Structural insights into the aggregation mechanism of huntingtin exon 1 protein fragment with different polyQ-lengths

Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study

Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.

Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers

Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures and aggregation mechanism are still poorly understood. We performed microsecond-long all-atom molecular dynamics simulations to study the folding and dimerization of Htt-ex1 (about 100 residues) with non-pathogenic and pathogenic polyQ lengths, and uncovered substantial differences. The non-pathogenic monomer adopts a long α-helix that includes most of the polyQ residues, which forms the interaction interface for dimerization, and a PPII-turn-PPII motif in the proline-rich region. In the pathogenic monomer, the polyQ region is disordered, leading to compact structures with many intra-protein interactions and the formation of short β-sheets. Dimerization can proceed via different modes, where those involving the N-terminal headpiece bury more hydrophobic residues and are thus more stable. Moreover, in the pathogenic Htt-ex1 dimers the proline-rich region interacts with the polyQ region, which slows the formation of β-sheets.

Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation

Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.

Possible Co-Evolution of Polyglutamine and Polyproline in Huntingtin Protein: Proline-Rich Domain as Transient Folding Chaperone

Huntington's disease is an inherited neurodegenerative disorder caused by the overduplication of CAG repeats in the Huntingtin gene. Recent findings revealed that among the orthologs, the expansion of CAG repeats (polyQ) in the Huntingtin gene occurs in tandem with the duplication of CCG repeats (polyP). However, the molecular mechanism of this possible co-evolution remains unknown. We examined the structures of Huntingtin exon 1 (HttEx1) from six species along with five designed mutants. We found that the polyP segments "chaperone" the rest of the HttEx1 by forming ad hoc polyP binding grooves. Such a process elongates the otherwise poorly solvated polyQ domain, while modulating its secondary structure propensity from β-strands to α-helices. This chaperoning effect is achieved mostly through transient hydrogen bond interactions between polyP and the rest of HttEx1, resulting in a striking golden ratio of ∼2:1 between the chain lengths of polyQ and polyP.

Pharmacological characterization of mutant huntingtin aggregate-directed PET imaging tracer candidates

Huntington’s disease (HD) is caused by a CAG trinucleotide repeat expansion in the first exon of the huntingtin (HTT) gene coding for the huntingtin (HTT) protein. The misfolding and consequential aggregation of CAG-expanded mutant HTT (mHTT) underpin HD pathology. Our interest in the life cycle of HTT led us to consider the development of high-affinity small-molecule binders of HTT oligomerized/amyloid-containing species that could serve as either cellular and in vivo imaging tools or potential therapeutic agents. We recently reported the development of PET tracers CHDI-180 and CHDI-626 as suitable for imaging mHTT aggregates, and here we present an in-depth pharmacological investigation of their binding characteristics. We have implemented an array of in vitro and ex vivo radiometric binding assays using recombinant HTT, brain homogenate-derived HTT aggregates, and brain sections from mouse HD models and humans post-mortem to investigate binding affinities and selectivity against other pathological proteins from indications such as Alzheimer’s disease and spinocerebellar ataxia 1. Radioligand binding assays and autoradiography studies using brain homogenates and tissue sections from HD mouse models showed that CHDI-180 and CHDI-626 specifically bind mHTT aggregates that accumulate with age and disease progression. Finally, we characterized CHDI-180 and CHDI-626 regarding their off-target selectivity and binding affinity to beta amyloid plaques in brain sections and homogenates from Alzheimer’s disease patients.

The regulatory roles of microRNAs toward pathogenesis and treatments in Huntington's disease

Huntington's disease (HD) is one of neurodegenerative diseases, and is defined as a monogenetic disease due to the mutation of Huntingtin gene. This disease affects several cellular functions in neurons, and further influences motor and cognitive ability, leading to the suffering of devastating symptoms in HD patients. MicroRNA (miRNA) is a non-coding RNA, and is responsible for gene regulation at post-transcriptional levels in cells. Since one miRNA targets to several downstream genes, it may regulate different pathways simultaneously. As a result, it raises a potential therapy for different diseases using miRNAs, especially for inherited diseases. In this review, we will not only introduce the update information of HD and miRNA, but also discuss the development of potential miRNA-based therapy in HD. With the understanding toward the progression of miRNA studies in HD, we anticipate it may provide an insight to treat this devastating disease, even applying to other genetic diseases.

