Development of an α-synuclein positron emission tomography tracer for imaging synucleinopathies.

Synucleinopathies are characterized by the accumulation of α-synuclein (α-Syn) aggregates in the brain. Positron emission tomography (PET) imaging of synucleinopathies requires radiopharmaceuticals that selectively bind α-Syn deposits. We report the identification of a brain permeable and rapid washout PET tracer [18F]-F0502B, which shows high binding affinity for α-Syn, but not for Aß or Tau fibrils, and preferential binding to α-Syn aggregates in the brain sections. Employing several cycles of counter screenings with in vitro fibrils, intraneuronal aggregates, and neurodegenerative disease brain sections from several mice models and human subjects, [18F]-F0502B images α-Syn deposits in the brains of mouse and non-human primate PD models. We further determined the atomic structure of the α-Syn fibril-F0502B complex by cryo-EM and revealed parallel diagonal stacking of F0502B on the fibril surface through an intense noncovalent bonding network via inter-ligand interactions. Therefore, [18F]-F0502B is a promising lead compound for imaging aggregated α-Syn in synucleinopathies.

Phase Separation of Disease-Associated SHP2 Mutants Underlies MAPK Hyperactivation.

The non-receptor protein tyrosine phosphatase (PTP) SHP2, encoded by PTPN11, plays an essential role in RAS-mitogen-activated protein kinase (MAPK) signaling during normal development. It has been perplexing as to why both enzymatically activating and inactivating mutations in PTPN11 result in human developmental disorders with overlapping clinical manifestations. Here, we uncover a common liquid-liquid phase separation (LLPS) behavior shared by these disease-associated SHP2 mutants. SHP2 LLPS is mediated by the conserved well-folded PTP domain through multivalent electrostatic interactions and regulated by an intrinsic autoinhibitory mechanism through conformational changes. SHP2 allosteric inhibitors can attenuate LLPS of SHP2 mutants, which boosts SHP2 PTP activity. Moreover, disease-associated SHP2 mutants can recruit and activate wild-type (WT) SHP2 in LLPS to promote MAPK activation. These results not only suggest that LLPS serves as a gain-of-function mechanism involved in the pathogenesis of SHP2-associated human diseases but also provide evidence that PTP may be regulated by LLPS that can be therapeutically targeted.

Structural mechanism for specific binding of chemical compounds to amyloid fibrils.

Amyloid fibril is an important pharmaceutical target for diagnostic and therapeutic treatment of neurodegenerative diseases. However, rational design of chemical compounds that interact with amyloid fibrils is unachievable due to the lack of mechanistic understanding of the ligand-fibril interaction. Here we used cryoelectron microscopy to survey the amyloid fibril-binding mechanism of a series of compounds including classic dyes, (pre)clinical imaging tracers and newly identified binders from high-throughput screening. We obtained clear densities of several compounds in complex with an α-synuclein fibril. These structures unveil the basic mechanism of the ligand-fibril interaction, which exhibits remarkable difference from the canonical ligand-protein interaction. In addition, we discovered a druggable pocket that is also conserved in the ex vivo α-synuclein fibrils from multiple system atrophy. Collectively, these findings expand our knowledge of protein-ligand interaction in the amyloid fibril state, which will enable rational design of amyloid binders in a medicinally beneficial way.

Mechanistic basis for receptor-mediated pathological α-synuclein fibril cell-to-cell transmission in Parkinson's disease.

The spread of pathological α-synuclein (α-syn) is a crucial event in the progression of Parkinson's disease (PD). Cell surface receptors such as lymphocyte activation gene 3 (LAG3) and amyloid precursor-like protein 1 (APLP1) can preferentially bind α-syn in the amyloid over monomeric state to initiate cell-to-cell transmission. However, the molecular mechanism underlying this selective binding is unknown. Here, we perform an array of biophysical experiments and reveal that LAG3 D1 and APLP1 E1 domains commonly use an alkaline surface to bind the acidic C terminus, especially residues 118 to 140, of α-syn. The formation of amyloid fibrils not only can disrupt the intramolecular interactions between the C terminus and the amyloid-forming core of α-syn but can also condense the C terminus on fibril surface, which remarkably increase the binding affinity of α-syn to the receptors. Based on this mechanism, we find that phosphorylation at serine 129 (pS129), a hallmark modification of pathological α-syn, can further enhance the interaction between α-syn fibrils and the receptors. This finding is further confirmed by the higher efficiency of pS129 fibrils in cellular internalization, seeding, and inducing PD-like α-syn pathology in transgenic mice. Our work illuminates the mechanistic understanding on the spread of pathological α-syn and provides structural information for therapeutic targeting on the interaction of α-syn fibrils and receptors as a potential treatment for PD.

