The structural basis of protein folding and its links with human disease

Minimum model for the alpha-helix-beta-hairpin transition in proteins

We present a minimal model for proteins, which is able to capture the structural conversion between the alpha-helix and beta-hairpin. In most regimes of the parameter space, the model produces a stable structure at a low temperature; in a few limited regimes of the parameter space, the model displays an beta-hairpin transition as the physical conditions vary. These variations include a perturbation on hydrogen bonding propensity at the middle of the modeled chain, or the change of the hydrophobicity of a designated pair along the chain. Using Monte Carlo simulations, we demonstrate the structural conversion by means of state diagrams, heat capacity maps, and free energy maps.

Two-dimensional Raman and Raman optical activity correlation analysis of the alpha-helix-to-disordered transition in poly(L-glutamic acid)

Rich and complex Raman scattering and Raman optical activity (ROA) spectra have been measured monitoring the pH induced alpha-helix-to-disordered conformational transition in poly(L-glutamic acid). Two-dimensional (2D) correlation techniques have been applied to facilitate a comprehensive analysis of these two complementary spectral sets. Synchronous contour plots have identified band assignments of alpha-helical and disordered conformations, and have revealed bands characteristic of changes in the protonation state of the polypeptide. Asynchronous plots, on the other hand, have probed the relative sequential orders of intensity changes indicating a decrease in intensity of alpha-helical bands in the backbone skeletal stretch region, followed by a subsequent decrease in intensity in the extended amide III and amide I regions, underlying the appearance of disordered structure, including poly(L-proline) II (PPII) helix. The application of a 2D correlation 'moving' window has also disclosed two distinct phases during helix unfolding in the alpha-helix-to-disordered transition, occurring at approximately pH 4.9 and approximately pH 5.2, possibly a result of the difference in helical stability between the end and central regions of the alpha-helix. This paper demonstrates the potential value of combining 2D Raman, 2D ROA and moving window correlation techniques for the detailed investigation of complex and subtle changes of secondary structure during the unfolding mechanisms of polypeptides and proteins.

Localization of ligand binding site in proteins identified in silico

Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabilize the structure of the protein in its natural environment. The fuzzy-oil-drop model is employed to represent the idealized hydrophobicity distribution in the protein molecule. Comparing it with the one empirically observed in the protein molecule reveals that they are not in agreement. It is shown in this study that the irregularity of hydrophobic distributions is aim-oriented. The character and strength of these irregularities in the organization of the hydrophobic core point to the specificity of a particular protein's structure/function. When the location of these irregularities is determined versus the idealized fuzzy-oil-drop, function-related areas in the protein molecule can be identified. The presented model can also be used to identify ways in which protein-protein complexes can possibly be created. Active sites can be predicted for any protein structure according to the presented model with the free prediction server at http://www.bioinformatics.cm-uj.krakow.pl/activesite. The implication based on the model presented in this work suggests the necessity of active presence of ligand during the protein folding process simulation.

A particular hydrophobic cluster in the residual structure of reduced lysozyme drastically affects the amyloid fibrils formation

Six hydrophobic clusters involved in long-range interaction have been identified in the residual structure of reduced lysozyme at pH 2. Recently, it was found that modulation in the residual structure affected amyloid formation. In this paper, we examined the effect of the hydrophobic cluster containing W111 (cluster 5) on amyloid fibril formation of reduced lysozyme. The reduced W62G lysozyme, in which most of the hydrophobic clusters except for cluster 5 are disrupted, formed hardly any amyloid fibrils in comparison with the reduced wild-type. However, the disruption of cluster 5 by the mutation of Trp111 to Gly allowed significant amyloid fibril formation of reduced W62G lysozyme. Moreover, the extent of amyloid formation in the reduced W62G/W111G lysozyme was greater than that of the reduced wild-type lysozyme. From the above results, it became clear that cluster 5 contributed to retarding the amyloid fibrils formation of the W62G lysozyme.

4-Phenylbutyrate restores the functionality of a misfolded mutant low-density lipoprotein receptor

Familial hypercholesterolemia is an autosomal dominant disease caused by mutations in the gene encoding the low-density lipoprotein receptor. To date, more than 900 different mutations have been described. Transport-defective mutations (class 2) causing partial or complete retention of the receptor in the endoplasmic reticulum are the predominant class of mutations. In a cell culture system (Chinese hamster ovary cells), we show that chemical chaperones are able to mediate rescue of a transport-defective mutant (G544V), and that the ability to obtain rescue is mutation dependent. In particular, the low molecular mass fatty acid derivative 4-phenylbutyrate mediated a marked increase in the transport of G544V-mutant low-density lipoprotein receptor to the plasma membrane. Thirty per cent of the mutant receptor was able to escape from the endoplasmic reticulum and reach the cell surface. The rescued receptor had reduced stability, but was found to be as efficient as the wild-type low-density lipoprotein receptor in binding and internalizing low-density lipoprotein. In addition to 4-phenylbutyrate, we also studied 3-phenylpropionate and 5-phenylvalerate, and compared their effect on rescue of the G544V-mutant low-density lipoprotein receptor with their ability to increase overall gene expression caused by their histone deacetylase inhibitor activity. No correlation was found. Our results indicate that the effect of these agents was not solely mediated by their ability to induce gene expression of proteins involved in intracellular transport, but rather could be due to a direct chemical chaperone activity. These data suggest that rescue of mutant low-density lipoprotein receptor is possible and that it might be feasible to develop pharmacologic chaperones to treat familial hypercholesterolemia patients with class 2 mutations.

SEROSURVEY OF INFECTIOUS DISEASE AGENTS OF CARNIVORES IN CAPTIVE RED PANDAS (AILURUS FULGENS) IN CHINA

The future of the endangered red panda (Ailurusfulgens) depends in part on the development of protective measures against infectious diseases. The present study is a first step toward improved understanding of infectious diseases in the species' home regions. Serum samples obtained from 73 red pandas in 10 captive facilities in southwest, east, and northeast China from October to December 2004 were tested for antibodies against nine common infectious pathogens of carnivores. Antibody titers against canine distemper virus (CDV), canine parvovirus (CPV), and canine adenovirus (CAV) in the three facilities in which red pandas were vaccinated were highly variable. The CAV titer in one vaccinated red panda was high enough to suggest infection with the field virus following vaccination. Together with anecdotal reports of vaccine-associated morbidity and mortality, our results suggest that the Chinese vaccine is not suitable for this species. In the seven unvaccinated groups, CDV titers were low and occurred in 20-100% of the animals; antibody titers against CPV were found in seven of eight areas. Only one of 61 and two of 61 unvaccinated red pandas had CAV and canine coronavirus titers, respectively, and these titers were all low. Positive titers to Toxoplasma gondii were found in four locations (33-94% seropositive); the titers in 52% of seropositive individuals were of a magnitude consistent with active disease in other species (1:1,024 to > or = 1:4,096). One red panda in each of three locations was seropositive for Neospora caninum. Antibodies against canine herpesvirus and Brucella canis were not detected in any of the samples. Only one of the 73 red pandas had a weak positive influenza A titer. The results of this study emphasize the need for research on and protection against infectious diseases of red pandas and other endangered species in China.

