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1. Design of parallel 𝛽‐sheet nanofibrils using Monte Carlo search, coarse‐grained simulations, and experimental testing

   https://doi.org/10.1002/pro.5102  

   Sarma, Sudeep; Sudarshan, Tarunya Rao; Nguyen, Van; Robang, Alicia S; Xiao, Xingqing; Le, Justin V; Helmicki, Michael E; Paravastu, Anant K; Hall, Carol K (August 2024, Protein Science)

   Ben-Tai, Nir (Ed.)

   Abstract Peptide self‐assembly into amyloid fibrils provides numerous applications in drug delivery and biomedical engineering applications. We augment our previously‐established computational screening technique along with experimental biophysical characterization to discover 7‐mer peptides that self‐assemble into “parallelβ‐sheets”, that is,β‐sheets with N‐terminus‐to‐C‐terminus 𝛽‐strand vectors oriented in parallel. To accomplish the desiredβ‐strand organization, we applied thePepADamino acid sequence design software to the Class‐1 cross‐βspine defined by Sawaya et al. This molecular configuration includes two layers of parallelβ‐sheets stacked such that N‐terminus‐to‐C‐terminus vectors are oriented antiparallel for molecules on adjacentβ‐sheets. The first cohort ofPepADidentified peptides were examined for their fibrillation behavior in DMD/PRIME20 simulations, and the top performing sequence was selected as a prototype for a subsequent round of sequence refinement. The two rounds of design resulted in a library of eight 7‐mer peptides. In DMD/PRIME20 simulations, five of these peptides spontaneously formed fibril‐like structures with a predominantly parallel 𝛽‐sheet arrangement, two formed fibril‐like structure with <50% in parallel 𝛽‐sheet arrangement and one remained a random coil. Among the eight candidate peptides produced by PepAD and DMD/PRIME20, five were synthesized and purified. All five assembled into amyloid fibrils composed of parallelβ‐sheets based on Fourier transform infrared spectroscopy, circular dichroism, electron microscopy, and thioflavin‐T fluorescence spectroscopy measurements. 

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2. Analysis of AlphaFold2 for Modeling Structures of Wildtype and Variant Protein Sequences

   https://doi.org/10.29007/5g4v  

   Kabir, Anowarul; Inan, Toki; Shehu, Amarda (March 2022, EPiC Series in Computing)

   ResNet and, more recently, AlphaFold2 have demonstrated that deep neural networks can now predict a tertiary structure of a given protein amino-acid sequence with high accuracy. This seminal development will allow molecular biology researchers to advance various studies linking sequence, structure, and function. Many studies will undoubtedly focus on the impact of sequence mutations on stability, fold, and function. In this paper, we evaluate the ability of AlphaFold2 to predict accurate tertiary structures of wildtype and mutated sequences of protein molecules. We do so on a benchmark dataset in mutation modeling studies. Our empirical evaluation utilizes global and local structure analyses and yields several interesting observations. It shows, for instance, that AlphaFold2 performs similarly on wildtype and variant sequences. The placement of the main chain of a protein molecule is highly accurate. However, while AlphaFold2 reports similar confidence in its predictions over wildtype and variant sequences, its performance on placements of the side chains suffers in comparison to main-chain predictions. The analysis overall supports the premise that AlphaFold2-predicted structures can be utilized in further downstream tasks, but that further refinement of these structures may be necessary. 

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3. Antimicrobial α-defensins as multi-target inhibitors against amyloid formation and microbial infection

   https://doi.org/10.1039/D1SC01133B  

   Zhang, Yanxian; Liu, Yonglan; Tang, Yijing; Zhang, Dong; He, Huacheng; Wu, Jiang; Zheng, Jie (July 2021, Chemical Science)