Rational design of functional amyloid fibrillar assemblies.

Amyloid fibrillar assemblies, originally identified as pathological entities in neurodegenerative diseases, have been widely adopted by various proteins to fulfill diverse biological functions in living organisms. Due to their unique features, such as hierarchical assembly, exceptional mechanical properties, environmental stability, and self-healing properties, amyloid fibrillar assemblies have been employed as functional materials in numerous applications. Recently, with the rapid advancement in synthetic biology and structural biology tools, new trends in the functional design of amyloid fibrillar assemblies have begun to emerge. In this review, we provide a comprehensive overview of the design principles for functional amyloid fibrillar assemblies from an engineering perspective, as well as through the lens of structural insights. Initially, we introduce the fundamental structural configurations of amyloid assemblies and highlight the functions of representative examples. We then focus on the underlying design principles of two prevalent strategies for the design of functional amyloid fibrillar assemblies: (1) introducing new functions via protein modular design and/or hybridization, with typical applications encompassing catalysis, virus disinfection, biomimetic mineralization, bio-imaging, and biotherapy; and (2) dynamically regulating living amyloid fibrillar assemblies using synthetic gene circuits, with typical applications in pattern formation, leakage repair, and pressure sensing. Next, we summarize how breakthroughs in characterization techniques have contributed to unveiling the structural polymorphism of amyloid fibrils at the atomic level, and further clarifying the highly diverse regulation mechanisms of amyloid fibrillar assembly and disassembly fine-tuned by various factors. The structural knowledge may significantly aid in the structure-guided design of amyloid fibrillar assemblies with diverse bio-activities and adjustable regulatory properties. Finally, we envision that a new trend in functional amyloid design may emerge by integrating structural tunability, synthetic biology and artificial intelligence.

Conformational Dynamics of an α-Synuclein Fibril upon Receptor Binding Revealed by Insensitive Nuclei Enhanced by Polarization Transfer-Based Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy.

Many amyloid fibrils associated with neurodegenerative diseases consist of an ordered fibril core (FC) and disordered terminal regions (TRs). The former represents a stable scaffold, while the latter is rather active in binding with various partners. Current structural studies mainly focus on the ordered FC since the high flexibility of TRs hinders structural characterization. Here, by combining insensitive nuclei enhanced by polarization transfer-based 1H-detected solid-state NMR and cryo-EM, we explored the intact structure of an α-syn fibril including both FC and TRs and further studied the conformational dynamics of the fibril upon binding to lymphocyte activation gene 3 (LAG3)─a cell surface receptor that is involved in α-syn fibril transmission in brains. We found that both the N- and C-TRs of α-syn are disordered in free fibrils featuring similar conformation ensembles as those in soluble monomers. While in the presence of the D1 domain of LAG3 (L3D1), the C-TR directly binds to L3D1, meanwhile the N-TR folds into a ß-strand and further integrates with the FC, which leads to alteration of the overall fibril structure and surface property. Our work reveals synergistic conformational transition of the intrinsically disordered TRs of α-syn, which sheds light on mechanistic understanding of the essential role of TRs in regulating the structure and pathology of amyloid fibrils.

Parkinson's disease-related phosphorylation at Tyr39 rearranges α-synuclein amyloid fibril structure revealed by cryo-EM.

Posttranslational modifications (PTMs) of α-synuclein (α-syn), e.g., phosphorylation, play an important role in modulating α-syn pathology in Parkinson's disease (PD) and α-synucleinopathies. Accumulation of phosphorylated α-syn fibrils in Lewy bodies and Lewy neurites is the histological hallmark of these diseases. However, it is unclear how phosphorylation relates to α-syn pathology. Here, by combining chemical synthesis and bacterial expression, we obtained homogeneous α-syn fibrils with site-specific phosphorylation at Y39, which exhibits enhanced neuronal pathology in rat primary cortical neurons. We determined the cryo-electron microscopy (cryo-EM) structure of the pY39 α-syn fibril, which reveals a fold of α-syn with pY39 in the center of the fibril core forming an electrostatic interaction network with eight charged residues in the N-terminal region of α-syn. This structure composed of residues 1 to 100 represents the largest α-syn fibril core determined so far. This work provides structural understanding on the pathology of the pY39 α-syn fibril and highlights the importance of PTMs in defining the polymorphism and pathology of amyloid fibrils in neurodegenerative diseases.

Performance optimization and nitrogen removal mechanism of up-flow partial denitrification/anammox process.