Early Kinetics of Amyloid Fibril Formation Reveals Conformational Reorganisation of Initial Aggregates

Understanding the initial steps of protein aggregation leading to the formation of amyloid fibrils remains a challenge. Here, the kinetics of such a process is determined for a misfolding protein model, ADA2h. The double nature of the very early kinetics suggests a step model of aggregation, where the denatured polypeptide folds into an aggregated beta-intermediate that subsequently reorganises into a more organised beta-sheet-richer structure that finally results in amyloid fibre formation. To determine the regions of the protein involved in amyloidosis, we have analysed a series of mutants previously made to study ADA2h folding. Using the algorithm TANGO, we have designed mutants that should enhance or decrease aggregation. Experimental analysis of the mutants shows that the C terminus of the molecule (comprising the last and edge beta-strand) is the major contributor to amyloid fibril formation, in good agreement with theoretical predictions. Comparison with proteins with similar topology reveals that family folds do not necessarily share the same principles of protein folding and/or aggregation.

Analytical model for studying how environmental factors influence protein conformational stability in solution

We introduce an analytical modeling strategy for probing the conformational stability of globular proteins in aqueous solution. In this approach, the intrinsic (i.e., infinite dilution) thermodynamic stability and coarse structural properties of the proteins, as well as the effective protein-protein interactions, derive from a heteropolymer collapse theory that incorporates predicted temperature- and pressure-dependent hydrophobic interactions. Protein concentration effects are estimated by integrating this information into a molecular thermodynamic model, which is an ad hoc generalization of the exact equilibrium theory of a one-dimensional binary mixture of square-well particles that interconvert through an isomerization (i.e., folding) reaction. The end result is an analytical multiscale modeling approach which, although still schematic, can predict that folded proteins exhibit a closed-loop region of stability in the pressure-temperature plane and that protein concentration has a nonmonotonic effect on protein stability, results consistent with qualitative trends observed in both experiments of protein solutions and simulations of coarse-grained protein models.

Amyloid-linked cellular toxicity triggered by bacterial inclusion bodies

The aggregation of proteins in the form of amyloid fibrils and plaques is the characteristic feature of some pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. The mechanisms by which the aggregation processes result in cell damage are under intense investigation but recent data indicate that prefibrillar aggregates are the most proximate mediators of toxicity rather than mature fibrils. Since it has been shown that prefibrillar forms of the nondisease-related misfolded proteins are highly toxic to cultured mammalian cells we have studied the cytoxicity associated to bacterial inclusion bodies that have been recently described as protein deposits presenting amyloid-like structures. We have proved that bacterial inclusion bodies composed by a misfolding-prone beta-galactosidase fusion protein are clearly toxic for mammalian cells but the beta-galactosidase wild type enzyme forming more structured thermal aggregates does not impair cell viability, despite it also binds and enter into the cells. These results are in the line that the most cytotoxic aggregates are early prefibrilar assemblies but discard the hypothesis that the membrane destabilization is the key event to subsequent disruption of cellular processes, such as ion balance, oxidative state and the eventually cell death.

Polymorphism in the intermediates and products of amyloid assembly

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

Kinetic studies of protein L aggregation and disaggregation

We have investigated the aggregation of protein L in 25% (vol/vol) TFE and 10 mM HCl. Under both conditions, aggregates adopt a fibrillar structure and bind dyes Congo Red and Thioflavin T consistent with the presence of amyloid fibrils. The kinetics of aggregation in 25% TFE suggest a linear-elongation mechanism with critical nucleus size of either two or three monomers. Aggregation kinetics in 10 mM HCl show a prolonged lag phase prior to a rapid increase in aggregation. The lag phase is time-dependent, but the time dependence can be eliminated by the addition of pre-formed seeds. Disaggregation studies show that for aggregates formed in TFE, aggregate stability is a strong function of aggregate age. For example, after 200 min of aggregation, 40% of the aggregation reaction is irreversible, while after 3 days over 60% is irreversible. When the final concentration of the denaturant, TFE, is reduced from 5% to 0, the amount of reversible aggregation doubles. Disaggregation studies of aggregates formed in TFE and 10 mM HCl reveal a complicated effect of pH on aggregate stability.

Thermodynamics of folding and association of lattice-model proteins

Closely related to the "protein folding problem" is the issue of protein misfolding and aggregation. Protein aggregation has been associated with the pathologies of nearly 20 human diseases and presents serious difficulties during the manufacture of pharmaceutical proteins. Computational studies of multiprotein systems have recently emerged as a powerful complement to experimental efforts aimed at understanding the mechanisms of protein aggregation. We describe the thermodynamics of systems containing two lattice-model 64-mers. A parallel tempering algorithm abates problems associated with glassy systems and the weighted histogram analysis method improves statistical quality. The presence of a second chain has a substantial effect on single-chain conformational preferences. The melting temperature is substantially reduced, and the increase in the population of unfolded states is correlated with an increase in interactions between chains. The transition from two native chains to a non-native aggregate is entropically favorable. Non-native aggregates receive approximately 25% of their stabilizing energy from intraprotein contacts not found in the lowest-energy structure. Contact maps show that for non-native dimers, nearly 50% of the most probable interprotein contacts involve pairs of residues that form native contacts, suggesting that a domain-swapping mechanism is involved in self-association.

