Modulation of human IAPP fibrillation: cosolutes, crowders and chaperones

Effect of trimethylamine-N-oxide on the phase separation of aqueous polyethylene glycol-600-Dextran-75 two-phase systems

The emergence of phase separation in both intracellular biomolecular condensates (membrane-less organelles) and in vitro aqueous two-phase systems (ATPS) relies on the formation of immiscible water-based phases/domains. The solvent properties and arrangement of hydrogen bonds within these domains have been shown to differ and can be modulated with the addition of various inorganic salts and osmolytes. The naturally occuring osmolyte, trimethylamine-N-oxide (TMAO), is well established as a biological condensate stabilizer whose presence results in enhanced phase separation of intracellular membrane-less compartments. Here, we show the unique effect of TMAO on the mechanism of phase separation in model PEG-600-Dextran-75 ATPS using dynamic and static light scattering in conjunction with ATR-FTIR and solvatochromic analysis. We observe that the presence of TMAO may enhance or destabilize phase separation depending on the concentration of phase forming components. Additionally, the behavior and density of mesoscopic polymer agglomerates, which arise prior to macroscopic phase separation, are altered by the presence and concentration of TMAO.

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

Nonspecific interaction and overlap concentration influence macromolecular crowding effect on glucose oxidase activity

Macromolecular crowding can change kinetics of enzyme catalysis. How interaction between enzymes and neighboring macromolecules contributes to the crowding effect on enzyme catalysis has not been quantitatively revealed. In this study, crowding effects of dextran and poly(ethylene glycol) (PEG) on glucose oxidase (GOx) are studied. Fluorescence resonance energy transfer experiments show the high transfer efficiency and stable interaction between the dextran and GOx. Further fluorescence quenching analysis also proves that the association of the dextran-GOx pair can become stronger than that of the PEG-GOx pair. Dextrans with concentrations above or below their chain overlap concentrations (c*) reduce Michaelis constants (K_m) of GOx catalysis by 90 % or 45 %, respectively, through volume exclusion mechanism, and in the meantime elevate the enzymatic efficiency (k_cat/K_m) by 8-fold or by 3-fold, respectively, which is more dramatic than that found in other enzymes before. Strong association between the enzyme and the dextran results in slow turnover rates (k_cat). Intermediate crowding with weak to moderate affinity to the enzyme below the c* can tune the k_cat higher than in the free state. Catalysis under crowded conditions is a joint effect of the enzyme-crowder nonspecific interaction, volume exclusion and overlap condition of the crowders.

Physiological models to study the effect of molecular crowding on multi-drug bound proteins: insights from SARS-CoV-2 main protease

Molecular Dynamics simulations are often used in drug design. However, such simulations do not account for the physiological environment of the receptor; hence overlook its impact on biomolecular interactions. To address this lacuna, we identified three objectives to pursue - develop models of physiological environment, study a drug-receptor complex in such environments, and identify methods to analyze these complicated simulations. Two novel physiological models were developed and studied. The first, called 'm10', comprises of 10 of the most abundant cytoplasmic metabolites at physiological concentrations. The second, called 'phy', supplements m10 with an additional crowder protein to elicit macromolecular crowding effect. The main protease (M^pro) of SARS-CoV-2, being essential for viral replication, is an attractive drug target for COVID-19. Hence, we chose M^pro docked with multiple drugs as our model drug-receptor system. With a plethora of compounds, physiological systems can be exceedingly large and complex. A novel Spark-based software (SparkTraj) was developed to rapidly analyze non-specific contacts and water interactions. Our study shows that crowding enhances the difference in the dynamics of apo- vs drug-bound complexes. Metabolites, at times as a cluster, were seen interacting with the protease, drugs, and binding sites in drug-free receptor. Except one that crawled to an adjacent pocket in phy, the drugs remained in their respective pockets in all simulations. Given these observations, we hope that the models and approach presented here would help the optimization, evaluation, and selection of potential drugs. Generic biomolecular dynamics could also benefit from such models and tools.Communicated by Ramaswamy H. Sarma.

Interaction of Human Resistin with Human Islet Amyloid Polypeptide at Charged Phospholipid Membranes

An X-ray reflectivity study on the interaction of recombinant human resistin (hRes) with fibrillation-prone human islet amyloid polypeptide (hIAPP) at anionic phospholipid Langmuir films as model membranes is presented. Aggregation and amyloid formation of hIAPP is considered the main mechanism of pancreatic β-cell loss in patients with type 2 diabetes mellitus. Resistin shows a chaperone-like ability, but also tends to form aggregates by itself. Resistin and hIAPP cross multiply metabolism pathways. In this study, we researched the potential protective effects of resistin against hIAPP-induced lipid membrane rupture. The results demonstrate that resistin can inhibit or prevent hIAPP adsorption even in the presence of aggregation-promoting negatively charged lipid interfaces. Moreover, we found strong hydrophobic interactions of resistin at the bare buffer-air interface.

