Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43307-319 Aggregation.

Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the ß-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.

Catalytic Cross Talk between Key Peptide Fragments That Couple Alzheimer's Disease with Amyotrophic Lateral Sclerosis.

Protein aggregation is a common feature in prominent neurodegenerative diseases, usually thought to be due to the assembly of a single peptide or protein. Recent studies have challenged this notion and suggested several proteins may be involved in promoting and amplifying disease. For example, the TDP-43 protein associated with Amyotrophic Lateral Sclerosis has been found in the brain along with Aß assemblies associated with Alzheimer's disease, and those patients that show the presence of TDP-43 are 10 times more likely to demonstrate cognitive impairment compared to TDP-43-negative Alzheimer's patients. Here we examine the interactions between the amyloidogenic core of TDP-43, TDP-43307-319, and a neurotoxic physiologically observed fragment of Aß, Aß25-35. Utilizing ion mobility mass spectrometry in concert with atomic force microscopy and molecular dynamics simulations, we investigate which oligomers are involved in seeding aggregation across these two different protein systems and gain insight into which structures initiate and result from these interactions. Studies were conducted by mixing Aß25-35 with the toxic wild type TDP-43307-319 peptide and with the nontoxic synthetic TDP-43307-319 mutant, G314V. Our findings identify a strong catalytic effect of TDP-43307-319 WT monomer in the acceleration of Aß25-35 aggregation to its toxic cylindrin and ß barrel forms. This observation is unprecedented in both its speed and specificity. Interestingly, the nontoxic G314V mutant of TDP-43307-319 and dimers or higher order oligomers of WT TDP-43307-319 do not promote aggregation of Aß25-35 but rather dissociate preformed toxic higher order oligomers of Aß25-35. Reasons for these very different behaviors are reported.

Modulating ALS-Related Amyloidogenic TDP-43307-319 Oligomeric Aggregates with Computationally Derived Therapeutic Molecules.

TDP-43 aggregates are a salient feature of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and a variety of other neurodegenerative diseases, including Alzheimer's disease (AD). With an anticipated growth in the most susceptible demographic, projections predict neurodegenerative diseases will potentially affect 15 million people in the United States by 2050. Currently, there are no cures for ALS, FTD, or AD. Previous studies of the amyloidogenic core of TDP-43 have demonstrated that oligomers greater than a trimer are associated with toxicity. Utilizing a joint pharmacophore space (JPS) method, potential drugs have been designed specifically for amyloid-related diseases. These molecules were generated on the basis of key chemical features necessary for blood-brain barrier permeability, low adverse side effects, and target selectivity. Combining ion-mobility mass spectrometry and atomic force microscopy with the JPS computational method allows us to more efficiently evaluate a potential drug's efficacy in disrupting the development of putative toxic species. Our results demonstrate the dissociation of higher-order oligomers in the presence of these novel JPS-generated inhibitors into smaller oligomer species. Additionally, drugs approved by the Food and Drug Administration for the treatment of ALS were also evaluated and demonstrated to maintain higher-order oligomeric assemblies. Possible mechanisms for the observed action of the JPS molecules are discussed.

Catalytic Prion-Like Cross-Talk between a Key Alzheimer's Disease Tau-Fragment R3 and the Type 2 Diabetes Peptide IAPP.

The aberrant association of proteins/peptides is implicated in the etiology and pathogenesis of a variety of human diseases. In general, the primary protein component responsible for the formation of aggregates is different in each case and is specific to a particular disease condition. However, there are instances where multiple protein aggregates have been found to coexist in the same or different tissue(s), thereby leading to mixed pathologies and exacerbation of disease symptoms. In this context, a strong link has been established between Alzheimer's disease (AD) and type 2 diabetes (T2D). However, the underlying molecular details still remain elusive. Here, we report the direct interaction of an AD-associated amyloidogenic cytotoxic fragment of Tau (R3:306-336) with islet amyloid polypeptide (IAPP) implicated in T2D. Using ion-mobility mass spectrometry (IM-MS) in conjunction with fluorescence spectroscopy, circular dichroism, and transmission electron microscopy, we have been able to provide critical mechanistic insights into these interactions. Our IM-MS data showed the formation of hetero-oligomers of R3 and IAPP. Additionally, using IM-MS, we found that the amyloidogenic extended beta hairpin conformation of IAPP is favored much more in the R3-IAPP mixture, when compared with IAPP alone. Furthermore, we found that the oligomerization of R3 occurs much faster in the presence of IAPP. We also observed a secondary nucleation step in our kinetics data for the R3-IAPP mixture. We believe that the secondary nucleation step is demonstrative of R3 aggregation which otherwise requires the presence of anionic cofactors. Our results provide the first experimental evidence for direct molecular interaction between Tau and IAPP and highlights the repercussion of possible "prion-like" cross-talk in the proliferation of diseases that are associated with different tissues/organs.