This study aimed to remediate the problems of sludge floating and uneven mass transfer in up-flow partial denitrification/anammox (PDA) reactors and dissect the nitrogen removal mechanism. Two up-flow PDA reactors were operated, whereby in R1 combined biological carriers were added, while in R2 mechanical stirring was applied, the reactors were inoculated with PD sludge and anammox sludge. Results showed the TN removal rates at the end of the operation were 89% (R1) and 92% (R2). The addition of both strategies suppressed the occurrence of sludge upwelling and deterioration of settling performance, even when the granule diameter of the granular zone in R1 and R2 reached 1.921 and 2.006 mm, respectively. 16SrRNA sequencing revealed R1 had a higher abundance of anammox bacteria (AAOB, 14.53%-R1, 9.06%-R2, respectively), and R2 had a higher quantity of denitrifying bacteria (61.92%-R1, 67.11%-R2, respectively). And the nitrogen removal was contributed by anammox and denitrification in combination, with contributions of 82.17%, 17.83% (R1), and 85.07%, 14.93% (R2), respectively. In summary, both strategies prevented sludge flotation and uneven nitrogen mass transfer. However, mechanical agitation had a more substantial positive effect on the performance of PDA than the addition of biocarriers because it achieved a more adequate mass transfer.

Starting up anammox system with high efficiency nitrogen removal at low temperatures: Performance optimization, sludge characterization and microbial community analysis.

Anaerobic ammonia oxidation (anammox) has potential advantages for nitrogen removal when operating at medium temperatures, but the increased operation costs of heating limit its application. It would be advantageous to start and operate anammox at low temperatures, the feasibility of which was studied here on a lab scale. Two identical expanded granular sludge bed (EGSB) reactors were inoculated at 35 ± 1 °C (Amed) and 15 ± 3 °C (Alow). Results showed that anammox was successful after 138 d for Alow, only 7 d longer than Amed. Stable operation to 194 d in Alow, the nitrogen loading rate (NLR) increased to 1.01 kg m-3·d-1, giving a high nitrogen removal efficiency (NRE) of 85%, which was only slightly lower than that of Amed (90%). More extracellular polymeric substance (EPS) was produced by the microbes of Alow compared to Amed, which prevented anaerobic ammonia oxidizing bacteria (AnAOB) against low temperature stress. Microbial community revealed presence of Candidatus Jettenia in Amed with relative abundance 7.4%, while the "cold-tolerant" Candidatus Kuenenia with 4% was the dominant anammox bacteria in Alow. The anammox granules adapted well to low temperatures and demonstrated high efficiency in anammox process without heating. Therefore, constructing an energy-saving and cost-effective anammox system in high latitudes or high altitudes can be considered.

Creating an Amyloid 'Kaleidoscope' Using Short Iodinated Peptides.

Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1 GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid "kaleidoscope" by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.

A novel partially open state of SHP2 points to a "multiple gear" regulation mechanism.

The protein tyrosine phosphatase SHP2 mediates multiple signal transductions in various cellular pathways, controlled by a variety of upstream inputs. SHP2 dysregulation is causative of different types of cancers and developmental disorders, making it a promising drug target. However, how SHP2 is modulated by its different regulators remains largely unknown. Here, we use single-molecule fluorescence resonance energy transfer and molecular dynamics simulations to investigate this question. We identify a partially open, semiactive conformation of SHP2 that is intermediate between the known open and closed states. We further demonstrate a "multiple gear" regulatory mechanism, in which different activators (e.g., insulin receptor substrate-1 and CagA), oncogenic mutations (e.g., E76A), and allosteric inhibitors (e.g., SHP099) can shift the equilibrium of the three conformational states and regulate SHP2 activity to different levels. Our work reveals the essential role of the intermediate state in fine-tuning the activity of SHP2, which may provide new opportunities for drug development for relevant cancers.

Treatment of high-concentration phosphorus wastewater based on foamed concrete.

Phosphorus is a nonrenewable resource, and the recovery of phosphorus from wastewater containing high concentrations of phosphorus is of great importance. In this work, a novel method for highly efficient treatment of high-concentration phosphorus-containing wastewater (50 mg/L, 100 mg/L and 150 mg/L) with low energy consumption was developed by using the block waste foam concrete (FC) as a potential phosphorus recovery material. The results showed that acid leaching significantly improved the accumulation efficiency of phosphorus in calcium hydroxyphosphate (HAP) via accelerating the release of calcium in wastewater. The recovery rate of phosphorus could reach 99.0% under the pH value of 9.0 at 25 °C, using 2.0 g FC. It was also found that the microporous structure of the surface of FC provided the adsorption sites for phosphorus, resulting in the adsorption rate in different concentrations of phosphorus-containing wastewater up to 14.5%. It indicated that FC achieved the recovery of phosphorus from high-concentration phosphorus-containing wastewater by coupling HAP crystallization and physical adsorption to polyphosphorus.