Human islet amyloid polypeptide: A therapeutic target for the management of type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) and other metabolic disorders are often silent and go unnoticed in patients because of the lack of suitable prognostic and diagnostic markers. The current therapeutic regimens available for managing T2DM do not reverse diabetes; instead, they delay the progression of diabetes. Their efficacy (in principle) may be significantly improved if implemented at earlier stages. The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) or amylin has been associated with a gradual decrease in pancreatic β-cell function and mass in patients with T2DM. Hence, hIAPP has been recognized as a therapeutic target for managing T2DM. This review summarizes hIAPP's role in mediating dysfunction and apoptosis in pancreatic β-cells via induction of endoplasmic reticulum stress, oxidative stress, mitochondrial dysfunction, inflammatory cytokine secretion, autophagy blockade, etc. Furthermore, it explores the possibility of using intermediates of the hIAPP aggregation pathway as potential drug targets for T2DM management. Finally, the effects of common antidiabetic molecules and repurposed drugs; other hIAPP mimetics and peptides; small organic molecules and natural compounds; nanoparticles, nanobodies, and quantum dots; metals and metal complexes; and chaperones that have demonstrated potential to inhibit and/or reverse hIAPP aggregation and can, therefore, be further developed for managing T2DM have been discussed.

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Misfolded species of hIAPP form toxic oligomers in pancreatic β-cells.

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hIAPP amyloids has been detected in the pancreas of about 90% subjects with T2DM.

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Inhibitors of hIAPP aggregation can help manage T2DM.

Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo

The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Macromolecular Crowding Effect on the Structure, Function, Conformational Dynamics and Relative Domain Movement of a Multi-Domain Protein as a function of Crowder Shape and Interaction

The cellular environment is crowded by macromolecules of various sizes, shapes, and charges, which modulate protein structure, function and dynamics. Herein, we contemplated the effect of three different macromolecular crowders:...

Amyloidogenicity of peptides targeting diabetes and obesity

Since the discovery of insulin, a century ago, the repertoire of therapeutic polypeptides targeting diabetes - and now also obesity - have increased substantially. The focus on quality has shifted from impure and unstable preparations of animal insulin to highly pure, homologous recombinant insulin, along with other peptide-based hormones and analogs such as amylin analogs (pramlintide, davalintide, cagrilintide), glucagon and glucagon-like peptide-1 receptor agonists (GLP-1, liraglutide, exenatide, semaglutide). Proper formulation, storage, manipulation and usage by professionals and patients are required in order to avoid agglomeration into high molecular weight products (HMWP), either amorphous or amyloid, which could result in potential loss of biological activity and short- or long-term immune reaction and silent inactivation. In this narrative review, we present perspective of the aggregation of therapeutic polypeptides used in diabetes and other metabolic diseases, covering the nature and mechanisms, analytical techniques, physical and chemical stability, strategies aimed to hamper the formation of HMWP, and perspectives on future biopharmaceutical developments.

Brazilin Removes Toxic Alpha-Synuclein and Seeding Competent Assemblies from Parkinson Brain by Altering Conformational Equilibrium

Alpha-synuclein (α-syn) fibrils, a major constituent of the neurotoxic Lewy Bodies in Parkinson's disease, form via nucleation dependent polymerization and can replicate by a seeding mechanism. Brazilin, a small molecule derived from red cedarwood trees in Brazil, has been shown to inhibit the fibrillogenesis of amyloid-beta (Aβ) and α-syn as well as remodel mature fibrils and reduce cytotoxicity. Here we test the effects of Brazilin on both seeded and unseeded α-syn fibril formation and show that the natural polyphenol inhibits fibrillogenesis of α-syn by a unique mechanism that alters conformational equilibria in two separate points of the assembly mechanism: Brazilin preserves the natively unfolded state of α-syn by specifically binding to the compact conformation of the α-syn monomer. Brazilin also eliminates seeding competence of α-syn assemblies from Parkinson's disease patient brain tissue, and reduces toxicity of pre-formed assemblies in primary neurons by inducing the formation of large fibril clusters. Molecular docking of Brazilin shows the molecule to interact both with unfolded α-syn monomers and with the cross-β sheet structure of α-syn fibrils. Our findings suggest that Brazilin has substantial potential as a neuroprotective and therapeutic agent for Parkinson's disease.