Heme binding inhibits the fibrillization of amyloidogenic apomyoglobin and determines lack of aggregate cytotoxicity

Myoglobin is an alpha-helical globular protein containing two highly conserved tryptophanyl residues at positions 7 and 14 in the N-terminal region. The double W/F replacement renders apomyoglobin highly susceptible to aggregation and amyloid-like fibril formation under physiological conditions. In this work we analyze the early stage of W7FW14F apomyoglobin aggregation following the time dependence of the process by far-UV CD, Fourier-transform infrared (FTIR) spectroscopy, and heme-binding properties. The results show that the aggregation of W7FW14F apomyoglobin starts from a native-like globin state able to bind the prosthetic group with spectroscopic properties similar to those observed for wild-type apoprotein. Nevertheless, it rapidly aggregates, forming amyloid fibrils. However, when the prosthetic group is added before the beginning of aggregation, amyloid fibrillization is inhibited, although the aggregation process is not prevented. Moreover, the apomyoglobin aggregates formed in these conditions are not cytotoxic differently from what is observed for all amyloidogenic proteins. These results open new insights into the relationship between the structure adopted by the protein into the aggregates and their ability to trigger the impairment of cell viability.

Destabilization of non-pathological variants of ataxin-3 by metal ions results in aggregation/fibrillogenesis

Ataxin-3 (AT3), a protein that causes spinocerebellar ataxia type 3, has a C-terminus containing a polyglutamine stretch, the length of which can be expanded in its pathological variants. Here, we report on the role of Cu(2+), Mn(2+), Zn(2+) and Al(3+) in the induction of defective protein structures and subsequent aggregation/fibrillogenesis of three different non-pathological forms of AT3, i.e. murine (Q6), human non-expanded (Q26) and human moderately expanded (Q36). AT3 variants showed an intrinsic propensity to misfolding/aggregation; on the other hand, Zn(2+) and Al(3+) strongly stimulated the amplitude and kinetics of these conformational conversions. While both metal ions induced a time-dependent aggregation into amyloid-like fibrillar forms, only small oligomers and/or short protofibrillar species were detected for AT3s alone. The rate and extent of the metal-induced aggregation/fibrillogenesis processes increased with the size of the polyglutamine stretch. Mn(2+) and Cu(2+) had no effect on (Q6) or actually prevented (Q26 and Q36) the AT3 structural transitions. The observation that Zn(2+) and Al(3+) promote AT3 fibrillogenesis is consistent with similar results found for other amyloidogenic molecules, such as beta-amyloid and prion proteins. Plausibly, these metal ions are a major common factor/cofactor in the etiopathogenesis of neurodegenerative diseases. Studies of liposomes as membrane models showed dramatic changes in the structural properties of the lipid bilayer in the presence of AT3, which were enhanced after supplementing the protein with Zn(2+) and Al(3+). This suggests that cell membranes could be a potential primary target in the ataxin-3 pathogenesis and metals could be a biological factor capable of modulating their interaction with AT3.

Functionality and the evolution of marginal stability in proteins: inferences from lattice simulations

It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit motion, flexibility, or general disorder, some have suggested that marginally stable proteins should have an evolutionary advantage over proteins of differing stability. Others have suggested that stability and functionality are contradictory qualities, and that selection for both criteria results in marginally stable proteins, optimised to satisfy the competing design pressures. While these explanations are plausible, recent research simulating the evolution of model proteins has shown that selection for stability, ignoring any aspects of functionality, can result in marginally stable proteins because of the underlying makeup of protein sequence-space. We extend this research by simulating the evolution of proteins, using a computational protein model that equates functionality with binding and catalysis. In the model, marginal stability is not required for ligand-binding functionality and we observe no competing design pressures. The resulting proteins are marginally stable, again demonstrating that neutral evolution is sufficient for explaining marginal stability in observed proteins.

Role of neurofilament aggregation in motor neuron disease

A major question in the pathogenesis of motor neuron disease is why motor neurons are selectively susceptible to mutations in widely expressed gene products. Reexamination of motor neuron degeneration due to alterations of neurofilament (NF) expression suggests that disruption of assembly with aggregation of the light neurofilament (NFL) protein may be an upstream event and contributing factor leading to the preferential degeneration of motor neurons. The implications of these findings are that aggregation of NFL is not only a triggering mechanism to account for the hallmark aggregates of NF protein in sporadic and familial forms of amyotrophic lateral sclerosis, but that aggregates of NFL may also promote aggregation of wildly expressed proteins that are destabilized by missense mutations, such as by mutations in superoxide dismutase-1 protein. This review examines the potential role of NFs in determining and promoting the preferential degeneration of motor neurons in motor neuron disease. The underlying premise is that motor neurons are selectively susceptible to alterations in NF expression, that alterations in NF expression lead to NF aggregates in motor neurons, and that elevated levels of NF aggregates provide a favorable microenvironment for the formation of neurotoxic aggregation and degeneration of motor neurons.

Atrazine increases ranavirus susceptibility in the tiger salamander, Ambystoma tigrinum

Pathogenic diseases and environmental contaminants are two of the leading hypotheses for global amphibian declines, yet few studies have examined the influence of contaminants on disease susceptibility. In this study, we examined effects of ecologically relevant doses of atrazine (0, 1.6, 16, and 160 microg/L), sodium nitrate (0, 6.8, 68 mg/L), and their interactions on susceptibility of four laboratory-bred tiger salamander families to Ambystoma tigrinum virus (ATV), a pathogen implicated in global amphibian die-offs. Salamanders were from Arizona populations where a coevolutionary history with ATV is supported, and thus cofactors rather than recent introduction may contribute to disease epizootics. Use of atrazine and nitrogenous fertilizers are ubiquitous; therefore, the impact of these cofactors on disease susceptibility is an important consideration. Atrazine and sodium nitrate significantly decreased peripheral leukocyte levels, suggesting an impact of these contaminants on the immune system. As expected from this result, atrazine significantly increased susceptibility of larvae to ATV infection. In contrast, nitrate had a marginally significant main effect and significantly decreased infection rate at the highest level. However, neither atrazine nor sodium nitrate had significant effects on viral copy number per individual. These results suggest that ecologically relevant concentrations of atrazine and nitrates have immunosuppressive effects, and atrazine may contribute to ATV epizootics, raising concerns about the influence of contaminants on diseases in general.

