Evidence of the Reduced Abundance of Proline cis Conformation in Protein Poly Proline Tracts.

Proline is found in a cis conformation in proteins more often than other proteinogenic amino acids, where it influences structure and modulates function, being the focus of several high-resolution structural studies. However, until now, technical and methodological limitations have hampered the site-specific investigation of the conformational preferences of prolines present in poly proline (poly-P) homorepeats in their protein context. Here, we apply site-specific isotopic labeling to obtain high-resolution NMR data on the cis/trans equilibrium of prolines within the poly-P repeats of huntingtin exon 1, the causative agent of Huntington's disease. Screening prolines in different positions in long (poly-P11) and short (poly-P3) poly-P tracts, we found that, while the first proline of poly-P tracts adopts similar levels of cis conformation as isolated prolines, a length-dependent reduced abundance of cis conformers is observed for terminal prolines. Interestingly, the cis isomer could not be detected in inner prolines, in line with percentages derived from a large database of proline-centered tripeptides extracted from crystallographic structures. These results suggest a strong cooperative effect within poly-Ps that enhances their stiffness by diminishing the stability of the cis conformation. This rigidity is key to rationalizing the protection toward aggregation that the poly-P tract confers to huntingtin. Furthermore, the study provides new avenues to probe the structural properties of poly-P tracts in protein design as scaffolds or nanoscale rulers.

Site-Specific Isotopic Labeling (SSIL): Access to High-Resolution Structural and Dynamic Information in Low-Complexity Proteins.

Remarkable technical progress in the area of structural biology has paved the way to study previously inaccessible targets. For example, large protein complexes can now be easily investigated by cryo-electron microscopy, and modern high-field NMR magnets have challenged the limits of high-resolution characterization of proteins in solution. However, the structural and dynamic characteristics of certain proteins with important functions still cannot be probed by conventional methods. These proteins in question contain low-complexity regions (LCRs), compositionally biased sequences where only a limited number of amino acids is repeated multiple times, which hamper their characterization. This Concept article describes a site-specific isotopic labeling (SSIL) strategy, which combines nonsense suppression and cell-free protein synthesis to overcome these limitations. An overview on how poly-glutamine tracts were made amenable to high-resolution structural studies is used to illustrate the usefulness of SSIL. Furthermore, we discuss the potential of this methodology to give further insights into the roles of LCRs in human pathologies and liquid-liquid phase separation, as well as the challenges that must be addressed in the future for the popularization of SSIL.

A General Strategy to Access Structural Information at Atomic Resolution in Polyglutamine Homorepeats.

Homorepeat (HR) proteins are involved in key biological processes and multiple pathologies, however their high-resolution characterization has been impaired due to their homotypic nature. To overcome this problem, we have developed a strategy to isotopically label individual glutamines within HRs by combining nonsense suppression and cell-free expression. Our method has enabled the NMR investigation of huntingtin exon1 with a 16-residue polyglutamine (poly-Q) tract, and the results indicate the presence of an N-terminal α-helix at near neutral pH that vanishes towards the end of the HR. The generality of the strategy was demonstrated by introducing a labeled glutamine into a pathological version of huntingtin with 46 glutamines. This methodology paves the way to decipher the structural and dynamic perturbations induced by HR extensions in poly-Q-related diseases. Our approach can be extended to other amino acids to investigate biological processes involving proteins containing low-complexity regions (LCRs).

Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies.

Nuclear magnetic resonance (NMR) studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning frequencies to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. The general applicability of this approach for NMR assignment has been demonstrated by introducing isotopically labeled alanines into four distinct proteins: huntingtin exon-1, HMA8 ATPase, the 300 kDa molecular chaperone ClpP, and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enabled unambiguous assignments while avoiding potential artifacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observed that the helical stability is strongly dependent on the homorepeat length. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of challenging biomolecular systems.

Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1.

Huntington's disease neurodegeneration occurs when the number of consecutive glutamines in the huntingtin exon-1 (HTTExon1) exceeds a pathological threshold of 35. The sequence homogeneity of HTTExon1 reduces the signal dispersion in NMR spectra, hampering its structural characterization. By simultaneously introducing three isotopically labeled glutamines in a site-specific manner in multiple concatenated samples, 18 glutamines of a pathogenic HTTExon1 with 36 glutamines were unambiguously assigned. Chemical shift analyses indicate the α-helical persistence in the homorepeat and the absence of an emerging toxic conformation around the pathological threshold. Using the same type of samples, the recognition mechanism of Hsc70 molecular chaperone has been investigated, indicating that it binds to the N17 region of HTTExon1, inducing the partial unfolding of the poly-Q. The proposed strategy facilitates high-resolution structural and functional studies in low-complexity regions.

The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity.