Pharmacological Targeting of Endoplasmic Reticulum Stress in Pancreatic Beta Cells

Diabetes is a disease with pandemic dimensions and no pharmacological treatment prevents disease progression. Dedifferentiation has been proposed to be a driver of beta-cell dysfunction in both type 1 and type 2 diabetes. Regenerative therapies aim to re-establish function in dysfunctional or dedifferentiated beta cells and restore the defective insulin secretion. Unsustainable levels of insulin production, with increased demand at disease onset, strain the beta-cell secretory machinery, leading to endoplasmic reticulum (ER) stress. Unresolved chronic ER stress is a major contributor to beta-cell loss of function and identity. Restoring ER homeostasis, enhancing ER-associated degradation of misfolded protein, and boosting chaperoning activity, are emerging therapeutic approaches for diabetes treatment.

Self-Assembly of Pseudo-Isocyanine Chloride as a Sensor for Macromolecular Crowding In Vitro and In Vivo

Pseudo‐isocyanine chloride (PIC) is a cationic dyestuff that exhibits self‐assembly in aqueous solution, promoted either by increasing the PIC concentration or by decreasing the temperature. PIC‐aggregates exhibit a characteristic and sharp absorption band as well as a fluorescence band at a wavelength of 573 nm making PIC an interesting candidate to analyze the self‐assembly process in various environments. The present work developed PIC‐based, synthetic model systems, suitable to investigate how macromolecular crowding influences self‐assembly processes. Four synthetic additives were used as potential crowders: Triethylene glycol (TEG), polyethylene glycol (PEG), Ficoll 400 as a highly branched polysaccharide, and sucrose corresponding to the monomeric unit of Ficoll. Combined UV/Vis spectroscopy and time‐resolved light scattering revealed a strong impact of crowding based on excluded volume effects only for Ficoll 400. Sucrose had hardly any influence on the self‐assembly of PIC and PEG and TEG impeded the PIC self‐assembly. Development of such a PIC based model system led over to in‐cell experiments. HeLa cells were infiltrated with PIC solutions well below the aggregation threshold in the infiltrating solution. In the cellular environment, PIC was exposed to a significant crowding and immediately started to aggregate. As was demonstrated by fluorescence imaging, the extent of aggregation can be modulated by exposing the cells to salt‐induced osmotic stress. The results suggest future use of such a system as a sensor for the analysis of in vitro and in vivo crowding effects on self‐assembly processes.

Islet Amyloid Polypeptide: A Partner in Crime With Aβ in the Pathology of Alzheimer's Disease

Diabetes affects hundreds of millions of patients worldwide. Despite the advances in understanding the disease and therapeutic options, it remains a leading cause of death and of comorbidities globally. Islet amyloid polypeptide (IAPP), or amylin, is a hormone produced by pancreatic β-cells. It contributes to the maintenance of glucose physiological levels namely by inhibiting insulin and glucagon secretion as well as controlling adiposity and satiation. IAPP is a highly amyloidogenic polypeptide forming intracellular aggregates and amyloid structures that are associated with β-cell death. Data also suggest the relevance of unprocessed IAPP forms as seeding for amyloid buildup. Besides the known consequences of hyperamylinemia in the pancreas, evidence has also pointed out that IAPP has a pathological role in cognitive function. More specifically, IAPP was shown to impair the blood–brain barrier; it was also seen to interact and co-deposit with amyloid beta peptide (Aß), and possibly with Tau, within the brain of Alzheimer's disease (AD) patients, thereby contributing to diabetes-associated dementia. In fact, it has been suggested that AD results from a metabolic dysfunction in the brain, leading to its proposed designation as type 3 diabetes. Here, we have first provided a brief perspective on the IAPP amyloidogenic process and its role in diabetes and AD. We have then discussed the potential interventions for modulating IAPP proteotoxicity that can be explored for therapeutics. Finally, we have proposed the concept of a “diabetes brain phenotype” hypothesis in AD, which may help design future IAPP-centered drug developmentstrategies against AD.

Atomic Force Microscopy: The Characterisation of Amyloid Protein Structure in Pathology

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Proteins are versatile macromolecules that perform a variety of functions and participate in virtually all cellular processes. The functionality of a protein greatly depends on its structure and alterations may result in the development of diseases. Most well-known of these are protein misfolding disorders, which include Alzheimer’s and Parkinson’s diseases as well as type 2 diabetes mellitus, where soluble proteins transition into insoluble amyloid fibrils. Atomic Force Microscopy (AFM) is capable of providing a topographical map of the protein and/or its aggregates, as well as probing the nanomechanical properties of a sample. Moreover, AFM requires relatively simple sample preparation, which presents the possibility of combining this technique with other research modalities, such as confocal laser scanning microscopy, Raman spectroscopy and stimulated emission depletion microscopy. In this review, the basic principles of AFM are discussed, followed by a brief overview of how it has been applied in biological research. Finally, we focus specifically on its use as a characterisation method to study protein structure at the nanoscale in pathophysiological conditions, considering both molecules implicated in disease pathogenesis and the plasma protein fibrinogen. In conclusion, AFM is a userfriendly tool that supplies multi-parametric data, rendering it a most valuable technique.