Light-Controlled Tyrosine Nitration of Proteins.

Tyrosine nitration of proteins is one of the most important oxidative post-translational modifications in vivo. A major obstacle for its biochemical and physiological studies is the lack of efficient and chemoselective protein tyrosine nitration reagents. Herein, we report a generalizable strategy for light-controlled protein tyrosine nitration by employing biocompatible dinitroimidazole reagents. Upon 390 nm irradiation, dinitroimidazoles efficiently convert tyrosine residues into 3-nitrotyrosine residues in peptides and proteins with fast kinetics and high chemoselectivity under neutral aqueous buffer conditions. The incorporation of 3-nitrotyrosine residues enhances the thermostability of lasso peptide natural products and endows murine tumor necrosis factor-α with strong immunogenicity to break self-tolerance. The light-controlled time resolution of this method allows the investigation of the impact of tyrosine nitration on the self-assembly behavior of α-synuclein.

Phosphorylation and O-GlcNAcylation at the same α-synuclein site generate distinct fibril structures.

α-Synuclein forms amyloid fibrils that are critical in the progression of Parkinson's disease and serves as the pathological hallmark of this condition. Different posttranslational modifications have been identified at multiple sites of α-synuclein, influencing its conformation, aggregation and function. Here, we investigate how disease-related phosphorylation and O-GlcNAcylation at the same α-synuclein site (S87) affect fibril structure and neuropathology. Using semi-synthesis, we obtained homogenous α-synuclein monomer with site-specific phosphorylation (pS87) and O-GlcNAcylation (gS87) at S87, respectively. Cryo-EM revealed that pS87 and gS87 α-synuclein form two distinct fibril structures. The GlcNAc situated at S87 establishes interactions with K80 and E61, inducing a unique iron-like fold with the GlcNAc molecule on the iron handle. Phosphorylation at the same site prevents a lengthy C-terminal region including residues 73 to 140 from incorporating into the fibril core due to electrostatic repulsion. Instead, the N-terminal half of the fibril (1-72) takes on an arch-like fibril structure. We further show that both pS87 and gS87 α-synuclein fibrils display reduced neurotoxicity and propagation activity compared with unmodified α-synuclein fibrils. Our findings demonstrate that different posttranslational modifications at the same site can produce distinct fibril structures, which emphasizes link between posttranslational modifications and amyloid fibril formation and pathology.

Acetylation encodes Tau aggregation.

Post-translational modifications profoundly influence amyloid assembly. In this issue of Structure, Li et al. unravel the underlying mechanism by which specific lysine acetylation patterns facilitate fibril formation of Tau segments. Their cryo-electron microscopy structure further elucidates how acetyl groups act as stabilizers within the architecture of Tau fibrils.

Culturing partial-denitrification (PD) granules in continuous flow reactor with waste sludge as inoculum: performance, granular sludge characteristics and microbial community.

Partial denitrification granular sludge (PDGS) can provide long-term stable nitrite for anaerobic ammonia oxidation (anammox). The cultivation of ordinary activated sludge from wastewater treatment plants into PDGS can further promote the application of PD in practical engineering. In this study, the feasibility of fast start-up of PDGS was explored by inoculating waste sludge in up-flow anaerobic sludge blanket (UASB) reactor with synergistic control of nitrogen load rate (NLR, 0.05-0.65 kg N/m3/d) and electron donor starvation (EDS) (240-168 mg L-1), and system performance, particle characteristics and microbial structure were studied. The results showed that PD-UASB started successfully within 48 days, the average nitrite accumulation rate (NTR) and nitrate removal ratio (NRR) reached 79.6% and 82.5% after successful initiation, accompanied by high abundance of PD bacteria (Thauera, Pseudomonas, unclassflied commamonadaceae and Limnobacter) (25.3%). The increase of PD activity, and the difference between nitrate reductase (NAR) and nitrite reductase (NIR) contributed to nitrite production. Besides, the sludge shifted from flocculated (≤0.5 mm, 95.37%) to granulated state (0.5-2 mm, 64.74%), which could be due to the increase of extracellular polymers (EPS) (especially T-EPS) and metabolism of specific microorganisms (Bacteroidota and Chloroflexi, 19.92%). Good sludge granulation promoted the settleability of PD (the SVI5 was 47.248 mL/ g. ss after successful start-up). In summary, good PD sludge granulation process could be achieved in a short time by synergistically controlling NLR and EDS.