Huntington's disease is a neurodegenerative disorder caused by a CAG expansion in the first exon of the HTT gene, resulting in an extended polyglutamine (poly-Q) tract in huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood due to its intrinsic flexibility and the strong compositional bias. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. Integrative data analysis reveals that the poly-Q tract adopts long α-helical conformations propagated and stabilized by glutamine side chain to backbone hydrogen bonds. We show that α-helical stability is a stronger signature in defining aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. Our observations provide a structural perspective of the pathogenicity of expanded httex1 and pave the way to a deeper understanding of poly-Q-related diseases.

Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins.

The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.

Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins.

The causative agent of Huntington's disease, the poly-Q homo-repeat in the N-terminal region of huntingtin (httex1), is flanked by a 17-residue-long fragment (N17) and a proline-rich region (PRR), which promote and inhibit the aggregation propensity of the protein, respectively, by poorly understood mechanisms. Based on experimental data obtained from site-specifically labeled NMR samples, we derived an ensemble model of httex1 that identified both flanking regions as opposing poly-Q secondary structure promoters. While N17 triggers helicity through a promiscuous hydrogen bond network involving the side chains of the first glutamines in the poly-Q tract, the PRR promotes extended conformations in neighboring glutamines. Furthermore, a bioinformatics analysis of the human proteome showed that these structural traits are present in many human glutamine-rich proteins and that they are more prevalent in proteins with longer poly-Q tracts. Taken together, these observations provide the structural bases to understand previous biophysical and functional data on httex1.

LC-MS ion maps for the characterization of aniline derivatives of fatty acids and triglycerides in laboratory-denatured rapeseed oil.

In 1981 Spain went through a unique epidemic associated with a food-borne vector, affecting more than 20,000 people with over 800 deaths, which came to be known as the Toxic Oil Syndrome (TOS). Early epidemiological studies showed a link between this illness and the ingestion of rapeseed oil denatured with 2% aniline. This oil, originally aniline-denatured for industrial use, was fraudulently processed in an attempt to remove free aniline, and marketed as edible oil. Fatty acid anilides (FAA), monoesters and diesters of 3-(N-phenylamino)-1,2-propanediol (PAP) are present in oil samples as they arise in the refining process from reactions of aniline with constituent fatty acids and triglycerides of the oil matrix and are the only extraneous compounds found in these samples. To expand the search for the causative agents in TOS-associated oils and to look for new aniline-related compounds, an exhaustive characterization of laboratory-processed oils was undertaken. These oils, in the presence of aniline doped with 14C labelled aniline, were submitted to the laboratory conditions required for the generation of PAPs and FAAs. Laboratory-generated oil samples were submitted to a liquid-liquid extraction procedure to remove the unreacted aniline. The extract was processed by double solid-phase extraction to improve detection limits for minor amine-containing compounds in oils. The extracts enriched in aniline derivatives were submitted to on-line HPLC-UV-APCI-MS. Using two-dimensional ion maps, the components of several families of derivatives were readily identified. Additionally, the extracts were also fractionated by HPLC-UV and the fractions were analyzed by HPLC-APCI-MS/MS to obtain structural information. Standards of some of these compounds were synthesized and analyzed to confirm the results. A total of 115 aniline derivatives from 9 aniline-related families were identified in these oil samples. These included fatty acid anilides and an extensive array of phenylaminopropanediol esters distributed in eight major compound classes.

In vitro bioactivation of 3-(N-phenylamino)propane-1,2-diol by human and rat liver microsomes and recombinant P450 enzymes. Implications for toxic oil syndrome.

Toxic oil syndrome (TOS) was a massive food-borne intoxication that occurred in Spain in 1981. Epidemiological studies imputed 3-( N-phenylamino)propane-1,2-diol (PAP) derivatives as the toxic agents. The in vitro bioactivation of PAP by rat and human liver microsomes was studied. In both cases, 3-[ N-(4'-hydroxyphenyl)amino]propane-1,2-diol ( 1) was detected as the main metabolite. Inhibition studies with pooled human liver microsomes in the presence and absence of P450-specific inhibitors suggest that 2C8 and 2E1 are the main enzymes involved in PAP bioactivation, followed by 3A4/5, 1A1/2, and 2C9. Incubations of PAP with 10 different recombinant P450 enzymes showed that 2C8, 2C9, 2C18, 2D6, and 2E1 catalyzed PAP 4'-hydroxylation. Incubations of phenol 1 with rat and human liver microsomes in the presence of GSH resulted in the formation of a glutathione conjugate of a quinoneimine metabolite derived from 1. In rat liver microsomes, P450 enzymes play a key role in the bioactivation of 1, whereas in human liver microsomes, autoxidation appears to be the major mechanism. The implications of these results for toxic oil syndrome are discussed.

Synthesis and stability studies of the glutathione and N-acetylcysteine adducts of an iminoquinone reactive intermediate generated in the biotransformation of 3-(N-phenylamino)propane-1,2-diol: implications for toxic oil syndrome.