Blood-based protein mediators of senility with replications across biofluids and cohorts

Dementia severity can be quantitatively described by the latent dementia phenotype 'δ' and its various composite 'homologues'. We have explored δ's blood-based protein biomarkers in the Texas Alzheimer's Research and Care Consortium. However, it would be convenient to replicate them in the Alzheimer's Disease Neuroimaging Initiative. To that end, we have engineered a δ homologue from the observed cognitive performance measures common to both projects [i.e. 'd:Texas Alzheimer's Research and Care Consortium to Alzheimer's Disease Neuroimaging Initiative' (dT2A)]. In this analysis, we confirm 13/22 serum proteins as partial mediators of age's effect on dementia severity as measured by dT2A in the Texas Alzheimer's Research and Care Consortium and then replicate 4/13 in the Alzheimer's Disease Neuroimaging Initiative's plasma data. The replicated mediators of age-specific effects on dementia severity are adiponectin, follicle-stimulating hormone, pancreatic polypeptide and resistin. In their aggregate, the 13 confirmed age-specific mediators suggest that 'cognitive frailty' pays a role in dementia severity as measured by δ. We provide both discriminant and concordant support for that hypothesis. Weight, calculated low-density lipoprotein and body mass index are partial mediators of age's effect in the Texas Alzheimer's Research and Care Consortium. Biomarkers related to other disease processes (e.g. cerebrospinal fluid Alzheimer's disease-specific biomarkers in the Alzheimer's Disease Neuroimaging Initiative) are not. It now appears that dementia severity is the sum of multiple independent processes impacting δ. Each may have a unique set of mediating biomarkers. Age's unique effect appears to be at least partially mediated through proteins related to frailty. Age-specific mediation effects can be replicated across cohorts and biofluids. These proteins may offer targets for the remediation of age-specific cognitive decline (aka 'senility'), help distinguish it from other determinants of dementia severity and/or provide clues to the biology of Aging Proper.

Molecular Dynamics Simulations Reveal the Inhibitory Mechanism of Dopamine against Human Islet Amyloid Polypeptide (hIAPP) Aggregation and Its Destabilization Effect on hIAPP Protofibrils

The aberrant self-assembly of human islet amyloid polypeptide (hIAPP) into toxic oligomers, protofibrils, and mature fibrils is associated with the pathogenesis of type 2 diabetes (T2D). Inhibition of hIAPP aggregation and destabilization of preformed hIAPP fibrils are considered as two major therapeutic strategies for treating T2D. Previous experimental studies reported that dopamine prevented the formation of hIAPP oligomers and fibrils. However, the underlying inhibitory mechanism at the atomic level remains elusive. Herein we investigated the conformational ensembles of hIAPP dimer with and without dopamine using replica-exchange molecular dynamics simulations. The simulations demonstrated that dopamine preferentially bound to R11, L12, F15, H18, F23, I26, L27, and Y37 residues, inhibited the formation of β-sheets in the amyloidogenic regions spanning residues ¹¹RLANFLVH¹⁸, ²²NFGAIL²⁷, and ³⁰TNVGSNT³⁶, and resulted in more disordered hIAPP dimers, thus hindering the amyloid formation of hIAPP. Protonated and deprotonated dopamine molecules displayed distinct binding capabilities but bound to similar residue sites on hIAPP. Additional microsecond molecular dynamics simulations showed that dopamine mainly bound to the β1 and turn regions of hIAPP protofibril and destabilized the protofibril structure. This study not only revealed the molecular mechanism of dopamine toward the inhibition of hIAPP aggregation but also demonstrated the protofibril-destabilizing effects of dopamine, which may be helpful for the design of drug candidates to treat T2D.

Effects of in vivo conditions on amyloid aggregation

One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.

Melting Down Protein Stability: PAPS Synthase 2 in Patients and in a Cellular Environment

Within the crowded and complex environment of the cell, a protein experiences stabilizing excluded-volume effects and destabilizing quinary interactions with other proteins. Which of these prevail, needs to be determined on a case-by-case basis. PAPS synthases are dimeric and bifunctional enzymes, providing activated sulfate in the form of 3′-phosphoadenosine-5′-phosphosulfate (PAPS) for sulfation reactions. The human PAPS synthases PAPSS1 and PAPSS2 differ significantly in their protein stability as PAPSS2 is a naturally fragile protein. PAPS synthases bind a series of nucleotide ligands and some of them markedly stabilize these proteins. PAPS synthases are of biomedical relevance as destabilizing point mutations give rise to several pathologies. Genetic defects in PAPSS2 have been linked to bone and cartilage malformations as well as a steroid sulfation defect. All this makes PAPS synthases ideal to study protein unfolding, ligand binding, and the stabilizing and destabilizing factors in their cellular environment. This review provides an overview on current concepts of protein folding and stability and links this with our current understanding of the different disease mechanisms of PAPSS2-related pathologies with perspectives for future research and application.