In silico designing of putative peptides for targeting pathological protein Htt in Huntington's disease

Huntington's disease is a neurodegenerative disease caused by CAG repeat in the first exon of HTT (Huntingtin) gene, leading to abnormal form of Htt protein containing enlarged polyglutamine strands of variable length that stick together to form aggregates and is toxic to brain causing brain damage. Complete reversal of brain damage is not possible till date but recovery may be possible by peptide therapy. The peptide-based therapy for Huntington's disease includes both poly Q peptide as well as non poly Q peptides like (QBP1)2, p42, Exendin 4, ED11, CaM, BiP, Leuprorelin peptide. The novel approach that is currently being tested in this article is the peptide-based therapy to target the mutated protein. This approach is based on the principle of preventing the aggregation of mutant Htt by blocking the potential sites responsible for protein aggregation and thereby ameliorating the disease symptoms. Herein, we have screened a variety of potential peptides that were known to prevent the protein aggregation, comparatively analyzed their binding affinity with homology modeled Htt protein, designed novel peptides based upon conservation analysis among screened potential peptides as a therapeutic agent, comparatively analyzed the therapeutic potential of novel peptides against modeled Htt protein for investigating the therapeutic prospects of Huntington's disease. We have designed a peptide for the therapy of Huntington's disease by comparing several peptides, which are already in use for Huntington's disease.

Protein aggregation: in silico algorithms and applications

Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.

Mutations causing Lopes-Maciel-Rodan syndrome are huntingtin hypomorphs

Huntington's disease pathogenesis involves a genetic gain-of-function toxicity mechanism triggered by the expanded HTT CAG repeat. Current therapeutic efforts aim to suppress expression of total or mutant huntingtin, though the relationship of huntingtin's normal activities to the gain-of-function mechanism and what the effects of huntingtin-lowering might be are unclear. Here, we have re-investigated a rare family segregating two presumed HTT loss-of-function (LoF) variants associated with the developmental disorder, Lopes-Maciel-Rodan syndrome (LOMARS), using whole-genome sequencing of DNA from cell lines, in conjunction with analysis of mRNA and protein expression. Our findings correct the muddled annotation of these HTT variants, reaffirm they are the genetic cause of the LOMARS phenotype and demonstrate that each variant is a huntingtin hypomorphic mutation. The NM_002111.8: c.4469+1G>A splice donor variant results in aberrant (exon 34) splicing and severely reduced mRNA, whereas, surprisingly, the NM_002111.8: c.8157T>A NP_002102.4: Phe2719Leu missense variant results in abnormally rapid turnover of the Leu2719 huntingtin protein. Thus, although rare and subject to an as yet unknown LoF intolerance at the population level, bona fide HTT LoF variants can be transmitted by normal individuals leading to severe consequences in compound heterozygotes due to huntingtin deficiency.

Secondary Chemical Bonding between Insoluble Calcium Oxalate and Carbonyl Oxygen Atoms of GLY and VAL Residues Triggers the Formation of Aβ Aggregates and Their Deposition in the Brain

Despite intense efforts, the cause of Alzheimer's disease is still not fully understood. A chemical and biochemical perspective could shed light on this disorder. Secondary chemical bonding between calcium and carbonyl oxygen atoms of glycine and valine might give rise to aggregates in the brain, which may later result in cell senescence. The decrease of solubility caused by amino acid substitutions in specific risk factors compounds insolubility issue and likely triggers early-onset Alzheimer's disease. Occasionally the enhancement of hydrogen bonding by amino acid replacements can reinforce the aggregates. Therefore, secondary chemical bonding to cations can generate cellular stresses in patients with Alzheimer's disease in addition to other chemical and biochemical interactions such as salt bridge. The distinction between early-onset and late-onset Alzheimer's disease risk factors may lie in the total capacity of a protein or local potency of a protein fragment to bind calcium or/and oxalate as calcium oxalate is highly insoluble and stressful.

