Biophysical approaches for the study of interactions between molecular chaperones and protein aggregates

Electric-field induced modulation of amorphous protein aggregates: polarization, deformation, and reorientation

Proteins in their native state are only marginally stable and tend to aggregate. However, protein misfolding and condensation are often associated with undesired processes, such as pathogenesis, or unwanted properties, such as reduced biological activity, immunogenicity, or uncontrolled materials properties. Therefore, controlling protein aggregation is very important, but still a major challenge in various fields, including medicine, pharmacology, food processing, and materials science. Here, flexible, amorphous, micron-sized protein aggregates composed of lysozyme molecules reduced by dithiothreitol are used as a model system. The preformed amorphous protein aggregates are exposed to a weak alternating current electric field. Their field response is followed in situ by time-resolved polarized optical microscopy, revealing field-induced deformation, reorientation and enhanced polarization as well as the disintegration of large clusters of aggregates. Small-angle dynamic light scattering was applied to probe the collective microscopic dynamics of amorphous aggregate suspensions. Field-enhanced local oscillations of the intensity auto-correlation function are observed and related to two distinguishable elastic moduli. Our results validate the prospects of electric fields for controlling protein aggregation processes.

The binding of the small heat-shock protein αB-crystallin to fibrils of α-synuclein is driven by entropic forces

Molecular chaperones are key components of the cellular proteostasis network whose role includes the suppression of the formation and proliferation of pathogenic aggregates associated with neurodegenerative diseases. The molecular principles that allow chaperones to recognize misfolded and aggregated proteins remain, however, incompletely understood. To address this challenge, here we probe the thermodynamics and kinetics of the interactions between chaperones and protein aggregates under native solution conditions using a microfluidic platform. We focus on the binding between amyloid fibrils of α-synuclein, associated with Parkinson's disease, to the small heat-shock protein αB-crystallin, a chaperone widely involved in the cellular stress response. We find that αB-crystallin binds to α-synuclein fibrils with high nanomolar affinity and that the binding is driven by entropy rather than enthalpy. Measurements of the change in heat capacity indicate significant entropic gain originates from the disassembly of the oligomeric chaperones that function as an entropic buffer system. These results shed light on the functional roles of chaperone oligomerization and show that chaperones are stored as inactive complexes which are capable of releasing active subunits to target aberrant misfolded species.

Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition

Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.

Procyanidine resists the fibril formation of human islet amyloid polypeptide

Human islet amyloid polypeptide (hIAPP) is widely studied due to its close correlation with the pathogenic mechanism of type II diabetes mellitus (T2DM). Bioflavonoids have been used in the neurodegeneration and diabetes studies. However, the structure-activity relationship remains unclear in many of these compounds. In this work, we performed diverse biophysical and biochemical methods to explore the inhibition of procyanidine on hIAPP and compared with that on amyloid-β (Aβ) protein which is linked to Alzheimer's disease (AD). The procyanidine effectively inhibited the aggregation of hIAPP and Aβ through hydrophobic and hydrogen bonding interactions, it dissolved the aged fibrils into nanoscale particles. The compound also ameliorated the cytotoxicity and the membrane leakage by reducing the peptide oligomerization. The procyanidine showed better binding affinity and inhibitory effects on peptide aggregation and upregulated the cell viability to hIAPP than to Aβ, which could be a prospective inhibitor against hIAPP. This work also offered a possible strategy for T2DM and AD treatments.

A biophysical toolset to probe the microscopic processes underlying protein aggregation and its inhibition by molecular chaperones

Given the breadth and depth of the scientific contributions of Sir Christopher Dobson, with over 870 publications to date, it is inconceivable to convey in a single review the impact of his work and its legacy. This review therefore primarily focuses on his contributions to the development of strategies for preventing aberrant protein misfolding. The first section of this review highlights his seminal work on the elucidation of the microscopic nucleation processes underlying protein aggregation. Next, we discuss the specific inhibition of these steps by candidate drugs and biologics, with a particular emphasis on the role of molecular chaperones. In the final section, we review how protein aggregation principles can be exploited for the rational design of novel and more potent aggregation inhibitors. These milestones serve as excellent examples of the profound impact of Dobson's seminal work on fundamental science and its translation into drug discovery.

Resistance of nepetin and its analogs on the fibril formation of human islet amyloid polypeptide

The self-aggregation of human islet amyloid polypeptide (hIAPP) into toxic oligomers and fibrils is closely linked to the pathogenesis of type II diabetes mellitus. Inhibitors can resist hIAPP misfolding, and the resistance can be considered an alternative therapeutic strategy for this disease. Flavones have been applied in the field of diabetes research, however, the inhibition mechanism of many compounds on the fibril formation of related pathogenic peptides remains unclear. In this work, four flavones, namely, nepetin (1), genkwanin (2), luteolin (3), and apigenin (4), were used to impede the peptide aggregation of hIAPP and compared with that on Aβ protein, which is correlated with Alzheimer's disease. Results indicated that the four flavones effectively inhibited the aggregation of the two peptides and mostly dispersed the mature fibrils to monomers. The interactions of flavones with the two peptides demonstrated a spontaneous and exothermic reaction through predominant hydrophobic and hydrogen bonding interactions. The binding affinities of 1 and 3 were stronger than those of 2 and 4 possibly because of the difference in the substituent groups of these molecules. These flavones could also decrease membrane leakage and upregulate cell viability by reducing the formation of toxic oligomers. Moreover, the performance of these flavones in terms of binding affinity, cellular viability, and decreased oligomerization was better on hIAPP than on Aβ. This work offered valuable data about these flavones as prospective therapeutic agents against relevant diseases.

Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates

The pathological Aβ aggregates associated with Alzheimer's disease follow a nucleation-dependent path of formation. A nucleus represents an oligomeric assembly of Aβ peptides that acts as a template for subsequent incorporation of monomers to form a fibrillar structure. Nuclei can form de novo or via surface-catalyzed secondary nucleation, and the combined rates of elongation and nucleation control the overall rate of fibril formation. Transthyretin (TTR) obstructs Aβ fibril formation in favor of alternative non-fibrillar assemblies, but the mechanism behind this activity is not fully understood. This study shows that TTR does not significantly disturb fibril elongation; rather, it effectively interferes with the formation of oligomeric nuclei. We demonstrate that this interference can be modulated by altering the relative contribution of elongation and nucleation, and we show how TTR's effects can range from being essentially ineffective to almost complete inhibition of fibril formation without changing the concentration of TTR or monomeric Aβ.

Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry

Living organisms regularly need to cope with fluctuating environments during their life cycle, including changes in temperature, pH, the accumulation of reactive oxygen species, and more. These fluctuations can lead to a widespread protein unfolding, aggregation, and cell death. Therefore, cells have evolved a dynamic and stress-specific network of molecular chaperones, which maintain a "healthy" proteome during stress conditions. ATP-independent chaperones constitute one major class of molecular chaperones, which serve as first-line defense molecules, protecting against protein aggregation in a stress-dependent manner. One feature these chaperones have in common is their ability to utilize structural plasticity for their stress-specific activation, recognition, and release of the misfolded client. In this paper, we focus on the functional and structural analysis of one such intrinsically disordered chaperone, the bacterial redox-regulated Hsp33, which protects proteins against aggregation during oxidative stress. Here, we present a toolbox of diverse techniques for studying redox-regulated chaperone activity, as well as for mapping conformational changes of the chaperone, underlying its activity. Specifically, we describe a workflow which includes the preparation of fully reduced and fully oxidized proteins, followed by an analysis of the chaperone anti-aggregation activity in vitro using light-scattering, focusing on the degree of the anti-aggregation activity and its kinetics. To overcome frequent outliers accumulated during aggregation assays, we describe the usage of Kfits, a novel graphical tool which allows easy processing of kinetic measurements. This tool can be easily applied to other types of kinetic measurements for removing outliers and fitting kinetic parameters. To correlate the function with the protein structure, we describe the setup and workflow of a structural mass spectrometry technique, hydrogen-deuterium exchange mass spectrometry, that allows the mapping of conformational changes on the chaperone and substrate during different stages of Hsp33 activity. The same methodology can be applied to other protein-protein and protein-ligand interactions.

Cooperative Assembly of Hsp70 Subdomain Clusters

Many molecular chaperones exist as oligomeric complexes in their functional states, yet the physical determinants underlying such self-assembly behavior, as well as the role of oligomerization in the activity of molecular chaperones in inhibiting protein aggregation, have proven to be difficult to define. Here, we demonstrate direct measurements under native conditions of the changes in the average oligomer populations of a chaperone system as a function of concentration and time and thus determine the thermodynamic and kinetic parameters governing the self-assembly process. We access this self-assembly behavior in real time under native-like conditions by monitoring the changes in the micrometer-scale diffusion of the different complexes in time and space using a microfluidic platform. Using this approach, we find that the oligomerization mechanism of the Hsp70 subdomain occurs in a cooperative manner and involves structural constraints that limit the size of the species formed beyond the limits imposed by mass balance. These results illustrate the ability of microfluidic methods to probe polydisperse protein self-assembly in real time in solution and to shed light on the nature and dynamics of oligomerization processes.