Simultaneous Prediction of Cosolvent Influence on Reaction Equilibrium and Michaelis Constants of Enzyme-Catalyzed Ketone Reductions

Understanding and quantification of cosolvent influences on enzyme-catalyzed reactions are driven by a twofold interest. On the one hand, cosolvents can simulate the cellular environment for deeper understanding of in cellulo reaction conditions. On the other hand, cosolvents are applied in biotechnology to tune yield and kinetics of reactions. Further, cosolvents are even present inherently, for example, for reactions with cofactor regeneration or for enzymes that need cosolvents in a function of a stabilizer. As the experimental determination of yield and kinetics is costly and time consuming, this work aims at providing a thermodynamic predictive approach that might allow screening cosolvent influences on yield and Michaelis constants. Reactions investigated in this work are the reduction of butanone and 2-pentanone under the influence of 17 wt % of the cosolvent polyethylene glycol 6000, which is also often used as a crowder to simulate cellular environments. The considered reactions were catalyzed by a genetically modified alcohol dehydrogenase (ADH 270). Predictions of cosolvent influences are based on accounting for a cosolvent-induced change of molecular interactions among the reacting agents as well as between the reacting agents and the solvent. Such interactions were characterized by activity coefficients of the reacting agents that were predicted by means of electrolyte perturbed-chain statistical associating fluid theory. This allowed simultaneously predicting the cosolvent effects on yield and Michaelis constants for two-substrate reactions for the first time.

mHTT Seeding Activity: A Marker of Disease Progression and Neurotoxicity in Models of Huntington's Disease

Self-propagating, amyloidogenic mutant huntingtin (mHTT) aggregates may drive progression of Huntington's disease (HD). Here, we report the development of a FRET-based mHTT aggregate seeding (FRASE) assay that enables the quantification of mHTT seeding activity (HSA) in complex biosamples from HD patients and disease models. Application of the FRASE assay revealed HSA in brain homogenates of presymptomatic HD transgenic and knockin mice and its progressive increase with phenotypic changes, suggesting that HSA quantitatively tracks disease progression. Biochemical investigations of mouse brain homogenates demonstrated that small, rather than large, mHTT structures are responsible for the HSA measured in FRASE assays. Finally, we assessed the neurotoxicity of mHTT seeds in an inducible Drosophila model transgenic for HTTex1. We found a strong correlation between the HSA measured in adult neurons and the increased mortality of transgenic HD flies, indicating that FRASE assays detect disease-relevant, neurotoxic, mHTT structures with severe phenotypic consequences in vivo.

Cosolvent and Crowding Effects on the Temperature- and Pressure-Dependent Dissociation Process of the α/β-Tubulin Heterodimer

Tubulin is one of the main components of the cytoskeleton of eukaryotic cells. The formation of microtubules depends strongly on environmental and solution conditions, and has been found to be among the most pressure sensitive processes in vivo. We explored the effects of different types of cosolvents, such as trimethylamine-N-oxide (TMAO), sucrose and urea, and crowding agents to mimic cell-like conditions, on the temperature and pressure stability of the building block of microtubules, i. e. the α/β-tubulin heterodimer. To this end, fluorescence and FTIR spectroscopy, differential scanning and pressure perturbation calorimetry as well as fluorescence anisotropy and correlation spectroscopies were applied. The pressure and temperature of dissociation of α/β-tubulin as well as the underlying thermodynamic parameters upon dissociation, such as volume and enthalpy changes, have been determined for the different solution conditions. The temperature and pressure of dissociation of the α/β-tubulin heterodimer and hence its stability increases dramatically in the presence of TMAO and the nanocrowder sucrose. We show that by adjusting the levels of compatible cosolutes and crowders, cells are able to withstand deteriorating effects of pressure even up to the kbar-range.

Vibrational Approach to the Dynamics and Structure of Protein Amyloids

Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.

