150 Getting a grip on alpha-synuclein amyloid oligomers

Misfolding and aggregation of proteins into nanometer-scale fibrillar assemblies is a hallmark of many neurodegenerative diseases. Aggregation of the human alpha-synuclein protein is implicated in the etiology of Parkinson’s disease. A particularly relevant question is the role of early oligomeric aggregates of alpha-synuclein in modulating the dynamics of protein aggregation, and in the interactions with essential cellular components. However, very little is known about the molecular details of these aggregate species. For large protein aggregates, such as alpha-synuclein oligomers, it is very difficult to determine the number of monomers that form an oligomer using conventional techniques. We have developed a method that uses sub-stoichiometric labeling, that is, only a fraction of the monomers contains a fluorescent label, in combination with single-molecule photobleaching to determine the number of monomers per oligomer (Zijlstra et al., 2012). The number of bleaching steps gives the number of fluorescent labels per oligomer. Knowing the exact label density, that is, the fraction of labeled monomers at the start of the aggregation, we can correlate the number of fluorescent labels per oligomer to the total number of monomers. Using this method, we can determine the composition, probe the distribution in the number of monomers per oligomer, and investigate the influence of the fluorescent label on the aggregation process. For wild-type alpha-synuclein, we find no distribution in the number of monomers per oligomer and find a single, well-defined oligomeric species consisting of ～30 monomers per oligomer. On the other hand, for oligomers formed in the presence of dopamine, we find a distinctly bimodal distribution suggesting the existence of two populations of oligomeric species.     

Why is Leu55-->Pro55 transthyretin variant the most amyloidogenic: insights from molecular dynamics simulations of transthyretin monomers

Transthyretin (TTR) is one of the known human amyloidogenic proteins. Its native state is a homotetramer with each monomer having a beta-sandwich structure. Strong experimental evidence suggests that TTR dissociates into monomeric intermediates and that the monomers subsequently self-assemble to form amyloid deposits and insoluble fibrils. However, details on the early steps along the pathway of TTR amyloid formation are unclear, although various experimental approaches with resolutions at the molecular or residue level have provided some clues. It is highly likely that the stability and flexibility of monomeric TTR play crucial roles in the early steps of amyloid formation; thereby, it is essential to characterize initial conformational changes of TTR monomers. In this article we probe the possibility that the differences in the monomeric forms of wild-type (WT) TTR and its variants are responsible for differential amyloidogenesis. We begin with the simulations of WT, Val30-->Met (V30M), and Leu55-->Pro (L55P) TTR monomers. Nanosecond time scale molecular dynamics simulations at 300 K were performed using AMBER. The results indicate that the L55P-TTR monomer undergoes substantial structural changes relative to fluctuations observed in the WT and V30M TTR monomers. The observation supports earlier speculation that the L55P mutation may lead to disruption of the beta-sheet structure through the disorder of the "edge strands" that might facilitate amyloidogenesis.     

One-step affinity purification of fusion proteins with optimal monodispersity and biological activity: application to aggregation-prone HPV E6 proteins

Background

Bacterial expression and purification of recombinant proteins under homogeneous active form is often challenging. Fusion to highly soluble carrier proteins such as Maltose Binding Protein (MBP) often improves their folding and solubility, but self-association may still occur. For instance, HPV E6 oncoproteins, when produced as MBP-E6 fusions, are expressed as mixtures of biologically inactive oligomers and active monomers. While a protocol was previously developed to isolate MBP-E6 monomers for structural studies, it allows the purification of only one MBP-E6 construct at the time. Here, we explored a parallelizable strategy more adapted for biophysical assays aiming at comparing different E6 proteins.

Results

In this study, we took advantage of the distinct size and diffusion properties of MBP-E6 monomers and oligomers to separate these two species using a rapid batch preparation protocol on affinity resins. We optimized resin reticulation, contact time and elution method in order to maximize the proportion of monomeric MBP-E6 in the final sample. Analytical size-exclusion chromatography was used to quantify the different protein species after purification. Thus, we developed a rapid, single-step protocol for the parallel purification of highly monomeric MBP-E6 samples. MBP-fused HPV16 E6 samples obtained by this approach were validated by testing the binding to their prototypical peptide targets (the LXXLL motif from ubiquitine ligase E6AP) by BIAcore-SPR assay.

Conclusions

We have designed a rapid single-step batch affinity purification approach to isolate biologically active monomers of MBP-fused E6 proteins. This protocol should be generalizable to isolate the monomer (or the minimal biologically active oligomer) of other proteins prone to self-association.