Characterizing TDP-43307-319 Oligomeric Assembly: Mechanistic and Structural Implications Involved in the Etiology of Amyotrophic Lateral Sclerosis.

Aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is a salient feature of amyotrophic lateral sclerosis (ALS), a debilitating neurodegenerative disorder affecting over 200 000 people worldwide. The protein undergoes both functional and pathogenic aggregation; the latter is irreversible and hypothesized to produce soluble oligomers that are toxic to neurons in addition to inclusions made of stable fibrous deposits. Despite progress made toward identifying disease-related proteins, the underlying pathogenic mechanism associated with these toxic oligomers remains elusive. Utilizing a multimodal approach that combines several measurement techniques (circular dichroism (CD), thioflavin T spectroscopy (ThT), Fourier transform infrared spectroscopy (FTIR)) and high spatial resolution imaging tools (electron microscopy (EM) and atomic force microscopy (AFM)), with soft ion mobility mass spectrometry (IM-MS) and atomistic molecular dynamics (MD) simulations, we explore the oligomerization mechanisms, structures, and assembly pathways of TDP-43307-319. This fragment is both amyloidogenic and toxic and is within the glycine-rich C-terminal domain essential for both toxicity and aggregation of the full-length protein. In addition to the wild-type peptide, two ALS-related mutants (A315T and A315E) and a non-axon-toxic mutant (G314V) were investigated to determine how mutations affect the oligomerization of TDP-43307-319 and structures of toxic oligomers. The results of our study provide new insights into how ALS-related mutants, A315T and A315E, accelerate or alter the pathogenic mechanism and highlight the role of an internal glycine, G314, in maintaining efficient packing known to be critical for functional oligomer assembly. More importantly, our data demonstrate that G314 plays a vital role in TDP-43 assembly and prevents cytotoxicity via its unique aversion to oligomers larger than trimer. Our observation is consistent with previous studies showing that G314V mutation of the full-length TDP-43 induced remediation of both axonotoxicity and neuronal apoptosis. Our findings reveal a distinct aggregation mechanism for each peptide and elucidate oligomeric species and possible structures that may be involved in the pathology of ALS.

Oligomerization of the microtubule-associated protein tau is mediated by its N-terminal sequences: implications for normal and pathological tau action.

Despite extensive structure-function analyses, the molecular mechanisms of normal and pathological tau action remain poorly understood. How does the C-terminal microtubule-binding region regulate microtubule dynamics and bundling? In what biophysical form does tau transfer trans-synaptically from one neuron to another, promoting neurodegeneration and dementia? Previous biochemical/biophysical work led to the hypothesis that tau can dimerize via electrostatic interactions between two N-terminal 'projection domains' aligned in an anti-parallel fashion, generating a multivalent complex capable of interacting with multiple tubulin subunits. We sought to test this dimerization model directly. Native gel analyses of full-length tau and deletion constructs demonstrate that the N-terminal region leads to multiple bands, consistent with oligomerization. Ferguson analyses of native gels indicate that an N-terminal fragment (tau(45-230) ) assembles into heptamers/octamers. Ferguson analyses of denaturing gels demonstrates that tau(45-230) can dimerize even in sodium dodecyl sulfate. Atomic force microscopy reveals multiple levels of oligomerization by both full-length tau and tau(45-230) . Finally, ion mobility-mass spectrometric analyses of tau(106-144) , a small peptide containing the core of the hypothesized dimerization region, also demonstrate oligomerization. Thus, multiple independent strategies demonstrate that the N-terminal region of tau can mediate higher order oligomerization, which may have important implications for both normal and pathological tau action. The microtubule-associated protein tau is essential for neuronal development and maintenance, but is also central to Alzheimer's and related dementias. Unfortunately, the molecular mechanisms underlying normal and pathological tau action remain poorly understood. Here, we demonstrate that tau can homo-oligomerize, providing novel mechanistic models for normal tau action (promoting microtubule growth and bundling, suppressing microtubule shortening) and pathological tau action (poisoning of oligomeric complexes).