Inhibition of protein misfolding and aggregation by natural phenolic compounds

Protein misfolding and aggregation into fibrillar deposits is a common feature of a large group of degenerative diseases affecting the central nervous system or peripheral organs, termed protein misfolding disorders (PMDs). Despite their established toxic nature, clinical trials aiming to reduce misfolded aggregates have been unsuccessful in treating or curing PMDs. An interesting possibility for disease intervention is the regular intake of natural food or herbal extracts, which contain active molecules that inhibit aggregation or induce the disassembly of misfolded aggregates. Among natural compounds, phenolic molecules are of particular interest, since most have dual activity as amyloid aggregation inhibitors and antioxidants. In this article, we review many phenolic natural compounds which have been reported in diverse model systems to have the potential to delay or prevent the development of various PMDs, including Alzheimer's and Parkinson's diseases, prion diseases, amyotrophic lateral sclerosis, systemic amyloidosis, and type 2 diabetes. The lower toxicity of natural compounds compared to synthetic chemical molecules suggest that they could serve as a good starting point to discover protein misfolding inhibitors that might be useful for the treatment of various incurable diseases.

Role and Cytotoxicity of Amylin and Protection of Pancreatic Islet β-Cells from Amylin Cytotoxicity

Amylin, (or islet amyloid polypeptide; IAPP), a 37-amino acid peptide hormone, is released in response to nutrients, including glucose, lipids or amino acids. Amylin is co-stored and co-secreted with insulin by pancreatic islet β-cells. Amylin inhibits food intake, delays gastric emptying, and decreases blood glucose levels, leading to the reduction of body weight. Therefore, amylin as well as insulin play important roles in controlling the level of blood glucose. However, human amylin aggregates and human amylin oligomers cause membrane disruption, endoplasmic reticulum (ER) stress and mitochondrial damage. Since cytotoxicity of human amylin oligomers to pancreatic islet β-cells can lead to diabetes, the protection of pancreatic islet β cells from cytotoxic amylin is crucial. Human amylin oligomers also inhibit autophagy, although autophagy can function to remove amylin aggregates and damaged organelles. Small molecules, including β-sheet breaker peptides, chemical chaperones, and foldamers, inhibit and disaggregate amyloid formed by human amylin, suggesting the possible use of these small molecules in the treatment of diabetes. In this review, we summarize recent findings regarding the role and cytotoxicity of amylin and the protection of pancreatic islet β-cells from cytotoxicity of amylin.

Pressure and cosolvent modulation of the catalytic activity of amyloid fibrils

We report on the effects of pressure and cosolvents on the catalytic activity of a designed amyloid fibril by applying a high-pressure stopped-flow methodology with rapid spectroscopic detection. FTIR spectroscopic data revealed a remarkable pressure and temperature stability of the fibrillar catalyst. The activity is further enhanced by osmolytes and macromolecular crowding.

Changing relations between proteins and osmolytes: a choice of nature

The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.

Critical Influence of Cosolutes and Surfaces on the Assembly of Serpin-Derived Amyloid Fibrils

Many proteins and peptides self-associate into highly ordered and structurally similar amyloid cross-β aggregates. This fibrillation is critically dependent on properties of the protein and the surrounding environment that alter kinetic and thermodynamic equilibria. Here, we report on dominating surface and solution effects on the fibrillogenic behavior and amyloid assembly of the C-36 peptide, a circulating bioactive peptide from the α₁-antitrypsin serine protease inhibitor. C-36 converts from an unstructured peptide to mature amyloid twisted-ribbon fibrils over a few hours when incubated on polystyrene plates under physiological conditions through a pathway dominated by surface-enhanced nucleation. In contrast, in plates with nonbinding surfaces, slow bulk nucleation takes precedence over surface catalysis and leads to fibrillar polymorphism. Fibrillation is strongly ion-sensitive, underlining the interplay between hydrophilic and hydrophobic forces in molecular self-assembly. The addition of exogenous surfaces in the form of silica glass beads and polyanionic heparin molecules potently seeds the amyloid conversion process. In particular, heparin acts as an interacting template that rapidly forces β-sheet aggregation of C-36 to distinct amyloid species within minutes and leads to a more homogeneous fibril population according to solid-state NMR analysis. Heparin's template effect highlights its role in amyloid seeding and homogeneous self-assembly, which applies both in vitro and in vivo, where glycosaminoglycans are strongly associated with amyloid deposits. Our study illustrates the versatile thermodynamic landscape of amyloid formation and highlights how different experimental conditions direct C-36 into distinct macromolecular structures.

l-Proline and RNA Duplex m-Value Temperature Dependence

The temperature dependence of l-proline interactions with the RNA dodecamer duplex surface exposed after unfolding was quantified using thermal and isothermal titration denaturation monitored by uv-absorbance. The m-value quantifying proline interactions with the RNA duplex surface area exposed after unfolding was measured using RNA duplexes with GC content ranging between 17 and 83%. The m-values from thermal denaturation decreased with increasing GC content signifying increasingly favorable proline interactions with the exposed RNA surface area. However, m-values from isothermal titration denaturation at 25.0 °C were independent of GC content and less negative than those from thermal denaturation. The m-value from isothermal titration denaturation for a 50% GC RNA duplex decreased (became more negative) as the temperature increased and was in nearly exact agreement with the m-value from thermal denaturation. Since RNA duplex transition temperatures increased with GC content, the more favorable proline interactions with the high GC content duplex surface area observed from thermal denaturation resulted from the temperature dependence of proline interactions rather than the RNA surface chemical composition. The enthalpy contribution to the m-value was positive and small (indicating a slight increase in duplex unfolding enthalpy with proline) while the entropic contribution to the m-value was positive and increased with temperature. Our results will facilitate proline's use as a probe of solvent accessible surface area changes during biochemical reactions at different reaction temperatures.