Strong Impact of Ionic Strength on the Kinetics of Fibrilar Aggregation of Bovine β-Lactoglobulin

We investigate the effect of ionic strength on the kinetics of heat-induced fibrilar aggregation of bovine beta-lactoglobulin at pH 2.0. Using in situ light scattering we find an apparent critical protein concentration below which there is no significant fibril formation for all ionic strengths studied. This is an independent confirmation of our previous observation of an apparent critical concentration for 13 mM ionic strength by proton NMR spectroscopy. It is also the first report of such a critical concentration for the higher ionic strengths. The critical concentration decreases with increasing ionic strength. Below the critical concentration mainly "dead-end" species that cannot aggregate anymore are formed. We prove that for the lowest ionic strength this species consists of irreversibly denatured protein. Atomic force microscopy studies of the morphology of the fibrils formed at different ionic strengths show shorter and curvier fibrils at higher ionic strength. The fibril length distribution changes non-monotonically with increasing ionic strength. At all ionic strengths studied, the fibrils had similar thicknesses of about 3.5 nm and a periodic structure with a period of about 25 nm.

Absolute correlation between lag time and growth rate in the spontaneous formation of several amyloid-like aggregates and fibrils

The formation of polypeptide aggregates, including amyloid fibrils and prions, is a biochemical process of considerable interest in the context of its association with ageing and neurodegeneration. Aggregation occurs typically with a lag phase and a growth phase that reflect an underlying nucleation-polymerisation mechanism. While the propensity of nucleation can be estimated from the lag time t(l), the efficiency of growth is represented by the growth rate k(g). Here, I have analysed the absolute k(g) and t(l) values from a total of 298 samples prepared from insulin, glucagon and different sequence variants of the Alzheimer's Abeta(1-40) peptide. Although these samples differ in the conditions of aggregation, systematic comparison reveals an overall similarity in the plot of k(g)versus t(l). The plot fits readily with the simple equation k(g)=alpha/t(l) and by using a proportionality factor alpha of 4.5. In contrast to the individual values of k(g) and t(l) that depend substantially on sequential and environmental parameters, alpha seems much less affected by such factors. These data suggest mechanistic similarities in the nucleation behaviour of different amyloid-like fibrils and aggregates.

Patterning amyloid peptide fibrils by AFM charge writing

Surface charge patterns generated by atomic force microscopy-based charge writing were used to pattern amyloid-like peptide fibrils on a solid substrate. Fibrils of the short peptide TTR105-115 were encapsulated inside water droplets of a water-in-perfluorocarbon oil emulsion and retained their rod morphology. They were observed to deposit selectively with a lateral resolution of approximately 1 microm onto negatively charged patterns on a polymethyl-methacrylate substrate.

Side chain-dependent stacking modulates tau filament structure

The misfolding of proteins into highly ordered fibrils with similar physical properties is a hallmark of many degenerative diseases. Here, we use the microtubule associated protein tau as a model system to investigate the role of amino acid side chains in the formation of such fibrils. We identify a region (positions 272-289) in the tau protein that, in the fibrillar state, either forms part of a core of parallel, in-register, beta-strands, or remains unfolded. Single point mutations are sufficient to control this conformational switch with disease mutants G272V and DeltaK280 (found in familial forms of dementia) inducing a folded state. Through systematic mutagenesis we derive a propensity scale for individual amino acids to form fibrils with parallel, in-register, beta-strands. This scale should not only apply to tau fibrils but generally to all fibrils with same strand arrangement.

Apolipoprotein (apo) E4 and Alzheimer's disease: unique conformational and biophysical properties of apoE4 can modulate neuropathology

The unique structural and biophysical features of apolipoprotein (apo) E4 - domain interaction and molten globule formation - have been correlated with the detrimental effects of apoE4 in neuropathology. Two examples of how the structure of apoE4 determines the pathological outcome in neurons include apoE4 potentiation of amyloid beta-induced lysosomal leakage and apoptosis and the proteolytic cleavage of apoE synthesized by neurons. Thus, a new therapeutic target is to identify small molecules to modulate the inherent neuropathological structure of apoE4, i.e. to prevent domain interaction and to convert apoE4 to an apoE3-like molecule. A second therapeutic target is to inhibit the apoE-cleaving enzyme. This would prevent the generation of the reactive carboxyl-terminal fragments of apoE that enter the cytosol, disrupt the cytoskeleton, and cause neurodegeneration. ApoE4 is more susceptible than apoE3 to proteolytic cleavage and is thus more likely to cause detrimental effects in the central nervous system. It is predictable that apoE4 acts through various pathways to cause cognitive decline and neurodegeneration.

GroEL-mediated protein folding: making the impossible, possible

Protein folding is a spontaneous process that is essential for life, yet the concentrated and complex interior of a cell is an inherently hostile environment for the efficient folding of many proteins. Some proteins-constrained by sequence, topology, size, and function-simply cannot fold by themselves and are instead prone to misfolding and aggregation. This problem is so deeply entrenched that a specialized family of proteins, known as molecular chaperones, evolved to assist in protein folding. Here we examine one essential class of molecular chaperones, the large, oligomeric, and energy utilizing chaperonins or Hsp60s. The bacterial chaperonin GroEL, along with its co-chaperonin GroES, is probably the best-studied example of this family of protein-folding machine. In this review, we examine some of the general properties of proteins that do not fold well in the absence of GroEL and then consider how folding of these proteins is enhanced by GroEL and GroES. Recent experimental and theoretical studies suggest that chaperonins like GroEL and GroES employ a combination of protein isolation, unfolding, and conformational restriction to drive protein folding under conditions where it is otherwise not possible.

Insights into the architecture of the Ure2p yeast protein assemblies from helical twisted fibrils

The protein Ure2 from baker's yeast is associated with a heritable and transmissible phenotypic change in the yeast Saccharomyces cerevisiae. Such prion properties are thought to arise from the fact that Ure2p is able to self-assemble into insoluble fibrils. Assemblies of Ure2p are composed of full-length proteins in which the structure of the globular, functional, C-terminal domain is retained. We have carried out structural studies on full-length, wild-type Ure2p fibrils with a regularly twisted morphology. Using electron microscopy and cryo-electron microscopy with image analysis we show high-resolution images of the twisted filaments revealing details within the fibrillar structure. We examine these details in light of recent proposed models and discuss how this new information contributes to an understanding of the architecture of Ure2p yeast prion fibrils.

