Amyloid Fibril Formation by the Chain B Subunit of Monellin Occurs by a Nucleation-Dependent Polymerization Mechanism

Collective effect of Vigna sp. (mung) tubulin GTP hydrolysis rate divergence on microtubule filament assembly

Microtubules (MTs) are dynamic cytoskeletal filaments with highly conserved sequences across evolution, polymerizing by the GTP-dependent assembly of tubulin subunits. Despite the sequence conservation, MT polymerization kinetics diverge quantitatively between vertebrate brain, the model plant Arabidopsis and the protozoan Plasmodium. Previously, tubulin purified from seedlings of the plant Vigna sp. (mung) by temperature cycling was found to have a very low critical concentration. However, the lengths of MTs were sub-micron, much shorter than brain tubulin filaments. This was explained in simulations to be the result of the collective effect of high nucleation and GTP hydrolysis rates. Here, we test the effect of GTPase rates of affinity-purified Vigna sp. tubulin on microtubule polymerization and elongation. Affinity-purified mung tubulin is active and has a critical concentration of .37 μM. The GTP-dependent polymerization kinetics are transient, consistent with previous results. Polymerization is stabilized in the presence of either GTP analog GMPPNP (non-hydrolyzable) or GMPCPP (slow-hydrolyzable). Using interference reflection microscopy (IRM) we find polymerization with the non-hydrolysable analog significantly increases filament numbers, while lengths are unaffected for both GTP analogs. However, prolonged incubation with slow-hydrolyzable GMPCPP results in long filaments, pointing to GTP hydrolysis as a key factor determining MT length. We find the average GTPase turnover number of mung tubulin is 22.8 min-1, compared to 2.04 min-1 for goat brain tubulin. Thus modulating GTPase rates affects both nucleation and elongation. This quantitative divergence in kinetics despite high sequence conservation in the GTPase domains of α- and β-tubulin could help better understand the roles of selective pressure and function in the diverse organisms.

Citrullinated human and murine MOG35-55 display distinct biophysical and biochemical behavior

The peptide spanning residues 35 to 55 of the protein myelin oligodendrocyte glycoprotein (MOG) has been studied extensively in its role as a key autoantigen in the neuroinflammatory autoimmune disease multiple sclerosis. Rodents and nonhuman primate species immunized with this peptide develop a neuroinflammatory condition called experimental autoimmune encephalomyelitis, often used as a model for multiple sclerosis. Over the last decade, the role of citrullination of this antigen in the disease onset and progression has come under increased scrutiny. We recently reported on the ability of these citrullinated MOG35-55 peptides to aggregate in an amyloid-like fashion, suggesting a new potential pathogenic mechanism underlying this disease. The immunodominant region of MOG is highly conserved between species, with the only difference between the murine and human protein, a polymorphism on position 42, which is serine in mice and proline for humans. Here, we show that the biophysical and biochemical behavior we previously observed for citrullinated murine MOG35-55 is fundamentally different for human and mouse MOG35-55. The citrullinated human peptides do not show amyloid-like behavior under the conditions where the murine peptides do. Moreover, we tested the ability of these peptides to stimulate lymphocytes derived from MOG immunized marmoset monkeys. While the citrullinated murine peptides did not produce a proliferative response, one of the citrullinated human peptides did. We postulate that this unexpected difference is caused by disparate antigen processing. Taken together, our results suggest that further study on the role of citrullination in MOG-induced experimental autoimmune encephalomyelitis is necessary.

Multistep molecular mechanism of amyloid-like aggregation of nucleic acid-binding domain of TDP-43

TDP-43 protein is associated with many neurodegenerative diseases and has been shown to adopt various oligomeric and fibrillar states. However, a detailed kinetic understanding of the structural transformation of the native form of the protein to the fibrillar state is missing. In this study, we delineate the temporal sequence of structural events during the amyloid-like assembly of the functional nucleic acid-binding domain of TDP-43. We kinetically mapped the aggregation process using multiple probes such as tryptophan and thioflavin T (ThT) fluorescence, circular dichroism (CD), and dynamic light scattering (DLS) targeting different structural events. Our data reveal that aggregation occurs in four distinct steps-very fast, fast, slow, and very slow. The "very fast" change results in partially unfolded forms that undergo conformational conversion, oligomerization and bind to ThT in the "fast step" to form higher order intermediates (HOI). The temporal sequence of the formation of ThT binding sites and conformational conversion depends upon the protein concentration. The HOI further undergoes structural rearrangement to form protofibrils in the "slow" step, which, consequently, assembles in the "very slow" step to form an amyloid-like assembly. The spectroscopic properties of the amyloid-like assembly across the protein concentration remain similar. Additionally, we observe no lag phase across protein concentration for all the probes studied, suggesting that the aggregation process follows a linear polymerization reaction. Overall, our study demonstrates that the amyloid-like assembly forms in multiple steps, which is also supported by the temperature dependence of the kinetics.