The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation

Fibril formation of the amyloid-β peptide (Aβ) follows a nucleation-dependent polymerization process and is associated with Alzheimer's disease. Several different lengths of Aβ are observed in vivo, but Aβ1-40 and Aβ1-42 are the dominant forms. The fibril architectures of Aβ1-40 and Aβ1-42 differ and Aβ1-42 assemblies are generally considered more pathogenic. We show here that monomeric Aβ1-42 can be cross-templated and incorporated into the ends of Aβ1-40 fibrils, while incorporation of Aβ1-40 monomers into Aβ1-42 fibrils is very poor. We also show that via cross-templating incorporated Aβ monomers acquire the properties of the parental fibrils. The suppressed ability of Aβ1-40 to incorporate into the ends of Aβ1-42 fibrils and the capacity of Aβ1-42 monomers to adopt the properties of Aβ1-40 fibrils may thus represent two mechanisms reducing the total load of fibrils having the intrinsic, and possibly pathogenic, features of Aβ1-42 fibrils in vivo. We also show that the transfer of fibrillar properties is restricted to fibril-end templating and does not apply to cross-nucleation via the recently described path of surface-catalyzed secondary nucleation, which instead generates similar structures to those acquired via de novo primary nucleation in the absence of catalyzing seeds. Taken together these results uncover an intrinsic barrier that prevents Aβ1-40 from adopting the fibrillar properties of Aβ1-42 and exposes that the transfer of properties between amyloid-β fibrils are determined by their path of formation.

NMR Studies of Large Proteins

Recent breakthroughs in isotope-labeling and pulse sequence techniques have enabled the NMR characterization of large protein systems with molecular masses of hundreds of kilodaltons. NMR studies of a great variety of large proteins have provided unique insights into the binding, dynamic, and allosteric mechanisms. Here we present a brief summary of these developments by highlighting few cases that exemplify the uniqueness of NMR in providing atomic resolution information into key dynamic processes and structures of protein complexes with high degree of flexibility.

The Amyloid Phenomenon and Its Links with Human Disease

The ability of normally soluble proteins to convert into amyloid fibrils is now recognized to be a generic phenomenon. The overall cross-β architecture of the core elements of such structures is closely similar for different amino acid sequences, as this architecture is dominated by interactions associated with the common polypeptide main chain. In contrast, the multiplicity of complex and intricate structures of the functional states of proteins is dictated by specific interactions involving the variable side chains, the sequence of which is unique to a given protein. Nevertheless, the side chains dictate important aspects of the amyloid structure, including the regions of the sequence that form the core elements of the fibrils and the kinetics and mechanism of the conversion process. The formation of the amyloid state of proteins is of particular importance in the context of a range of medical disorders that include Alzheimer's and Parkinson's diseases and type 2 diabetes. These disorders are becoming increasingly common in the modern world, primarily as a consequence of increasing life spans and changing lifestyles, and now affect some 500 million people worldwide. This review describes recent progress in our understanding of the molecular origins of these conditions and discusses emerging ideas for new and rational therapeutic strategies by which to combat their onset and progression.

Detection, inhibition and disintegration of amyloid fibrils: the role of optical probes and macrocyclic receptors

This article provides a brief account of the recent reports on the early detection of amyloid fibril formation using fluorescent dyes and inhibition and disintegration of fibrils using macrocyclic receptors, which find applications in the treatment of fibril associated neurodegenerative diseases.

Trehalose Inhibits Protein Aggregation Caused by Transient Ischemic Insults Through Preservation of Proteasome Activity, Not via Induction of Autophagy

Protein aggregation has been proved to be a pathological basis accounting for neuronal death caused by either transient global ischemia or oxygen glucose deprivation (OGD), and inhibition of protein aggregation is emerging as a potential strategy of preventing brain damage. Trehalose was found to inhibit protein aggregation caused by neurodegenerative diseases via induction of autophagy, whereas its effect is still elusive on ischemia-induced protein aggregation. In this study, we investigated this issue by using rat model of transient global ischemia and SH-SY5Y model of OGD. We found that pretreatment with trehalose inhibited transient global ischemia-induced neuronal death in the hippocampus CA1 neurons and OGD-induced death in SH-SY5Y cells, which was associated with inhibition of the formation of ubiquitin-labeled protein aggregates and preservation of proteasome activity. In vitro study showed that the protection of trehalose against OGD-induced cell death and protein aggregation in SH-SY5Y cells was reversed when proteasome activity was inhibited by MG-132. Further studies revealed that trehalose prevented OGD-induced reduction of proteasome activity via suppression of both oxidative stress and endoplasmic reticulum stress. Particularly, our results showed that trehalose inhibited OGD-induced autophagy. Therefore, we demonstrated that proteasome dysfunction contributed to protein aggregation caused by ischemic insults and trehalose prevented protein aggregation via preservation of proteasome activity, not via induction of autophagy.

Solution NMR Spectroscopy Provides an Avenue for the Study of Functionally Dynamic Molecular Machines: The Example of Protein Disaggregation

Solution-based NMR spectroscopy has been an important tool for studying the structure and dynamics of relatively small proteins and protein complexes with aggregate molecular masses under approximately 50 kDa. The development of new experiments and labeling schemes, coupled with continued improvements in hardware, has significantly reduced this size limitation, enabling atomic-resolution studies of molecular machines in the 1 MDa range. In this Perspective, some of the important advances are highlighted in the context of studies of molecular chaperones involved in protein disaggregation. New insights into the structural biology of disaggregation obtained from NMR studies are described, focusing on the unique capabilities of the methodology for obtaining atomic-resolution descriptions of dynamic systems.