Natively folded HypF-N and its early amyloid aggregates interact with phospholipid monolayers and destabilize supported phospholipid bilayers

Recent data depict membranes as the main sites where proteins/peptides are recruited and concentrated, misfold, and nucleate amyloids; at the same time, membranes are considered key triggers of amyloid toxicity. The N-terminal domain of the prokaryotic hydrogenase maturation factor HypF (HypF-N) in 30% trifluoroethanol undergoes a complex path of fibrillation starting with initial 2-3-nm oligomers and culminating with the appearance of mature fibrils. Oligomers are highly cytotoxic and permeabilize lipid membranes, both biological and synthetic. In this article, we report an in-depth study aimed at providing information on the surface activity of HypF-N and its interaction with synthetic membranes of different lipid composition, either in the native conformation or as amyloid oligomers or fibrils. Like other amyloidogenic peptides, the natively folded HypF-N forms stable films at the air/water interface and inserts into synthetic phospholipid bilayers with efficiencies depending on the type of phospholipid. In addition, HypF-N prefibrillar aggregates interact with, insert into, and disassemble supported phospholipid bilayers similarly to other amyloidogenic peptides. These results support the idea that, at least in most cases, early amyloid aggregates of different peptides and proteins produce similar effects on the integrity of membrane assembly and hence on cell viability.

The effects of the flavonoid baicalein and osmolytes on the Mg 2+ accelerated aggregation/fibrillation of carboxymethylated bovine 1SS-α-lactalbumin

Many protein conformational diseases arise when proteins form alternative stable conformations, resulting in aggregation and accumulation of the protein as fibrillar deposits, or amyloids. Interestingly, numerous proteins implicated in amyloid protein formation show similar structural and functional properties. Given this similarity, we tested the notion that carboxymethylated bovine alpha-lactalbumin (1SS-alpha-lac) could serve as a general amyloid fibrillation/aggregation model system. Like most amyloid forming systems, Mg2+ ions accelerate 1SS-alpha-lac amyloid fibril formation. While osmolytes such as trimethylamine N-oxide (TMAO), and sucrose enhanced thioflavin T detected aggregation, a mixture of trehalose and TMAO substantially inhibited aggregation. Most importantly however, the flavonoid, baicalein, known to inhibit alpha-synuclein amyloid fibril formation, also inhibits 1SS-alpha-lac amyloid with the same apparent efficacy. These data suggest that the easily obtainable 1SS-alpha-lac protein can serve as a general amyloid model and that some small molecule amyloid inhibitors may function successfully with many different amyloid systems.

Characterization of the native and fibrillar conformation of the human Nalpha-acetyltransferase ARD1

ARD1 (arrest-defective protein 1), together with NAT1 (N-acetyltransferase protein 1), is part of the major N(alpha)-acetyltransferase complex in eukaryotes responsible for alpha-acetylation of proteins and peptides. Protein acetylation has been implicated in gene expression regulation and protein-protein interaction. We characterized the native folded and misfolded conformation of hARD1. Structural characterization of native hARD1 using size exclusion chromatography, circular dichroism, and fluorescence spectroscopy shows the protein consists of a compact globular region comprising two thirds of the protein and a flexible unstructured C terminus. In addition, hARD1 forms protofilaments under physiological conditions of pH and temperature, as judged by electron microscopy and staining with the dyes Congo red and thioflavin T. The process is accelerated by thermal denaturation and high protein concentrations. Limited proteolysis of aggregated hARD1 revealed a resistant fragment whose sequence matched a region contained within the acetyl transferase domain.

Apolipoprotein E structure: insights into function

Human apolipoprotein E (apoE) is a member of the family of soluble apolipoproteins. Through its interaction with members of the low-density lipoprotein receptor family, apoE has a key role in lipid transport both in the plasma and in the central nervous system. Its three common structural isoforms differentially affect the risk of developing atherosclerosis and neurodegenerative disorders, including Alzheimer's disease. Because the function of apoE is dictated by its structure, understanding the structural properties of apoE and its isoforms is required both to determine its role in disease and for the development of therapeutic strategies.

Hydrophobic collapse in (in silico) protein folding

A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) 'oil-drop' model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding process (energy minimization procedure) and interact with the external hydrophobic force field defined by a three-dimensional Gaussian function. The value of the Gaussian function usually interpreted as a probability distribution is treated as a normalized hydrophobicity distribution, with its maximum in the center of the ellipsoid and decreasing proportionally with the distance versus the center. The fuzzy-oil-drop is elastic and changes its shape and size during the simulated folding procedure.

Investigating the permanent electric dipole moment of β-lactoglobulin fibrils, using transient electric birefringence

Amyloid fibrils, which are polymeric assemblies of protein molecules, have been intensively studied on a structural level, yet due to complications such as the disorder within the molecules, several aspects of their structure remain mysterious. Similarly, the kinetics of assembly are not well understood. Here we investigate the electric dipole moment of beta-lactoglobulin fibrils, a model amyloid fibril system, by applying the technique of transient electric birefringence. This moment appears to be large, and comparable to the total moment of the constituent protein monomers if they were joined in a chain, head-to-tail, without changing conformation, suggesting an ordered joining of monomers in the fibril. Such an ordered assembly may have implications for the assembly mechanism of beta-lactoglobulin fibrils in particular, and amyloid fibrils in general.

Amyloid fibrils of glucagon characterized by high-resolution atomic force microscopy

Glucagon solutions at pH 2.0 were subjected to mechanical agitation at 37 degrees C in the presence of a hydrophobic surface to explore the details of aggregation and fiber formation. High-resolution intermittent-contact atomic force microscopy performed in solution revealed the presence of aggregates after 0.5 h; however, longer agitation times resulted in the formation of fibrillated structures with varying levels of higher-order assembly. Height, periodicity, and amplitude measurements of these structures allowed the identification of four distinct fiber types. The most elementary fiber form, designated a filament, self-associates in a specific wound fashion to produce protofibrils composed of two filaments. Subsequent self-assembly of these filaments and protofibrils leads to two well-defined fibrillar motifs, termed Type I and Type II. Atomic force microscopy imaging of pH 2.8 glucagon solutions not agitated or exposed to elevated temperature revealed the presence of amorphous aggregates before the formation of fibrillar structures similar to those seen at pH 2.0. Time-course solution Fourier transform infrared spectroscopy and thioflavin T binding studies suggested that glucagon aggregation and fibril formation were associated with the development of beta-sheet structure. The results of these studies are used to describe a possible mechanism for glucagon aggregation and fibrillation that is consistent with a hierarchical assembly model proposed for amyloid fibril formation.