Epidemiological studies have pointed to fatty acid mono- and diesters of 3-(N-phenylamino)propane-1,2-diol (PAP) as the biomarkers of the toxic oil batches that caused toxic oil syndrome (TOS), an intoxication episode that occurred in Spain in 1981, causing over 400 deaths and affecting more than 20000 people. The biotransformation of PAP administered intraperitoneally to two mouse strains produced potentially toxic metabolites. The identification of 3-(4'-hydroxyphenylamino)propane-1,2-diol among those metabolites was important because the compound can generate the quinoneimine intermediate 2. The potential toxicity of quinoneimines has been attributed primarily to their electrophilic character. Accordingly, the reactions of 2 with N-acetylcysteine, N-acetylcysteine methyl ester, and GSH were investigated. Quinoneimine 2 reacts with the N-acetylcysteine methyl ester to give the expected conjugate as a major product, accompanied by the corresponding bis and tris adducts. The monoadduct, when isolated in pure form, undergoes spontaneous oxidation to generate a new quinoneimine intermediate, which in turn rearranges and undergoes hydrolysis to afford the thiol adduct formally derived from the quinoneimine generated from p-aminophenol. The same overall pathway was observed for the reaction of 2 with N-acetylcysteine and GSH. Both thiol reagents reacted with the quinoneimine to give the corresponding adducts in which the addition took place at the ortho position with respect to the amino group. These conjugates were also unstable and ultimately afforded the corresponding adduct derived from p-aminophenol. The relevancy of these results to TOS, as well as their potential generalization for quinoneimines derived from other xenobiotics, is discussed herein.

On the generation and outcome of 3-(N-phenylamino)propane-1,2-diol derivatives in deodorized model oils related to toxic oil syndrome.

Toxic Oil Syndrome (TOS) was a massive food-born intoxication that occurred in Spain in 1981 and affected more than 20,000 people. TOS was attributed to the ingestion of rapeseed oil that had been adulterated with aniline, illegally refined, and delivered for human consumption. Two chemical species derived from aniline have been identified in oil batches: fatty acid anilides, qualified as biomarkers of the adulterated oil, and fatty acid esters of 3-(N-phenylamino)propane-1,2-diol (PAP), considered toxic oil biomarkers. These esters were generated by chemical processes during oil refining, specifically in the deodorization step, which involves treatment of the oil at high temperatures under vacuum to remove volatile contaminants. Since PAP derivatives are strongly associated with TOS, their formation and putative interconversion in a toxic oil model has been studied. The main results obtained are (i) only triglycerides and aniline are required to produce PAP esters, thus eliminating the possibility that unknown activators present in the deodorization tank were required for toxification of the oil; (ii) PAP and PAP mono- and diesters are chemically interrelated, as are anilides and PAP esters to an even higher degree. In addition to the reaction of aniline with triglycerides, anilides can be also formed via attack of PAP esters by aniline. However, the most important source of anilides during deodorization seems to be the thermal decomposition of PAP esters. Overall, these results suggest that the generation and outcome of PAP derivatives during deodorization is a complex scenario whereby PAP esters are not only generated from different reactions but decompose to produce anilides, among other compounds. In addition to providing a rapeseed oil model that reproduces the composition of case oils with respect to anilides and PAP derivatives, the results presented herein further support the hypothesis imputing PAP diesters or their metabolites for the intoxication episode.

Studies on toxic oil syndrome: stereoselective hydrolysis of 3-(phenylamino)propane-1,2-diol esters by human pancreatic lipase.

The ingestion of rapeseed oil batches denatured with aniline and illegally refined and distributed by street vendors was responsible for toxic oil syndrome (TOS), an intoxication episode that took place in Spain in 1981, causing over 400 deaths and affecting more than 20,000 people. Despite the intense research efforts carried out to date, the compounds responsible for that intoxication have not been elucidated. Nevertheless, epidemiological studies have pointed to fatty acid mono- and diesters of 3-phenylamino-1,2-propanediol (PAP) as the biomarkers of those toxic oil batches. The structure of these esters bears common features with that of triglycerides, which suggested that PAP esters could follow the route of lipids metabolism up to a certain extent. The incubation of racemic PAP dioleyl ester with human pancreatic lipase (hPL) led to the formation of the corresponding stereoisomeric monoesters bearing the oleyl residue at C-2, although a kinetic resolution in favor of the (S)-enantiomer was observed. These monoesters are unstable and in equilibrium with their corresponding regioisomers with the acyl residue at C-1, apparently without the intervention of the lipase. Finally, incubations of these latter monoesters with hPL led to the formation of the respective PAP enantiomers. Again, the kinetic resolution of this hydrolytic process favored the formation of the enantiomer with the (S)-configuration. Taken together, these results showed that PAP esters are substrates of hPL and that the two hydrolytic steps exhibit kinetic resolution in favor of the (S)-enantiomers.