     

Use of surface plasmon resonance to study the elongation kinetics and the binding properties of the highly amyloidogenic Aβ(1-42) peptide, synthesized by depsi-peptide technique

A wide variety of human diseases are associated with the formation of highly organized protein aggregates termed amyloid fibrils, whose growth (elongation) is due to the assembly of the basic molecular units (monomers) in a sequential polymerization process. Surface plasmon resonance (SPR) technology has been proposed as a powerful approach to study in detail the fibril elongation of some amyloidogenic peptides. In particular, the injection of monomers over immobilized fibrils allows to follow in real time, and on a very short time-scale, the kinetics of fibril growth. In the present study we confirmed and extended this application of SPR to Aβ(1-42), hampered till now by the very pronounced aggregation propensity of this peptide, involved in Alzheimer disease. We took advantage of a new synthetic strategy ("depsi-peptide" technique) which allows to obtain reliable seed-free solutions (monomers) as well as fibrils of Aβ(1-42). SPR data were consistent with a "dock-and-lock" mechanism underlying Aβ(1-42) elongation process. The setup of an assay monitoring the elongation kinetics is very useful for investigating potential anti-amyloidogenic compounds. Moreover, the possibility to reliably immobilize both Aβ(1-42) monomers and fibrils allows to measure the binding affinities of putative ligands for these different species. The approach applied here to Aβ(1-42) might well be also applied to the study of other fibrillogenic peptides/proteins or to the study of polymerization reactions in general.     

A Generalized Michaelis–Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon

The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a ‘biologically motivated’ generalization of the Michaelis–Menten formula for the average rate of enzymatic reactions. This generalized Michaelis–Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.     

Which 3-ribofuranosyl-substituted purine 5′-phosphates undergo template-directed oligomerization?

Summary We have studied the oligomerization reactions of the 2-methylimidazolide derivatives of 3-isoisoguanosine 5-phosphate (2) and 3-isoxanthosine 5-phosphate (5) in the presence of a variety of homopolynucleotide templates. In no case did we observe a substantial template-facilitated production of long oligomers. Polyuridylic acid directed the synthesis of low molecular-weight products from both monomers. Polycytidylic acid, polyadenylic acid, polyinosinic acid, and polyguanylic acid were ineffective as templates in the systems that we investigated.     

Continuous flow reactor for the production of stable amyloid protein oligomers

The predominant working hypothesis of Alzheimer's disease is that the proximate pathologic agents are oligomers of the amyloid β-protein (Aβ). "Oligomer" is an ill-defined term. Many different types of oligomers have been reported, and they often exist in rapid equilibrium with monomers and higher-order assemblies. This has made formal structure-activity determinations difficult. Recently, Ono et al. [Ono, K., et al. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 14745-14750] used rapid, zero-length, in situ chemical cross-linking to stabilize the oligomer state, allowing the isolation and study of pure populations of oligomers of a specific order (number of Aβ monomers per assembly). This approach was successful but highly laborious and time-consuming, precluding general application of the method. To overcome these difficulties, we developed a "continuous flow reactor" with the ability to produce theoretically unlimited quantities of chemically stabilized Aβ oligomers. We show, in addition to its utility for Aβ, that this method can be applied to a wide range of other amyloid-forming proteins.     

Property and application of novel ferrocenyl-azobenzene labeled peptide nucleic acid monomers with the dual stimulus-response characteristics

In this work, three novel types of peptide nucleic acid (PNA) monomers labeled by ferrocenyl-azobenzene units (Fc-Azo-PNAs, 1a, 1b, and 1c) have been synthesized and they all exhibited good reversible photoswitch and redox properties. In the different solvents of ethanol (EtOH) and acetonitrile (ACN), photoisomerization rate constants (K) of three PNA monomers under UV light irradiation have also been analyzed and compared, discovering that the values of K are closely correlative to their molecular structures. The electrochemical properties of the synthesized PNA monomers are also investigated and the typical redox properties are displayed, demonstrating that they can be regarded as the anchor to be grafted at the end of PNA oligomers for detecting themselves. Finally, according to the analyses of UV-Vis absorption spectrum and differential pulse voltammetry (DPV), the synthesized PNA monomers afford the best detection limit down to 10⁻⁸ M in EtOH. The results also illuminate that PNA monomers with new photo-redox dual stimulus-response characteristics can be realized to detect themselves by the metal complex unit together with azo moiety; moreover, the hybridization with DNA also can be tuned by the isomerization of azo moiety.     