A molecular dynamics study of human serum albumin binding sites

A 2.0 ns unrestrained Molecular Dynamics was used to elucidate the geometric and dynamic properties of the HSA binding sites. The structure is not stress affected and the rmsds calculated from the published crystallographic data are almost constant for all the simulation time, with an averaged value of 2.4A. The major variability is in the C-terminus region. The trajectory analysis of the IIA binding site put in evidence fast oscillations for the Cgamma@Leu203...Cgamma@Leu275 and Cgamma@Leu219...Cgamma@Leu260 distances, with fluctuations around 250 ps, 1000 ps and over for the first, while the second is smoothly increasing with the simulation time from 7 to 10A. These variations are consistent with a volume increase up to 20% confirmed by the inter-domain contacts analysis, in particular for the pair O@Pro148...Ogamma@Ser283, representing the change of distance between IB-h9 and IIA-h6, O@Glu149...Ogamma@Ser189 for sub-domains IB-h9/IIA-h1 and N@Val339...Odelta2@Asp447 sub-domains IIB-h9/IIIA-h1. These inter-domain motions confirm the flexibility of the unfatted HSA with possible binding site pre-formation.

The role of lipid–protein interactions in amyloid-type protein fibril formation

Structural transition of polypeptide chains into the beta-sheet state followed by amyloid fibril formation is the key characteristic of a number of the so-called conformational diseases. The multistep process of protein fibrillization can be modulated by a variety of factors, in particular by lipid-protein interactions. A wealth of experimental evidence provides support to the notion that amyloid fibril assembly and the toxicity of pre-fibrillar aggregates are closely related and are both intimately membrane associated phenomena. The present review summarizes the principal factors responsible for the enhancement of fibril formation in a membrane environment, viz. (i) structural transformation of polypeptide chain into a partially folded conformation, (ii) increase of the local concentration of a protein upon its membrane binding, (iii) aggregation-favoring orientation of the bound protein, and (iv) variation in the depth of bilayer penetration affecting the nucleation propensity of the membrane associated protein. The molecular mechanisms of membrane-mediated protein fibrillization are discussed. Importantly, the toxicity of lipid-induced pre-fibrillar aggregates is likely to have presented a very strong negative selection pressure in the evolution of amino acid sequences.

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant

The structure and stabilities of the intermediates affect protein folding as well as misfolding and amyloid formation. By applying Kramer's theory of barrier crossing and a Morse-function-like energy landscape, we show that intermediates with medium stability dramatically increase the rate of amyloid formation; on the other hand, very stable and very unstable intermediates sharply decrease amyloid formation. Remarkably, extensive molecular dynamics simulations and conformational energy landscape analysis of Abeta25-35 and its N27Q mutant corroborate the mathematical description. Both experimental and current simulation results indicate that the core of the amyloid structure of Abeta25-35 formed from residues 28-35. A single mutation of N27Q of Abeta25-35 makes the Abeta25-35 N27Q amyloid-free. Energy landscape calculations show that Abeta25-35 has extended intermediates with medium stability that are prone to form amyloids, whereas the extended intermediates for Abeta25-35 N27Q split into stable and very unstable species that are not disposed to form amyloids. The results explain the contribution of both alpha-helical and beta-strand intermediates to amyloid formation. The results also indicate that the structure and stability of the intermediates, as well as of the native folded and the amyloid states can be targeted in drug design. One conceivable approach is to stabilize the intermediates to deter amyloid formation.

Mitochondria maintain maturation and secretion of lipoprotein lipase in the endoplasmic reticulum

Considering the physiological Ca2+ dynamics within the ER (endoplasmic reticulum), it remains unclear how efficient protein folding is maintained in living cells. Thus, utilizing the strictly folding-dependent activity and secretion of LPL (lipoprotein lipase), we evaluated the impact of ER Ca2+ content and mitochondrial contribution to Ca2+-dependent protein folding. Exhaustive ER Ca2+ depletion by inhibition of sarcoplasmic/endoplasmic reticulum Ca2+-ATPases caused strong, but reversible, reduction of cell-associated and released activity of constitutive and adenovirus-encoded human LPL in CHO-K1 (Chinese-hamster ovary K1) and endothelial cells respectively, which was not due to decline of mRNA or intracellular protein levels. In contrast, stimulation with the IP3 (inositol 1,4,5-trisphosphate)-generating agonist histamine only moderately and transiently affected LPL maturation in endothelial cells that paralleled a basically preserved ER Ca2+ content. However, in the absence of extracellular Ca2+ or upon prevention of transmitochondrial Ca2+ flux, LPL maturation discontinued upon histamine stimulation. Collectively, these data indicate that Ca2+-dependent protein folding in the ER is predominantly controlled by intraluminal Ca2+ and is largely maintained during physiological cell stimulation owing to efficient ER Ca2+ refilling. Since Ca2+ entry and mitochondrial Ca2+ homoeostasis are crucial for continuous Ca2+-dependent protein maturation in the ER, their pathological alterations may result in dysfunctional protein folding.

Fuzzy-oil-drop hydrophobic force field--a model to represent late-stage folding (in silico) of lysozyme

A model of hydrophobic collapse (in silico), which is generally considered to be the driving force for protein folding, is presented in this work. The model introduces the external field in the form of a fuzzy-oil-drop assumed to represent the environment. The drop is expressed in the form of a three-dimensional Gauss function. The usual probability value is assumed to represent the hydrophobicity distribution in the three-dimensional space of the virtual environment. The differences between this idealized hydrophobicity distribution and the one represented by the folded polypeptide chain is the parameter to be minimized in the structure optimization procedure. The size of fuzzy-oil-drop is critical for the folding process. A strong correlation between protein length and the dimension of the native and early-stage molecular form was found on the basis of single-domain proteins analysis. A previously presented early-stage folding (in silico) model was used to create the starting structure for the procedure of late-stage folding of lysozyme. The results of simulation were found to be promising, although additional improvements for the formation of beta-structure and disulfide bonds as well as the participation of natural ligand in folding process seem to be necessary.