   Amyloid aggregation and microbial infection are considered as pathological risk factors for developing amyloid diseases, including Alzheimer's disease (AD), type II diabetes (T2D), Parkinson's disease (PD), and medullary thyroid carcinoma (MTC). Due to the multifactorial nature of amyloid diseases, single-target drugs and treatments have mostly failed to inhibit amyloid aggregation and microbial infection simultaneously, thus leading to marginal benefits for amyloid inhibition and medical treatments. Herein, we proposed and demonstrated a new “anti-amyloid and antimicrobial hypothesis” to discover two host-defense antimicrobial peptides of α-defensins containing β-rich structures (human neutrophil peptide of HNP-1 and rabbit neutrophil peptide of NP-3A), which have demonstrated multi-target, sequence-independent functions to (i) prevent the aggregation and misfolding of different amyloid proteins of amyloid-β (Aβ, associated with AD), human islet amyloid polypeptide (hIAPP, associated with T2D), and human calcitonin (hCT, associated with MTC) at sub-stoichiometric concentrations, (ii) reduce amyloid-induced cell toxicity, and (iii) retain their original antimicrobial activity upon the formation of complexes with amyloid peptides. Further structural analysis showed that the sequence-independent amyloid inhibition function of α-defensins mainly stems from their cross-interactions with amyloid proteins via β-structure interactions. The discovery of antimicrobial peptides containing β-structures to inhibit both microbial infection and amyloid aggregation greatly expands the new therapeutic potential of antimicrobial peptides as multi-target amyloid inhibitors for better understanding pathological causes and treatments of amyloid diseases. 

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4. Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases

   https://doi.org/10.1039/D0TB02958K  

   Zhang, Yanxian; Zhang, Mingzhen; Liu, Yonglan; Zhang, Dong; Tang, Yijing; Ren, Baiping; Zheng, Jie (April 2021, Journal of Materials Chemistry B)

   Amyloid cross-seeding, as a result of direct interaction and co-aggregation between different disease-causative peptides, is considered as a main mechanism for the spread of the overlapping pathology across different cells and tissues between different protein-misfolding diseases (PMDs). Despite the biomedical significance of amyloid cross-seeding in amyloidogenesis, it remains a great challenge to discover amyloid cross-seeding systems and reveal their cross-seeding structures and mechanisms. Herein, we are the first to report that GNNQQNY – a short fragment from yeast prion protein Sup35 – can cross-seed with both amyloid-β (Aβ, associated with Alzheimer's disease) and human islet amyloid polypeptide (hIAPP, associated with type II diabetes) to form β-structure-rich assemblies and to accelerate amyloid fibrillization. Dry, steric β-zippers, formed by the two β-sheets of different amyloid peptides, provide generally interactive and structural motifs to facilitate amyloid cross-seeding. The presence of different steric β-zippers in a variety of GNNQQNY-Aβ and GNNQQNY-hIAPP assemblies also explains amyloid polymorphism. In addition, alteration of steric zipper formation by single-point mutations of GNNQQNY and interactions of GNNQQNY with different Aβ and hIAPP seeds leads to different amyloid cross-seeding efficiencies, further confirming the existence of cross-seeding barriers. This work offers a better structural-based understanding of amyloid cross-seeding mechanisms linked to different PMDs. 

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5. Multi-target amyloid probing and inhibition using basic orange fluorescence

   https://doi.org/10.1039/D3SD00124E  

   Tang, Yijing; Zhang, Dong; Gong, Xiong; Zheng, Jie (November 2023, Sensors & Diagnostics)

   Misfolding and aggregation of amyloid peptides are critical pathological events in numerous protein misfolding diseases (PMDs), such as Alzheimer's disease (AD), type II diabetes (T2D), and medullary thyroid carcinoma (MTC). While developing effective amyloid detectors and inhibitors to probe and prevent amyloid aggregation is a crucial diagnostic and therapeutic strategy for treating debilitating diseases, it is important to recognize that amyloid detection and amyloid prevention are two distinct strategies for developing pharmaceutical drugs. Here, we reported novel fluorescent BO21 as a versatile “dual-function, multi-target” amyloid probe and inhibitor for detecting and preventing amyloid aggregates of different sequences (Aβ, hIAPP, or hCT) and sizes (monomers, oligomers, or fibrils). As an amyloid probe, BO21 demonstrated a higher sensitivity and binding affinity to oligomeric and fibrillar amyloids compared to ThT, resulting in up to 18–39 fold fluorescence enhancements. As an amyloid inhibitor, BO21 also demonstrated its strong amyloid inhibition property by effectively preventing amyloid aggregation, disaggregating preformed amyloid fibrils, and reducing amyloid-induced cytotoxicity. The findings of this study offer a new perspective for the discovery of dual-functional amyloid probes and inhibitors, which have the potential to greatly expand the diagnostic and therapeutic treatments available for PMDs. 

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