Characterization of dimeric ATP synthase and cristae membrane ultrastructure from Saccharomyces and Polytomella mitochondria

There is increasing evidence now that F(1)F(0) ATP synthase is arranged in dimers in the inner mitochondrial membrane of several organisms. The dimers are also considered to be the building blocks of oligomers. It was recently found that the monomers in beef and the alga Polytomella ATP synthase dimer make an angle of approximately 40 degrees and approximately 70 degrees, respectively. This arrangement is considered to induce a strong local bending of the membrane. To further understand the packing of dimers into oligomers we performed an electron microscopy analysis of ATP synthase dimers purified from Saccharomyces cerevisiae. Two types of dimers were found in which the angle between the monomers is either approximately 90 degrees or approximately 35 degrees. According to our interpretation, the wide-angle dimers (70-90 degrees) are "true-dimers" whereas the small-angle dimers (35-40 degrees) rather are "pseudo-dimers", which represent breakdown products of two adjacent true dimers in the oligomer. Ultrathin sectioning of intact Polytomella mitochondria indicates that the inner mitochondrial or cristae membrane is folded into lamellae and tubuli. Oligomers of ATP synthase can arrange in a helical fashion in tubular-shaped cristae membranes. These results strongly support the hypothesized role of ATP synthase oligomers in structural determination of the mitochondrial inner membrane.     

Clustering of identical oligomers in coding and noncoding DNA sequences.

We develop a quantitative method for analyzing repetitions of identical short oligomers in coding and noncoding DNA sequences. We analyze sequences presently available in the GenBank separately for primate, mammal, vertebrate, rodent, invertebrate and plant taxonomic partitions. We find that some oligomers "cluster" more than they would if randomly distributed, while other oligomers "repel" each other. To quantify this degree of clustering, we define clustering measures. We find that (i) clustering significantly differs in coding and noncoding DNA; (ii) in most cases, monomers, dimers and tetramers cluster in noncoding DNA but appear to repel each other in coding DNA. (iii) The degree of clustering for different sources (primates, invertebrates, and plants) is more conserved among these sources in the case of coding DNA than in the case of noncoding DNA. (iv) In contrast to other oligomers, we find that trimers always prefer to cluster. (v) Clustering of each particular oligomer is conserved within the same organism.     

In silico modeling of pH-optimum of protein-protein binding

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity (pH-optimum of binding) or pH interval at which affinity is almost pH-independent (pH-flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH-dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH-optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH-optimum of binding. These findings are used to propose empirical rule for predicting pH-optimum of binding provided that the amino acid compositions of the corresponding monomers are available.     

Characterization of three regulatory states of the striated muscle thin filament

The troponin-tropomyosin-linked regulation of striated muscle contraction occurs through allosteric control by both Ca(2+) and myosin. The thin filament fluctuates between two extreme states: the inactive "off" state and the active "on" state. Intermediate states have been proposed from structural studies and transient kinetic measurements. However, in contrast to the well-characterised, on and off states, the mechanochemical properties of the intermediate states are much less well understood because of the instability of those states. In the present study, we have characterized a myosin-induced intermediate that is stabilized by cross-linking myosin motor domains (S1) to actin filaments (with a maximum of one S1 molecule for 50 actin monomers). A single S1 molecule is known to interact with two adjacent actin monomers. A detailed analysis revealed that thin filaments containing S1 molecules cross-linked to just one actin monomer (actin(1)-S1 complexes) are regulated with a 79% inhibition of the ATPase in the absence of Ca(2+). In contrast, filaments containing S1 molecules cross-linked at two positions, to two adjacent actin monomers (actin(2)-S1 complexes) totally lose their regulation in a highly cooperative manner. This loss of regulation was due both to an enhancement of the ATPase activity without calcium and an inhibition of the ATPase with calcium. Filaments containing actin(2)-S1 complexes, with significant ATPase activity in the absence of calcium (about 50%), did not move on a myosin-coated surface unless calcium was present. This partial uncoupling between the ATPase activity and in vitro motility in the absence of calcium demonstrates that the mechanical steps require actin-myosin contacts, which take place only in the on state and not in the off or intermediate states. These data provide new insights concerning the difference in cooperativity of Ca(2+) regulation that exists between the biochemical and mechanical cycles of the actin-myosin motor.     