DYNAMICS AND MANAGEMENT OF INFECTIOUS DISEASE IN COLONIZING POPULATIONS

The introduction of chronic, infectious diseases by colonizing populations (invasive or reintroduced) is a serious hazard in conservation biology, threatening the original host and other spillover species. Most research on spatial invasion of diseases has pertained to established host populations, either at steady state or fluctuating through time. Within a colonizing population, however, the spread of disease may be influenced by the expansion process of the population itself. Here we explore the simultaneous expansion of a colonizing population and a chronic, nonlethal disease introduced with it, describing basic patterns in homogeneous and structured landscapes and discussing implications for disease management. We describe expected outcomes of such introductions for three qualitatively distinct cases, depending on the relative velocities at which the population and epidemic expand. (1) If transmissibility is low the disease cannot be sustained, although it may first expand its range somewhat around the point of introduction. (2) If transmissibility is moderate but the wave-front velocity for the population, vp, is higher than that for the disease, vd, the disease wave front lags behind that of the population. (3) A highly transmissible disease, with vd > vp, will invade sufficiently rapidly to track the spread of the host. To test these elementary theoretical predictions, we simulated disease outbreaks in a spatially structured host population occupying a real landscape. We used a spatially explicit, individual-based model of Persian fallow deer (Dama mesopotamica) reintroduced in northern Israel, considering a hypothetical introduction of bovine tuberculosis. Basic patterns of disease expansion in this realistic setting were similar to our conceptual predictions for homogeneous landscapes. Landscape heterogeneity, however, induced the establishment of population activity centers and disease foci within them, leading to jagged wave fronts and causing local variation in the relative velocities at which the population and epidemic expanded. Based on predictions from simple theory and simulations of managed outbreaks, we suggest that the relative velocities at which the population and epidemic expand have important implications for the impact of different management strategies. Recognizing which of our three general cases best describes a particular outbreak will aid in planning an efficient strategy to contain the disease.

Characterization of Intra-molecular Distances and Site-specific Dynamics in Chemically Unfolded Barstar: Evidence for Denaturant-dependent Non-random Structure

The structure and dynamics of the unfolded form of a protein are expected to play critical roles in determining folding pathways. In this study, the urea and guanidine hydrochloride (GdnHCl)-unfolded forms of the small protein barstar were explored by time-resolved fluorescence techniques. Barstar was labeled specifically with thionitrobenzoate (TNB), by coupling it to the thiol side-chain of a cysteine residue at one of the following positions on the sequence: 14, 25, 40, 42, 62, 82 and 89, in single cysteine-containing mutant proteins. Seven intra-molecular distances (R(DA)) under unfolding conditions were estimated from measurements of time-resolved fluorescence resonance energy transfer between the donor Trp53 and the non-fluorescent acceptor TNB coupled to one of the seven cysteine side-chains. The unfolded protein chain expands with an increase in the concentration of the denaturants. The extent of expansion was found to be non-uniform, with different intra-molecular distances expanding to different extents. In general, shorter distances were found to expand less when compared to longer spans. The extent of expansion was higher in the case of GdnHCl when compared to urea. A comparison of the measured values of R(DA) with those derived from a model based on excluded volume, revealed that while shorter spans showed good agreement, the experimental values of R(DA) of longer spans were smaller when compared to the theoretical values. Sequence-specific flexibility of the polypeptide was determined by time-resolved fluorescence anisotropy decay measurements on acrylodan or 1,5-IAEDANS labeled single cysteine-containing proteins under unfolding conditions. Rotational dynamics derived from these measurements indicated that the level of flexibility increased with increase in the concentration of denaturants and showed a graded increase towards the C-terminal end. Taken together, these results appear to indicate the presence of specific non-random coil structures and show that the deviation from random coil structure is different for the two denaturants.

Apolipoprotein E4: a causative factor and therapeutic target in neuropathology, including Alzheimer's disease

The premise of this review is that apolipoprotein (apo) E4 is much more than a contributing factor to neurodegeneration. ApoE has critical functions in redistributing lipids among CNS cells for normal lipid homeostasis, repairing injured neurons, maintaining synapto-dendritic connections, and scavenging toxins. In multiple pathways affecting neuropathology, including Alzheimer's disease, apoE acts directly or in concert with age, head injury, oxidative stress, ischemia, inflammation, and excess amyloid beta peptide production to cause neurological disorders, accelerating progression, altering prognosis, or lowering age of onset. We envision that unique structural features of apoE4 are responsible for apoE4-associated neuropathology. Although the structures of apoE2, apoE3, and apoE4 are in dynamic equilibrium, apoE4, which is detrimental in a variety of neurological disorders, is more likely to assume a pathological conformation. Importantly, apoE4 displays domain interaction (an interaction between the N- and C-terminal domains of the protein that results in a compact structure) and molten globule formation (the formation of stable, reactive intermediates with potentially pathological activities). In response to CNS stress or injury, neurons can synthesize apoE. ApoE4 uniquely undergoes neuron-specific proteolysis, resulting in bioactive toxic fragments that enter the cytosol, alter the cytoskeleton, disrupt mitochondrial energy balance, and cause cell death. Our findings suggest potential therapeutic strategies, including the use of "structure correctors" to convert apoE4 to an "apoE3-like" molecule, protease inhibitors to prevent the generation of toxic apoE4 fragments, and "mitochondrial protectors" to prevent cellular energy disruption.

Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor

Hydrophobic collapse is commonly considered as a process of significance for protein folding. Many models have been applied for description of this event. A model introducing an external force field mimicking the hydrophobic environment and simultaneously the driving force for the folding process is presented in this paper. Bovine pancreatic trypsin inhibitor (BPTI) was taken as a test protein. An early-stage folding (in silico) model presented elsewhere was used to create the starting structure for hydrophobic collapse. The resulting structure was energy-refined using molecular dynamics simulation in an explicit solvent. The similarity versus the crystal structure of BPTI is estimated using visual analysis, residue-residue contacts, phi, psi angle distributions, RMSD, accessible solvent area, radii of gyration and hydrodynamic radii. A program allowing creation of early-stage folding structural forms to be created for any protein is available from http://bioinformatics.cm-uj.krakow.pl/earlystage. The program for late-stage folding simulation is available on request.

Effect of single-point sequence alterations on the aggregation propensity of a model protein

Sequences of contemporary proteins are believed to have evolved through a process that optimized their overall fitness, including their resistance to deleterious aggregation. Biotechnological processing may expose therapeutic proteins to conditions that are much more conducive to aggregation than those encountered in a cellular environment. An important task of protein engineering is to identify alternative sequences that would protect proteins when processed at high concentrations without altering their native structure associated with specific biological function. Our computational studies exploit parallel tempering simulations of coarse-grained model proteins to demonstrate that isolated amino acid residue substitutions can result in significant changes in the aggregation resistance of the protein in a crowded environment while retaining protein structure in isolation. A thermodynamic analysis of protein clusters subject to competing processes of folding and association shows that moderate mutations can produce effects similar to those caused by changes in system conditions, including temperature, concentration, and solvent composition, that affect the aggregation propensity. The range of conditions where a protein can resist aggregation can therefore be tuned by sequence alterations, although the protein generally may retain its generic ability for aggregation.