Template-assisted design of monomeric polyQ models to unravel the unique role of glutamine side chains in disease-related aggregation

PolyQ model peptides reveal the effect of individual glutamine side chains on fibril formation.

Expanded polyglutamine (polyQ) sequences cause numerous neurodegenerative diseases which are accompanied by the formation of polyQ fibrils. The unique role of glutamines in the aggregation onset is undoubtedly accepted and a lot structural data of the fibrils have been acquired, however side-chain specific structural dynamics inducing oligomerization are not well understood yet. To analyze spectroscopically the nucleation process, we designed various template-assisted glutamine-rich β-hairpin monomers mimicking the structural motif of a polyQ fibril. In a top-down strategy, we use a template which forms a well-defined stable hairpin in solution, insert polyQ-rich sequences into each strand and monitor the effects of individual glutamines by NMR, CD and IR spectroscopic approaches. The design was further advanced by alternating glutamines with other amino acids (T, W, E, K), thereby enhancing the solubility and increasing the number of cross-strand interacting glutamine side chains. Our spectroscopic studies reveal a decreasing hairpin stability with increased glutamine content and demonstrate the enormous impact of only a few glutamines – far below the disease threshold – to destabilize structure. Furthermore, we could access sub-ms conformational dynamics of monomeric polyQ-rich peptides by laser-excited temperature-jump IR spectroscopy. Both, the increased number of interacting glutamines and higher concentrations are key parameters to induce oligomerization. Concentration-dependent time-resolved IR measurements indicate an additional slower kinetic phase upon oligomer formation. The here presented peptide models enable spectroscopic molecular analyses to distinguish between monomer and oligomer dynamics in the early steps of polyQ fibril formation and in a side-chain specific manner.

Specific Key-Point Mutations along the Helical Conformation of Huntingtin-Exon 1 Protein Might Have an Antagonistic Effect on the Toxic Helical Content's Formation

The polyglutamine tract length represents a key regulator for the Huntington's disease toxicity level and its aggregation rates, often being related to helical structural conformations. In this study, we performed all-atom MD simulations on mutant Huntingtin-Exon1 protein with additional mutation spots, aiming to observe the corresponding structural and dynamical changes at the level of the helix. The simulated structures consist of three sets of Q residue mutations into P residues (4P, 7P, and 9P), with each set including different spots of mutations: random along the mutant sequence (R models), at the edges of the helix (E models), as well as at the edges and in the middle of the helix (EM models). At the helical level, our results predict less compactness profiles for a higher number of P mutations (7P and 9P models) with particular mutation spots at the edges and at the edges-middle of the helix. Moreover, the C-alpha atom distances decreased for 7P and 9P models in comparison to 4P models, and the RMSF values show the highest fluctuation rates for 9P models with point mutations at the edges and in the middle of the helix. The secondary structure analysis suggests greater structural transitions from α-helices to bends, turns, and random coils for 7P and 9P models, particularly for point mutations considered at the edges and in the middle of the helical content. The obtained results support our hypothesis that specific key-point mutations along the helical conformation might have an antagonistic effect on the toxic helical content's formation.

Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review

Over the recent years, Huntington's disease (HD) has become widely discussed in the scientific literature especially because at the mutant level there are several contradictions regarding the aggregation mechanism. The specific role of the physiological huntingtin protein remains unknown, due to the lack of characterization of its entire crystallographic structure, making the experimental and theoretical research even harder when taking into consideration its involvement in multiple biological functions and its high affinity for different interacting partners. Different types of models, containing fewer (not more than 35 Qs) polyglutamine residues for the WT structure and above 35 Qs for the mutants, were subjected to classical or advanced MD simulations to establish the proteins' structural stability by evaluating their conformational changes. Outside the polyQ tract, there are two other regions of interest (the N17 domain and the polyP rich domain) considered to be essential for the aggregation kinetics at the mutant level. The polymerization process is considered to be dependent on the polyQ length. As the polyQ tract's dimension increases, the structures present more β-sheet conformations. Contrarily, it is also considered that the aggregation stability is not necessarily dependent on the number of Qs, while the initial stage of the aggregation seed might play the decisive role. A general assumption regarding the polyP domain is that it might preserve the polyQ structures soluble by acting as an antagonist for β-sheet formation.