Sucrose modulates insulin amyloid-like fibril formation: effect on the aggregation mechanism and fibril morphology

Sucrose modifies the human insulin fibrillation pathways, affecting the fibril morphology.

Insulin Formulation Characterization-the Thioflavin T Assays

The insulin molecule was discovered in 1921. Shortly thereafter, its propensity towards amyloid fibril formation, fibrillation, was observed and described in the literature as a "precipitate." In the past decades, the increased incidence of type 2 diabetes has reached global epidemic proportions. This has emphasized the demands for both insulin production and the development of modern insulin products for unmet medical needs. Bringing such new insulin drug products to the market for the benefit of patients requires that many CMC-related processes are understood, described, and controlled. One potential undesired process is insulin fibril formation. The compound thioflavin T (ThT) is known as a fluorescent probe for amyloid fibrils. As such, ThT is utilized in a versatile research assay in microtiter plate format, the ThT assay. This review will describe an experimental set-up using not only a ThT microtiter plate assay but also two orthogonal methods. The use of the ThT assay in research and characterization of insulin analogues, as well as formulations of insulin, is described by cases drawn from the scientific literature and patents. The ThT assay is compared to other physical stability tests and in conclusion the advantages and limitations of the assay are compared.

Regulation of the assembly and amyloid aggregation of murine amylin by zinc

The secretory granule of the pancreatic β-cells is a zinc-rich environment copopulated with the hormones amylin and insulin. The human amylin is shown to interact with zinc ions with major contribution from the single histidine residue, which is absent in amylin from other species such as cat, rhesus and rodents. We report here the interaction of murine amylin with zinc ions in vitro. The self-assembly of murine amylin is tightly regulated by zinc and pH. Ion mobility mass spectrometry revealed zinc interaction with monomers and oligomers. Nuclear magnetic resonance confirms the binding of zinc to murine amylin. The aggregation process of murine amylin into amyloid fibrils is accelerated by zinc. Collectively these data suggest a general role of zinc in the modulation of amylin variants oligomerization and amyloid fibril formation.

Understanding and predicting protein misfolding and aggregation: Insights from proteomics

Protein misfolding and aggregation are being found to be associated with an increasing number of human diseases and premature aging, either because they promote a loss of protein function or, more frequently, because the aggregated species gain a toxic activity. Despite potentially harmful, aggregation seems to be a generic property of polypeptide chains and aggregation-prone protein sequences seem to be ubiquitous, which, counterintuitively, suggests that they serve evolutionary conserved functions. The in vitro study of individual aggregation reactions of a large number of proteins has provided important insights on the structural and sequential determinants of this process. However, it is clear that understanding the role played by protein aggregation and its regulation in health and disease at the cellular, developmental, and evolutionary levels require more global approaches. The use of model organisms and their proteomic analysis hold the power to provide answers to such issues. In the present review, we address how, initially, computational large-scale analysis and, more recently, experimental proteomics are helping us to rationalize how, why and when proteins aggregate, as well as to decipher the strategies organisms have developed to control proteins aggregation propensities.

The inhibitory mechanism of a fullerene derivative against amyloid-β peptide aggregation: an atomistic simulation study

Alzheimer's disease (AD) is associated with the pathological self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. Aβ dimers formed in the initial step of Aβ aggregation were reported to be the smallest toxic species. Inhibiting the formation of β-sheet-rich oligomers and fibrils is considered as the primary therapeutic strategy for AD. Previous studies reported that fullerene derivatives strongly inhibit Aβ fibrillation. However, the underlying inhibitory mechanism remains elusive. As a first step to understand fullerene-modulated full-length Aβ aggregation, we investigated the conformational ensemble of the Aβ1-42 dimer with and without 1,2-(dimethoxymethano)fullerene (DMF) - a more water-soluble fullerene derivative - by performing a 340 ns explicit-solvent replica exchange molecular dynamics simulation. Our simulations show that although disordered states are the most abundant conformations of the Aβ1-42 dimer, conformations containing diverse extended β-hairpins are also populated. The first most-populated β-hairpins involving residues L17-D23 and A30-V36 strongly resemble the engineered β-hairpin which is a building block of toxic Aβ oligomers. We find that the interaction of DMFs with Aβ peptides greatly impedes the formation of such β-hairpins and inter-peptide β-sheets. Binding energy analyses demonstrate that DMF preferentially binds not only to the central hydrophobic motif LVFFA of the Aβ peptide as suggested experimentally, but also to the aromatic residues including F4 and Y10 and the C-terminal hydrophobic region I31-V40. This study reveals a complete picture of the inhibitory mechanism of full-length Aβ1-42 aggregation by fullerenes, providing theoretical insights into the development of drug candidates against AD.