Domain interactions direct misfolding and amyloid formation of yeast phosphoglycerate kinase

There are proteins that are built of two structural domains and are deposited full-length in amyloid plaques formed in various diseases. In spite of the known differences in the mechanisms of folding of single- and multidomain proteins, no published studies can be found that address the role of the domain-domain interactions during misfolding and amyloid formation. By the discovery of the role of domain-domain interactions, here we provide important insight in the submolecular mechanism of amyloid formation. A model system based on yeast phosphoglycerate kinase was designed. This system includes the wild-type yeast phosphoglycerate kinase and single-tryptophan mutants of the individual N and C terminal domains and the complete protein. Electron microscopic measurements proved that amyloid fibrils grow from all mutants under identical conditions as for the wild-type protein. Misfolding and amyloid formation was followed in stopped-flow and manual mixing experiments on the 1 ms to 4 days timescale. Tryptophan fluorescence was used for selective detection of conformational changes accompanying the formation of the amyloidogenic intermediates and the growth of amyloid fibrils. The interactions between the polypeptide chains of the two domains direct the misfolding process from the early steps to the amyloid formation, and influence the final structure. The kinetics of misfolding is different for the individual domains, pointing to the significance of the amino acid sequence. Misfolding of the domains within the complete protein is synchronized indicating that domain-domain interactions direct the misfolding and amyloid formation mechanism.

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior

We use highly efficient transition-matrix Monte Carlo simulations to determine equilibrium unfolding curves and fluid phase boundaries for solutions of coarse-grained globular proteins. The model we analyze derives the intrinsic stability of the native state and protein-protein interactions from basic information about protein sequence using heteropolymer collapse theory. It predicts that solutions of low hydrophobicity proteins generally exhibit a single liquid phase near their midpoint temperatures for unfolding, while solutions of proteins with high sequence hydrophobicity display the type of temperature-inverted, liquid-liquid transition associated with aggregation processes of proteins and other amphiphilic molecules. The phase transition occurring in solutions of the most hydrophobic protein we study extends below the unfolding curve, creating an immiscibility gap between a dilute, mostly native phase and a concentrated, mostly denatured phase. The results are qualitatively consistent with the solution behavior of hemoglobin (HbA) and its sickle variant (HbS), and they suggest that a liquid-liquid transition resulting in significant protein denaturation should generally be expected on the phase diagram of high-hydrophobicity protein solutions. The concentration fluctuations associated with this transition could be a driving force for the nonnative aggregation that can occur below the midpoint temperature.

A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments

Identifying sequence determinants of fibril-forming proteins is crucial for understanding the processes causing >20 proteins to form pathological amyloid depositions. Our approach to identifying which sequences form amyloid-like fibrils is to screen the amyloid-forming proteins human insulin and beta(2)-microglobulin for segments that form fibrils. Our screen is of 60 sequentially overlapping peptides, 59 being six residues in length and 1 being five residues, covering every noncysteine-containing segment in these two proteins. Each peptide was characterized as amyloid-like or nonfibril-forming. Amyloid-like peptides formed fibrils visible in electron micrographs or needle-like microcrystals showing a cross-beta diffraction pattern. Eight of the 60 peptides (three from insulin and five from beta(2)-microglobulin) were identified as amyloid-like. The results of the screen were used to assess the computational method, and good agreement between prediction and experiments was found. This agreement suggests that the pair-of-sheets, zipper spine model on which the computational method is based is at least approximately correct for the structure of the fibrils and suggests the nature of the sequence signal for formation of amyloid-like fibrils.

Refolding studies using pressure: The folding landscape of lysozyme in the pressure–temperature plane

Refolding of hen egg white lysozyme after pressure unfolding was measured by FTIR spectroscopy. The high-pressure treatment was found to be useful for unfolding/refolding studies because pressure acts against aggregation, and therefore no irreversible aggregation takes place during the pressure treatment. After the release of the pressure, folding intermediate structures were found which were formed during the decompression of the lysozyme. These were aggregation prone when heated, as indicated by their lower stability against aggregation. The intermediates were only formed if the protein was unfolded, subdenaturing pressures could not populate these intermediates. We introduced the notion of a superfunnel to describe the free energy landscape of interacting polypeptide chains. This can explain the propensity of folding intermediates to aggregate. A possible Gibbs-free energy landscape for lysozyme was constructed for the whole pressure-temperature plane.

Extracellular disulfide exchange and the regulation of cellular function

An emerging concept is that disulfide bonds can act as a dynamic scaffold to present mature proteins in different conformational and functional states on the cell surface. Two examples are the conversion of the receptor, integrin alphaIIbbeta3, from a low affinity to a high affinity state, and the interaction of CD4 receptor with the HIV-1 envelope glycoprotein gp120 to promote virus-cell fusion. In both of these cases there is a remodeling of the protein disulfide bonding pattern. The formation and rearrangement of disulfide bonds is modulated by a family of enzymes known as the thiol isomerases, which include protein disulfide isomerase (PDI), ERp5, ERp57, and ERp72. While these enzymes were reported originally to be restricted in location to the endoplasmic reticulum, in some cells thiol isomerases are found on the cell surface. This may indicate a wider role for these enzymes in cell function. In platelets it has been shown that reagents that react with cell surface sulfhydryl groups are capable of blocking a number of functional responses, including integrin-mediated aggregation, adhesion, and granule secretion. Furthermore, the use of function blocking antibodies to either PDI or ERp5 causes inhibition of these functional responses. This review summarizes current knowledge of the extracellular regulation of disulfide exchange and the implications of this in the regulation of cell function.

Kinetics of amyloid aggregation of mammal apomyoglobins and correlation with their amino acid sequences

In protein deposition disorders, a normally soluble protein is deposited as insoluble aggregates, referred to as amyloid. The intrinsic effects of specific mutations on the rates of protein aggregation and amyloid formation of unfolded polypeptide chains can be correlated with changes in hydrophobicity, propensity to convert alpha-helical to beta sheet conformation and charge. In this paper, we report the aggregation rates of buffalo, horse and bovine apomyoglobins. The experimental values were compared with the theoretical ones evaluated considering the amino acid differences among the sequences. Our results show that the mutations which play critical roles in the rate-determining step of apomyoglobin aggregation are those located within the N-terminal region of the molecule.

Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations

Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.