Sticking coefficient-orchestrated selection in a kinetic model for the first origin

The mathematical formalism of the steady-state Poisson equation is applied to a variant of Freeman Dyson's "Toy Model" for a first origin. Our kinetic approach allows for an examination of the requisite conditions under which metabolism is quantized into discrete eigenstates (e.g. Dyson's disordered, saddle point, and metabolically active toy cell states). The surface reaction machinery additionally allows for more realistic modeling, whence the crucial role of sticking coefficients (catalyst precursors) as prebiotic selectors emerges. In our interior source model, a steady influx of vent nutrients fuels the intracellular synthesis of (impermeable) monomers within a rock-encradled cavity. Random adsorptions and desorptions occur at inactive "cell" wall sites (where the inert monomers remain impermeable until their eventual return to the intracellular metabolite pool). Occasionally, metabolizing reactions also occur due to endogeneous source monomers adsorbing at their "active" sites. Dyson's mean field approach is used to simplify the species-specific sticking coefficients at empty active (substrate) sites to functions of the fraction x of sites occupied by (catalytically) active monomers. In short, our work suggests that disorder-order transition models based on random drift between discrete metabolic eigenstates (Dyson's Toy Model) do not, in general, extend to more realistic metabolisms. From a perspective based on quasi-random feedback kinetics, the contraindication for discretization (spontaneous generation) in non-autocatalytic metabolisms is consistent with the emergence of ordered metabolism under hydrothermal driving forces, a provisio the occurrence of each period of vent dormancy coincides with a discrete zero-source (dormant) metabolic state. Cell drift to higher order is induced by the random reactions which happen to enhance the substrate specificity (chemical selectivity) of the sticking coefficients for active monomers. The result is stronger sink effects for metabolizing species, whence active adsorptions are promoted in favor of inactive adsorptions at substrate sites. Positive feedback plays a crucial role in preserving ("propagating") order in the cell wall reaction kinetics and is held in check by negative feedback inhibition of excessive cell growth. Finally, the eventual desorption of randomly growing dysfunctional proteins is postulated as a deterrent to deterioration catastrophes.     

Nuclear protein modification and chromatin substructure. 2. Internucleosomal localization of poly(adenosine diphosphate-ribose) polymerase.

Definitive evidence for poly(ADP-Rib) polymerase activity is localized within internucleosomal "linker" regions of HeLa cell chromatin is presented. This evidence was based on the following criteria: the enzyme activity did not coincide with the position of core particles in a sucrose gradient but was displaced to that part of the gradient which is enriched in monomers with linker regions. This was not due to dimer contamination, since resedimentation did not affect the enzyme activity in relation to the monomer. A new method of assaying enzyme activity directly in polyacrylamide gels following the separation of monomers and dimers showed that only dimers and monomers with linker regions contained activity. When dimers were digested, the enzyme activity moved from the dimer to the monomer with linker.     

Messenger RNA isolation using novel PNA analogues

Homo-Thy hetero-oligomer probes composed of trans-4-hydroxy-L-proline based PNA-like (HypNA) monomers and phosphono PNA (pPNA) monomers demonstrated strong binding to complementary poly A+ RNA strands. We used a mixture of chimeric oligomers containing both "linear" and "clamping" PNA-analogues to develop an mRNA isolation procedure and demonstrate the improved recovery of RNA molecules with secondary structure at the 3'end as well as RNAs with short poly A tails.     

Reciprocal effects of substitutions at the subunit interfaces in hexameric pyrophosphatase of Escherichia coli. Dimeric and monomeric forms of the enzyme

A homohexameric molecule of Escherichia coli pyrophosphatase is arranged as a dimer of trimers, with an active site present in each of its six monomers. Earlier we reported that substitution of His(136) and His(140) in the intertrimeric subunit interface splits the molecule into active trimers (Velichko, I. S., Mikalahti, K., Kasho, V. N., Dudarenkov, V. Y., Hyyti?, T., Goldman, A., Cooperman, B. S., Lahti, R., and Baykov, A. A. (1998) Biochemistry 37, 734-740). Here we demonstrate that additional substitutions of Tyr(77) and Gln(80) in the intratrimeric interface give rise to moderately active dimers or virtually inactive monomers, depending on pH, temperature, and Mg(2+) concentration. Successive dissociation of the hexamer into trimers, dimers, and monomers progressively decreases the catalytic efficiency (by 10(6)-fold in total), and conversion of a trimer into dimer decreases the affinity of one of the essential Mg(2+)-binding sites/monomer. Disruptive substitutions predominantly in the intratrimeric interface stabilize the intertrimeric interface and vice versa, suggesting that the optimal intratrimeric interaction is not compatible with the optimal intertrimeric interaction. Because of the resulting "conformational strain," hexameric wild-type structure appears to be preformed to bind substrate. A hexameric triple variant substituted at Tyr(77), Gln(80), and His(136) exhibits positive cooperativity in catalysis, consistent with this model.     