Polymerization kinetics of tubulin from mung seedlings modeled as a competition between nucleation and GTP-hydrolysis rates

Microtubules (MTs) form physiologically important cytoskeletal structures that assemble by tubulin polymerization in a nucleation- and GTP-dependent manner. GTP-hydrolysis competes with the addition of monomers, to determine the GTP-cap size, and onset of shrinkage, which alternates with growth. Multiple theoretical models of MT polymerization dynamics have been reconciled to the kinetics of animal brain tubulins, but more recently rapid kinetics seen in Arabidopsis tubulin polymerization suggest the need to sample a wider diversity in tubulin polymerization kinetics and reconcile it to theory. Here, we have isolated tubulin from seedlings of Vigna sp. (mung bean), compared polymerization kinetics to animal brain tubulin and used a computational model to understand the di_erences. We _nd that activity isolated mung tubulin polymerizes in a nucleation-dependent manner, based on turbidimetry, qualitatively similar to brain tubulin, but with a ten-fold smaller critical critical concentration. GTP-dependent polymerization kinetics also appear to be transient, indicative of high rates of GTP-hydrolysis. Computational modeling of tubulin nucleation and vectorial GTP-hydrolysis to examine the e_ect of high nucleation and GTP-hydrolysis rates predicts a dominance of the latter in determining MT lengths and numbers. Microscopy of mung tubulin _laments stabilized by GMPCPP or taxol result in few and short MTs, compared to the many long MTs arising from goat tubulin, qualitatively matching the model predictions. We _nd GTP-hydrolysis outcompetes nucleation rates in determining MT lengths and numbers. This article is protected by copyright. All rights reserved.

The amyloidogenicity of a C-terminal region of TDP-43 implicated in Amyotrophic Lateral Sclerosis can be affected by anions, acetylation and homodimerization

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease associated with accumulation of hyper-phosphorylated, and ubiquitinated TAR DNA-binding protein-43 (TDP-43) as inclusion deposits in neuronal cells. Recently, amyloid-like fibrillar aggregates of TDP-43 have been reported from several ALS patients. The C-terminal region of TDP-43 is central to TDP-43's pathological aggregation and most of the familial ALS mutations in the encoding TARDBP gene are located in this domain. Also, aberrant proteolytic cleavages of TDP-43 produce cytotoxic C-terminal fragments of ∼15-35 kDa. The C-terminal end harbours a glycine-rich region and a Q/N rich prion-like aggregation-prone domain which has been shown to form amyloid-like fibrillar aggregates in vitro. Previously, TDP-43 protein has also been shown to undergo several other post-translational modifications such as acetylation and dimerization, however, their effects on TDP-43's amyloid-like in vitro aggregation have not been examined. Towards this, we have here examined effects of anions, acetylation and homodimerization on the in vitro aggregation of a C-terminal fragment (amino acid: 193-414) of TDP-43 termed TDP-43^2C. We find that kosmotropic anions greatly accelerate whereas chaotropic anions impede its aggregation. Also, we show that acetylation of certain lysines in C-terminal fragments significantly reduces the TDP-43^2C's amyloid-like aggregation. Furthermore, we separated spontaneously formed cysteine-linked homodimers of the recombinantly purified TDP-43^2C using size-exclusion chromatography and found that these dimers retain amyloidogenicity. These findings would be of significance to the TDP-43 aggregation-induced pathology in ALS.

The G126V Mutation in the Mouse Prion Protein Hinders Nucleation-Dependent Fibril Formation by Slowing Initial Fibril Growth and by Increasing the Critical Concentration

The middle disordered hydrophobic region of the prion protein plays a critical role in conformational conversion of the protein, with pathogenic as well as protective mutations being localized to this region. In particular, it has been shown that the G127V mutation in this region of the human prion protein (huPrP) is protective against the spread of prion disease, but the mechanism of protection remains unknown. In this study, quantitative analyses of the kinetics of fibril formation by wild-type mouse prion protein (moPrP) and G126V moPrP (equivalent to G127V huPrP) reveal important differences: the critical concentration is higher, the lag phase is longer, and the initial effective rate constant of fibril growth is slower for the mutant variant. The study offers a simple biophysical explanation for why the G127V mutation in huPrP would be protective in humans: the ∼5-fold increase in critical concentration caused by the mutation likely results in the critical concentration (below which fibril formation cannot occur) being higher that the concentration of the protein present in and on cells in vivo.

