniques such as x-ray crystallography, NMR, electron microscopy, and AFM. However, data regarding the structures formed during the early stages of the aggregation process were unknown. Experimental models of protein deposition diseases have demonstrated that the small oligomeric species have significant neurotoxicity. This highlights the urgent need to discover the properties of these species, to enable the development of efficient diagnostic and therapeutic strategies. The oligomers exist transiently, making it impossible to use traditional structural techniques to study their characteristics. The recent implementation of single-molecule imaging and probing techniques that are capable of probing transient states have enabled the properties of these oligomers to be characterized. Additionally, powerful computational techniques capable of structurally analyzing oligomers at the atomic level advanced our understanding of the amyloid aggregation problem. This review outlines the progress in AFM experimental studies and computational analyses with a primary focus on understanding the very first stage of the aggregation process. Experimental approaches can aid in the development of novel sensitive diagnostic and preventive strategies for protein deposition diseases, and several examples of these approaches will be discussed.

Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I

Several disease-linked mutations of apolipoprotein A-I, the major protein in high-density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N-terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril-associated disordered 1-93 fragment of this protein, in wild-type and mutated (G26R, S36A, K40L, W50R) forms. In atomic-level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position-dependent β-strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease-linked aggregation of apolipoprotein A-I.

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N(⁎)) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration ([C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N(⁎) states. Interestingly, the phase boundaries separating the folded and unfolded states at all [C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N(⁎) with a disordered solvent-exposed amino-terminal β-strand. The structure of the N(⁎) state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N(⁎) state, determined by the free energy gap separating the native structure and the N(⁎) state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N(⁎) state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain.

Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models

This Perspective highlights recent computational approaches to protein aggregation, from coarse-grained models to atomistic simulations, using the islet amyloid polypeptide (IAPP) as a case study. We review salient open questions where simulations can make an impact, discuss the successes and challenges met by simulations, and explore new directions.

A coarse-grained model for peptide aggregation on a membrane surface

The aggregation of peptides on a lipid bilayer is studied using coarse-grained molecular dynamics in implicit solvent. Peptides bind to and self-assemble on the membrane surface into β-rich fibrillar aggregates, even under conditions where only disordered oligomers form in bulk solution. Relative to a solid surface, the membrane surface facilitates peptide mobility and a more complex network of morphology transitions as aggregation proceeds. Additionally, final aggregate structures realized on the membrane surface are distinct from those observed on a comparable solid surface. The aggregated fibrils alter the local structure and material properties of the lipid bilayer in their immediate vicinity but have only a modest effect on the overall bending rigidity of the bilayer.

Minimal model of self-assembly: emergence of diversity and complexity

Molecular self-assembly is ubiquitous in nature, yet prediction of assembly pathways from fundamental interparticle interactions has yet to be achieved. Here, we introduce a minimal self-assembly model with two attractive and two repulsive beads bound into a tetrahedron. The model is associated with a single parameter η defined as the repulsive to attractive interaction ratio. We explore self-assembly pathways and resulting assembly morphologies for different η values by discrete molecular dynamics. Our results demonstrate that η governs the assembly dynamics and resulting assembly morphologies, revealing an unexpected diversity and complexity for 0.5 ≤ η < 1. One of the key processes that governs the assembly dynamics is assembly breakage, which emerges spontaneously at η > 0 with the breakage rate increasing with η. The observed assembly pathways display a broad variety of assembly structures characteristic of aggregation of amyloidogenic proteins, including quasi-spherical oligomers that coassemble into elongated protofibrils, followed by a conversion into ordered polymorphic fibril-like aggregates. We further demonstrate that η can be meaningfully mapped onto amyloidogenic protein sequences, with the majority of amyloidogenic proteins characterized by 0.5 ≤ η < 1. Prion proteins, which are known to form highly breakage-prone fibrils, are characterized by η > 1, consistent with the model predictions. Our model thus provides a theoretical basis for understanding the universal aspects of aggregation pathways of amyloidogenic proteins relevant to human disease. As the model is not specific to proteins, these findings represent an important step toward understanding and predicting assembly dynamics of not only proteins but also viruses, colloids, and nanoparticles.

Computational approaches to understanding protein aggregation in neurodegeneration

The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders.

Effects of environmental factors on MSP21-25 aggregation indicate the roles of hydrophobic and electrostatic interactions in the aggregation process

Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the merozoite surface of Plasmodium falciparum, is recognized to be important for the parasite's invasion into the host cell and is thus a promising malaria vaccine candidate. However, mediated mainly by its conserved N-terminal 25 residues (MSP21-25), MSP2 readily forms amyloid fibril-like aggregates under physiological conditions in vitro, which impairs its potential as a vaccine component. In addition, there is evidence that MSP2 exists in aggregated forms on the merozoite surface in vivo. To elucidate the aggregation mechanism of MSP21-25 and thereby understand the behavior of MSP2 in vivo and find ways to avoid the aggregation of relevant vaccine in vitro, we investigated the effects of agitation, pH, salts, 1-anilinonaphthalene-8-sulfonic acid (ANS), trimethylamine N-oxide dihydrate (TMAO), urea, and sub-micellar sodium dodecyl sulfate (SDS) on the aggregation kinetics of MSP21-25 using thioflavin T (ThT) fluorescence. The results showed that MSP21-25 aggregation was accelerated by agitation, while repressed by acidic pHs. The salts promoted the aggregation in an anion nature-dependent pattern. Hydrophobic surface-binding agent ANS and detergent urea repressed MSP21-25 aggregation, in contrast to hydrophobic interaction strengthener TMAO, which enhanced the aggregation. Notably, sub-micellar SDS, contrary to its micellar form, promoted MSP21-25 aggregation significantly. Our data indicated that hydrophobic interactions are the predominant driving force of the nucleation of MSP21-25 aggregation, while the elongation is controlled mainly by electrostatic interactions. A kinetic model of MSP21-25 aggregation and its implication were also discussed.