Protein osmotic pressure modulates actin filament length distribution

1.

The changes of the macromolecular osmotic pressure associated with F-actin solutions are related to the changes of the free energy of the free actin monomers.

2.

By making use of the model of Biron et al. [2006. Inter-filament attractions narrow the length distribution of actin filaments. Europhys. Lett. 73, 464-470], the changes of the free energy of the free actin monomers are related to the changes of the length distribution of the actin filaments.

On these bases, we propose that the length distribution of the actin filaments is regulated by (a) the free energy of hydrolysis of ATP and (b) the macromolecular osmotic pressure.

a.

While the free energy of hydrolysis of ATP tends to zero, the length distribution of the actin filaments shifts from an exponential curve to a straight line parallel to the abscissa axis (i.e. the concentration of the actin filaments becomes independent of their length). In the mean time, the total energy of the actin filaments reaches a minimum.

b.

With the increase of the macromolecular osmotic pressure the free energy of the actin monomers increases and a break is introduced in the curve that describes the length distribution of the actin filaments; the break is located at the mean length of the filaments.

     

Reverse engineering an amyloid aggregation pathway with dimensional analysis and scaling

Human islet amyloid polypeptide (hIAPP) is a cytotoxic protein that aggregates into oligomers and fibrils that kill pancreatic β-cells. Here we analyze hIAPP aggregation in vitro, measured via thioflavin-T fluorescence. We use mass-action kinetics and scaling analysis to reconstruct the aggregation pathway, and find that the initiation step requires four hIAPP monomers. After this step, monomers join the nucleus in pairs, until the first stable nucleus (of size approximately 20 monomers) is formed. This nucleus then elongates by successive addition of single monomers. We find that the best-fit of our data is achieved when we include a secondary fibril-dependent nucleation pathway in the reaction scheme. We predict how interventions that change rates of fibril elongation or nucleation rates affect the accumulation of potentially cytotoxic oligomer species. Our results demonstrate the power of scaling analysis in reverse engineering biochemical aggregation pathways.     

The effects of caldesmon on smooth muscle heavy actomeromyosin ATPase activity and binding of heavy meromyosin to actin

Caldesmon was purified to homogeneity from both chicken gizzard and bovine aortic smooth muscles. Caldesmon purified from bovine aorta was slightly larger than caldesmon purified from chicken gizzards (Mr = 140,000) when the two were compared electrophoretically. Caldesmon bound tightly to actin saturating at a molar ratio of 1 caldesmon monomer per 6.6 actin monomers. Ca2+-calmodulin appeared to reduce the affinity of caldesmon for actin. Caldesmon was also a potent inhibitor of heavy actomeromyosin ATPase activity producing a maximal effect at a ratio of 1 caldesmon monomer per 7-10 actin monomers. This effect was also antagonized by Ca2+-calmodulin. While caldesmon inhibited heavy actomeromyosin ATPase activity, it greatly enhanced binding of both unphosphorylated and phosphorylated heavy meromyosin to actin in the presence of MgATP, reducing the Kd for binding by a factor of 40 for each form of heavy meromyosin. Although we did identify a Ca2+-calmodulin-stimulated "caldesmon kinase" activity in caldesmon preparations purified under nondenaturing conditions, we observed no effect of phosphorylation (2 mol of PO4/mol of caldesmon) on the capacity to inhibit heavy actomeromyosin ATPase activity. Our results suggest that caldesmon could serve some role in smooth muscle function by enhancing cross-bridge affinity while inhibiting actomyosin ATPase activity.     

Structure optimization in a three-dimensional off-lattice protein model

We studied a three-dimensional off-lattice AB model with two species of monomers, hydrophobic (A) and hydrophilic (B), and present two optimization algorithms: face-centered-cubic (FCC)-lattice pruned-enriched-Rosenbluth method (PERM) and subsequent conjugate gradient (PERM++) minimization and heuristic conjugate gradient (HCG) simulation based on "off-trap" strategy. In PERM++, we apply the PERM to the FCC-lattice to produce the initial conformation, and conjugate gradient minimization is then used to reach the minimum energy state. Both algorithms have been tested in the three-dimensional AB model for all sequences with lengths 13 < or = n < or = 55. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we renew the putative ground states energy values.