Stabilization of α-Synuclein Fibril Clusters Prevents Fragmentation and Reduces Seeding Activity and Toxicity

Protein misfolding results in the accumulation of aggregated β-sheet-rich structures in Parkinson's disease (PD) and Alzheimer's disease. The toxic oligomer hypothesis stipulates that prefibrillar assemblies, such as soluble oligomers or protofibrils, are responsible for the poor prognosis of these diseases. Previous studies demonstrated that a small molecule related to the natural compound orcein, O4, directly binds to amyloid-β fibrils and stabilizes them, accelerating the formation of end-stage mature fibrils. Here we demonstrate a similar phenomenon during O4 treatment of α-synuclein (αsyn) aggregates, the protein responsible for PD pathology. While the drug did not change the kinetics of aggregate formation as measured by the amyloidophilic dye thioflavin T, O4 depleted αsyn oligomers and promoted the formation of sodium dodecyl sulfate and proteinase K resistant aggregates consisting of large fibril clusters. These fibril clusters exhibited reduced toxicity to human neuronal model cells and reduced seeding activity in vitro. The effectiveness of O4 decreased when it was added at later points in the αsyn aggregation pathway, which suggests that the incorporation of O4 into fibril assemblies stabilizes them against chemical, enzymatic, and mechanic degradation. These findings suggest that small molecules, which stabilize amyloid fibrils, can prevent fibril fragmentation and seeding and consequently prevent prion-like replication of misfolded αsyn. Inhibiting prion replication by fibril stabilization could thus be a therapeutic strategy for PD.

Competing processes of micellization and fibrillization in native and reduced casein proteins

Competition between micellization and fibrillization in milk caseins, intrinsically disordered proteins (IDPs).

A natural hyperbranched proteoglycan inhibits IAPP amyloid fibrillation and attenuates β-cell apoptosis

A natural amphiphilic hyperbranched proteoglycan efficiently inhibits IAPP fibrillation and attenuates β-cell apoptosis for type 2 diabetes treatment.

Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology

The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy.

Kinetic Insights into the Elongation Reaction of Actin Filaments as a Function of Temperature, Pressure, and Macromolecular Crowding

Actin polymerization is an essential process in eukaryotic cells that provides a driving force for motility and mechanical resistance for cell shape. By using preformed gelsolin-actin nuclei and applying stopped-flow methodology, we quantitatively studied the elongation kinetics of actin filaments as a function of temperature and pressure in the presence of synthetic and protein crowding agents. We show that the association of actin monomers to the pointed end of double-stranded helical actin filaments (F-actin) proceeds via a transition state that requires an activation energy of 56 kJ mol(-1) for conformational and hydration rearrangements, but exhibits a negligible activation volume, pointing to a compact transition state that is devoid of packing defects. Macromolecular crowding causes acceleration of the F-actin elongation rate and counteracts the deteriorating effect of pressure. The results shed new light on the combined effect of these parameters on the polymerization process of actin, and help us understand the temperature and pressure sensitivity of actin polymerization under extreme conditions.

The Effects of Lipid Membranes, Crowding and Osmolytes on the Aggregation, and Fibrillation Propensity of Human IAPP

Type 2 diabetes mellitus (T2DM) is an age-related and metabolic disease. Its development is hallmarked, among others, by the dysfunction and degeneration of β-cells of the pancreatic islets of Langerhans. The major pathological characteristic thereby is the formation of extracellular amyloid deposits consisting of the islet amyloid polypeptide (IAPP). The process of human IAPP (hIAPP) self-association, and the intermediate structures formed as well as the interaction of hIAPP with membrane systems seem to be, at least to a major extent, responsible for the cytotoxicity. Here we present a summary and comparison of the amyloidogenic propensities of hIAPP in bulk solution and in the presence of various neutral and charged lipid bilayer systems as well as biological membranes. We also discuss the cellular effects of macromolecular crowding and osmolytes on the aggregation pathway of hIAPP. Understanding the influence of different cellular factors on hIAPP aggregation will provide more insight into the onset of T2DM and help to develop novel therapeutic strategies.