Structural Insights of Fe3+ Induced α-synuclein Fibrillation in Parkinson's Disease.

Amyloid aggregation of α-synuclein (α-syn) in Lewy bodies (LBs) is the pathological hallmark of Parkinson's disease (PD). Iron, especially Fe3+, is accumulated in substantia nigra of PD patients and co-deposited with α-syn in LBs. However, how Fe3+ modulates α-syn fibrillation at molecular level remains unclear. In this study, we found that Fe3+ can promote α-syn fibrillation at low concentration while inhibit its fibrillation at high concentration. NMR titration study shows poor interaction between α-syn monomer and Fe3+. Instead, we found that Fe3+ binds to α-syn fibrils. By using cryo-electron microscopy (cryo-EM), we further determined the atomic structure of α-syn fibril in complex with Fe3+ at the resolution of 2.7 Å. Strikingly, two extra electron densities adjacent to His50 and Glu57 were observed as putative binding sites of Fe3+ and water molecules, suggesting that Fe3+ binds to the negative cleft of the fibril and stabilizes the fibril structure for promoting α-syn aggregation. Further mutagenesis study shows mutation of His50 abolishes the Fe3+-facilitated fibrillation of α-syn. Our work illuminates the structural basis of the interaction of Fe3+ and α-syn in both monomeric and fibrillar forms, and sheds light on understanding the pathological role of Fe3+ in α-syn aggregation in PD.

Conformational change of α-synuclein fibrils in cerebrospinal fluid from different clinical phases of Parkinson's disease.

α-Synuclein (α-syn) has been shown to form various conformational fibrils associated with different synucleinopathies. But whether the conformation of α-syn fibrils changes during disease progression is unclear. Here, we amplified α-syn aggregates from the cerebrospinal fluid (CSF) of patients with Parkinson's disease (PD) staged in preclinical PD (pre-PD), middle- to late-stage PD (mid-PD), and late-stage PD (late-PD). Our results show that α-syn fibrils derived from the late-PD patient are most potent in inducing endogenous α-syn aggregation in primary neurons, followed by the mid-PD and pre-PD fibrils. By using cryo-electron microscopy, we further determined the high-resolution structures of the CSF-amplified fibrils. The structures exhibit remarkable differences in a minor but significant population of conformational species in different staged samples. Our work demonstrates structural and pathological differences between α-syn fibrils derived from PD patients at a spectrum of clinical stages, which suggests potential conformational transition of α-syn fibrils during the progression of PD.

Molecular structure of an amyloid fibril formed by FUS low-complexity domain.

FUS is a multifunctional nuclear protein which undergoes liquid-liquid phase separation in response to stress and DNA damage. Dysregulation of FUS dynamic phase separation leads to formation of pathological fibril closely associated with neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. In this study, we determined the cryo-EM structure of a cytotoxic fibril formed by the low-complexity (LC) domain of FUS at 2.9 Å resolution. The fibril structure exhibits a new and extensive serpentine fold consisting of three motifs incorporating together via a Tyr triad. FUS LC employs 91 residues to form an enlarged and stable fibril core via hydrophilic interaction and hydrogen bonds, which is distinct from most of previously determined fibrils commonly stabilized by hydrophobic interaction. Our work reveals the structural basis underlying formation of a cytotoxic and thermostable fibril of FUS LC and sheds light on understanding the liquid-to-solid phase transition of FUS in disease.

Subtle change of fibrillation condition leads to substantial alteration of recombinant Tau fibril structure.

In vitro assembly of amyloid fibrils that recapitulate those in human brains is very useful for fundamental and applied research on the amyloid formation, pathology, and clinical detection. Recent success in the assembly of Tau fibrils in vitro enables the recapitulation of the paired helical filament (PHF) of Tau extracted from brains of patients with Alzheimer's disease (AD). However, following the protocol, we observed that Tau constructs including 297-391 and a mixture of 266-391 (3R)/297-391, which are expected to predominantly form PHF-like fibrils, form highly heterogeneous fibrils instead. Moreover, the seemingly PHF-like fibril formed by Tau 297-391 exhibits a distinctive atomic structure with a spindle-like fold, that is neither PHF-like or similar to any known Tau fibril structures revealed by cryo-electron microscopy (cryo-EM). Our work highlights the high sensitivity of amyloid fibril formation to subtle conditional changes and suggests high-resolution structural characterization to in vitro assembled fibrils prior to further laboratory use.