Glycerol inhibits the primary pathways and transforms the secondary pathway of insulin aggregation

Aggregation of insulin initiated from the monomeric form proceeds via the secondary pathway of fragmentation. It was interesting to find that glycerol had the potential to transform the secondary pathway of aggregation from fragmentation to heterogeneous nucleation in a concentration dependent manner. Such a change in the secondary pathway was manifested by a change in the fibrillar morphology, wherein, longer fibrils were formed in the presence of glycerol. Glycerol could inhibit all the major steps of insulin aggregation. The analysis of the kinetic traces suggested that the inhibitory effect was most significant on the primary pathways, although secondary nucleation and elongation were also inhibited. In fact, at higher glycerol concentrations, the primary pathways were inhibited to such an extent that the majority of the aggregation was now driven by the secondary pathways. Our data suggest that glycerol binds to the early intermediates in the insulin aggregation pathway, and inhibits them from forming the aggregation competent species capable of elongation. As higher order species are formed in the aggregation pathway, the relative stabilization rendered by glycerol diminishes due to the exclusion of glycerol from the interface.

Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein

MNEI is a single chain derivative of monellin, a plant protein that can interact with the human sweet taste receptor, being therefore perceived as sweet. This unusual physiological activity makes MNEI a potential template for the design of new sugar replacers for the food and beverage industry. Unfortunately, applications of MNEI have been so far limited by its intrinsic sensitivity to some pH and temperature conditions, which could occur in industrial processes. Changes in physical parameters can, in fact, lead to irreversible protein denaturation, as well as aggregation and precipitation. It has been previously shown that the correlation between pH and stability in MNEI derives from the presence of a single glutamic residue in a hydrophobic pocket of the protein. We have used molecular dynamics to study the consequences, at the atomic level, of the protonation state of such residue and have identified the network of intramolecular interactions responsible for MNEI stability at acidic pH. Based on this information, we have designed a pH-independent, stabilized mutant of MNEI and confirmed its increased stability by both molecular modeling and experimental techniques.

Differential influence of additives on the various stages of insulin aggregation

The different species in the aggregation pathway of insulin are stabilized/destabilized to different extent in the presence of various additives.

Kinetic Analysis as a Tool to Distinguish Pathway Complexity in Molecular Assembly: An Unexpected Outcome of Structures in Competition

While the sensitive dependence of the functional characteristics of self-assembled nanofibers on the molecular structure of their building blocks is well-known, the crucial influence of the dynamics of the assembly process is often overlooked. For natural protein-based fibrils, various aggregation mechanisms have been demonstrated, from simple primary nucleation to secondary nucleation and off-pathway aggregation. Similar pathway complexity has recently been described in synthetic supramolecular polymers and has been shown to be intimately linked to their morphology. We outline a general method to investigate the consequences of the presence of multiple assembly pathways, and show how kinetic analysis can be used to distinguish different assembly mechanisms. We illustrate our combined experimental and theoretical approach by studying the aggregation of chiral bipyridine-extended 1,3,5-benzenetricarboxamides (BiPy-1) in n-butanol as a model system. Our workflow consists of nonlinear least-squares analysis of steady-state spectroscopic measurements, which cannot provide conclusive mechanistic information but yields the equilibrium constants of the self-assembly process as constraints for subsequent kinetic analysis. Furthermore, kinetic nucleation-elongation models based on one and two competing pathways are used to interpret time-dependent spectroscopic measurements acquired using stop-flow and temperature-jump methods. Thus, we reveal that the sharp transition observed in the aggregation process of BiPy-1 cannot be explained by a single cooperative pathway, but can be described by a competitive two-pathway mechanism. This work provides a general tool for analyzing supramolecular polymerizations and establishing energetic landscapes, leading to mechanistic insights that at first sight may seem unexpected and counterintuitive.

Relationship between the initial rate of protein aggregation and the lag period for amorphous aggregation

Lag period is an inherent characteristic of the kinetic curves registered for protein aggregation. The appearance of a lag period is connected with the nucleation stage and the stages of the formation of folding or unfolding intermediates prone to aggregation (for example, the stage of protein unfolding under stress conditions). Discovering the kinetic regularities essential for elucidation of the protein aggregation mechanism comprises deducing the relationship between the lag period and aggregation rate. Fändrich proposed the following equation connecting the duration of the lag phase (tlag) and the aggregate growth rate (kg) in the amyloid fibrillation: kg=const/tlag. To establish the relationship between the initial rate of protein aggregation (v) and the lag period (t0) in the case of amorphous aggregation, the kinetics of dithithreitol-induced aggregation of holo-α-lactalbumin from bovine milk was studied (0.1M Na-phosphate buffer, pH 6.8; 37°C). The order of aggregation with respect to protein (n) was calculated from the dependence of the initial rate of protein aggregation on the α-lactalbumin concentration (n=5.3). The following equation connecting v and t0 has been proposed: v(1/n)=const/(t0-t0,lim), where t0,lim is the limiting value of t0 at high concentrations of the protein.