Tranilast binds to aβ monomers and promotes aβ fibrillation

The antiallergy and potential anticancer drug tranilast has been patented for treating Alzheimer's disease (AD), in which amyloid β-protein (Aβ) plays a key pathogenic role. We used solution NMR to determine that tranilast binds to Aβ40 monomers with ∼300 μM affinity. Remarkably, tranilast increases Aβ40 fibrillation more than 20-fold in the thioflavin T assay at a 1:1 molar ratio, as well as significantly reducing the lag time. Tranilast likely promotes fibrillation by shifting Aβ monomer conformations to those capable of seed formation and fibril elongation. Molecular docking results qualitatively agree with NMR chemical shift perturbation, which together indicate that hydrophobic interactions are the major driving force of the Aβ-tranilast interaction. These data suggest that AD may be a potential complication for tranilast usage in elderly patients.

Using a reduced dimensionality model to compute the thermodynamic properties of finite polypeptide aggregates

By implementing a simple reduced dimensionality model to describe the interactions in finite systems composed of two seven-amino-acid peptides, the thermodynamic properties of ordered and disordered aggregates were computed. Within this model, the hydrophobicity of each amino acid was varied, and the stability of the systems computed. Accurate averages in the canonical ensemble were obtained using various replica exchange Monte Carlo algorithms. Low and high temperature regions were encountered where the ordered and disordered aggregates were stabilized. It was observed that as the degree of hydrophobicity increased, the stability of the aggregates increased, with a significant energetic stabilization obtained for the ordered aggregates. Upon decreasing the concentration of the solution, the stability of the amorphous aggregates increased when compared to the ordered systems.

Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides

Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a 'hydrophobic wall' available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.

Molecular mechanism of misfolding and aggregation of Aβ(13-23)

The misfolding and self-assembly of the amyloid-beta (Aβ) peptide into aggregates is a molecular signature of the development of Alzheimer's disease, but molecular mechanisms of the peptide aggregation remain unknown. Here, we combined Atomic Force Microscopy (AFM) and Molecular Dynamics (MD) simulations to characterize the misfolding process of an Aβ peptide. Dynamic force spectroscopy AFM analysis showed that the peptide forms stable dimers with a lifetime of ∼1 s. During MD simulations, isolated monomers gradually adopt essentially similar nonstructured conformations independent from the initial structure. However, when two monomers approach their structure changes dramatically, and the conformational space for the two monomers become restricted. The arrangement of monomers in antiparallel orientation leads to the cooperative formation of β-sheet conformation. Interactions, including hydrogen bonds, salt bridges, and weakly polar interactions of side chains stabilize the structure of the dimer. Under the applied force, the dimer, as during the AFM experiments, dissociates in a cooperative manner. Thus, misfolding of the Aβ peptide proceeds via the loss of conformational flexibility and formation of stable dimers suggesting their key role in the subsequent Aβ aggregation process.

Conformational ensemble and polymorphism of the all-atom Alzheimer's Aβ(37-42) amyloid peptide oligomers

Although the Aβ(37-42) peptide has two opposite terminal charges, counterintuitively its current fibril amyloid structure reveals in register parallel β-strands, as formed by the full length Aβ peptide. In this study, we carried out a replica exchange molecular dynamics simulation of 16 all-atom Aβ(37-42) peptides in explicit water starting from randomized and dispersed chains. The extensive conformational sampling (48 replicas, 460 ns/replica) with a total simulation time of 23 μs allows us to obtain a full picture on the equilibrium conformational distribution of oligomers and β-sheet sizes and gain some insights into the oligomerization process at 300 K. At the peptide concentration of 12 mM, self-assembly is described by the condensation-polymerization mechanism with conversion from micelle-like to high β-sheet structures. At equilibrium, the oligomer distribution consists of large aggregates and free monomers, representing 70% and 25% of all species, respectively. Though the formation/dissociation of β-strand is high, the population of 4-5 fully parallel β-strands, consistent with the arrangement in the current fibril, is marginal and that of 4-5 fully antiparallel β-strands, consistent with amyloid polymorphism, is non-negligible. However, the system adopts essentially mixed parallel/antiparallel β-strands. This indicates that a system of 16 Aβ(37-42) chains in explicit solvent still does not form more stable species that will irreversibly grow to a fibril, independently of polymorphism. Our results also suggest that the Aβ(37-42) fibril may display packing polymorphism with antiparallel β-strands, in addition to the experimentally observed in register parallel β-strands.

Protein fibrillation and nanoparticle interactions: opportunities and challenges

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers, oligomers, critical nuclei, and other prefibrillar states, together with their influence on protein fibrillation kinetics has been described in detail. In addition, current and possible-future strategies for controlling the desired effect of NPs and their corresponding effects on the conformational changes of the proteins, which have significant roles in the fibrillation process, have been presented.

β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation

The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.

New method for determining size of critical nucleus of fibril formation of polypeptide chains

A new method for determining the size of critical nucleus of fibril formation of polypeptide chains is proposed. Based on the hypothesis that the fibril grows by addition of a nascent peptide to the preformed template, the nucleus size N(c) is defined as the number of forming template peptides above which the time to add a new monomer becomes independent of the template size. Using lattice models one can show that our method and the standard method which is based on calculation of the free energy, provide the same result for N(c).