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2022 ◽  
Vol 23 (2) ◽  
pp. 701
Author(s):  
Yuki Ito ◽  
Takuya Araki ◽  
Shota Shiga ◽  
Hiroyuki Konno ◽  
Koki Makabe

Top7 is a de novo designed protein whose amino acid sequence has no evolutional trace. Such a property makes Top7 a suitable scaffold for studying the pure nature of protein and protein engineering applications. To use Top7 as an engineering scaffold, we initially attempted structure determination and found that crystals of our construct, which lacked the terminal hexahistidine tag, showed weak diffraction in X-ray structure determination. Thus, we decided to introduce surface residue mutations to facilitate crystal structure determination. The resulting surface mutants, Top7sm1 and Top7sm2, crystallized easily and diffracted to the resolution around 1.7 Å. Despite the improved data, we could not finalize the structures due to high R values. Although we could not identify the origin of the high R values of the surface mutants, we found that all the structures shared common packing architecture with consecutive intermolecular β-sheet formation aligned in one direction. Thus, we mutated the intermolecular interface to disrupt the intermolecular β-sheet formation, expecting to form a new crystal packing. The resulting mutant, Top7sm2-I68R, formed new crystal packing interactions as intended and diffracted to the resolution of 1.4 Å. The surface mutations contributed to crystal packing and high resolution. We finalized the structure model with the R/Rfree values of 0.20/0.24. Top7sm2-I68R can be a useful model protein due to its convenient structure determination.


2022 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Mohammad Javad Khodayar ◽  
Masoud Mahdavinia ◽  
Masoumeh Baradaran ◽  
Amir Jalali

Background: Scorpions and other venomous animals are sought with great concern because venom is a source of novel peptides with exciting features. Some toxins of scorpion venom are effectors of potassium channels. Previous studies strongly support the importance of potassium channel toxins for use as pharmacological tools or potential drugs. Objectives: Here, a three-dimensional (3-D) structure and function of a potent acidic blocker of the human voltage-gated potassium ion channel, Kv1.3, previously identified in the scorpion Mesobuthus eupeus venom gland, were interpreted. Methods: The 3-D structure of meuK2-2 was generated using homology modeling. The interaction of meuK2-2 with the Kv1.3 channel was evaluated using a computational protocol employing peptide-protein docking experiments, pose clustering, and 100 ns molecular dynamic simulations to make the 3-D models of the meuK2-2/Kv1.3 complex trustworthy. Results: A CSα/β (cysteine-stabilized α-helical and β-sheet) fold was found for the 3-D structure of meuK2-2. In a different mechanism from what was identified so far, meuK2-2 binds to both turret and pore loop of Kv1.3 through two key residues (Ala28 and Ser11) and H-bonds. The binding of meuK2-2 induces some conformational changes to Kv1.3. Eventually, the side chain of a positively charged amino acid (His9) occupies the channel's pore. All together blocks the ion permeation pathway. Conclusions: MeuK2-2 could block Kv1.3 by a new mechanism. So, it could be a unique target for further investigations to develop a pharmacological tool and potential drug.


CrystEngComm ◽  
2022 ◽  
Author(s):  
Jiai Hua ◽  
Xueman Wei ◽  
Xiang Ma ◽  
Jinzhe Jiao ◽  
Binghui Chai ◽  
...  

A nanoscale polyoxometalate {[H2dap]6[Cd4Cl2(B-α-AsW9O34)2]} based on tetra-Cd cluster sandwiched trivacant Keggin-type tungstoarsenate was successfully designed and synthesized. It can modulate the β-sheet-rich fibrils of Aβ peptide efficiently; and thus inhibits...


Foods ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
Hao Chen ◽  
Hongwu Ji ◽  
Chuang Pan ◽  
Di Zhang ◽  
Weiming Su ◽  
...  

Pigment proteins play a vital role in the red colour change of the red swamp crayfish (Procambarus clarkii) shell after cooking. In this study, two red-change-related pigment proteins with molecular weights of approximately 170 and 43 kDa—denoted as F1 and F2, respectively—were purified by ammonium sulphate salting-out and size exclusion chromatography. F1 and F2 entirely comprised homomultimeric protein complexes composed of 21 kDa subunits. LC-MS/MS analysis showed that the 21 kDa protein subunit belonged to the crustacyanin family, named P. clarkii crustacyanin A2 (PcCRA2). The full-length cDNA of PcCRA2 was cloned, which encoded 190 amino acid residues and was highly homologous (91.58%) with Cherax quadricarinatus crustacyanin A. The predicted 3D structure showed that PcCRA2 had a β-barrel structure for pigment encapsulation. The colour change of F1 was first detected at 40 °C, and the red change occurred upon heating above 60 °C. Additionally, with increasing temperature, its β-sheet content increased, and its α-helix content reduced. Correlation analysis showed that the redness value of F1 was significantly related to the heating temperature and the β-sheet content.


Author(s):  
Truc Lam Pham ◽  
Michael Kovermann ◽  
Franziska Thomas
Keyword(s):  

2021 ◽  
pp. 2102342
Author(s):  
Boris Apter ◽  
Igor Lapsker ◽  
Alexandra Inberg ◽  
Gil Rosenman
Keyword(s):  

2021 ◽  
Author(s):  
Forrest Hoyt ◽  
Heidi G. Standke ◽  
Efrosini Artikis ◽  
Cindi L. Schwartz ◽  
Bryan Hansen ◽  
...  

Little is known about the structural basis of prion strains. Here we provide a high (3.0 Å) resolution cryo-electron microscopy-based structure of brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register β-sheet-based core. However, detailed comparisons reveal that variations in shared structural motifs provide a basis for prion strain determination.


2021 ◽  
Vol 5 (3) ◽  
pp. e202101185
Author(s):  
Irene Riera-Tur ◽  
Tillman Schäfer ◽  
Daniel Hornburg ◽  
Archana Mishra ◽  
Miguel da Silva Padilha ◽  
...  

The autophagy-lysosomal pathway is impaired in many neurodegenerative diseases characterized by protein aggregation, but the link between aggregation and lysosomal dysfunction remains poorly understood. Here, we combine cryo-electron tomography, proteomics, and cell biology studies to investigate the effects of protein aggregates in primary neurons. We use artificial amyloid-like β-sheet proteins (β proteins) to focus on the gain-of-function aspect of aggregation. These proteins form fibrillar aggregates and cause neurotoxicity. We show that late stages of autophagy are impaired by the aggregates, resulting in lysosomal alterations reminiscent of lysosomal storage disorders. Mechanistically, β proteins interact with and sequester AP-3 μ1, a subunit of the AP-3 adaptor complex involved in protein trafficking to lysosomal organelles. This leads to destabilization of the AP-3 complex, missorting of AP-3 cargo, and lysosomal defects. Restoring AP-3μ1 expression ameliorates neurotoxicity caused by β proteins. Altogether, our results highlight the link between protein aggregation, lysosomal impairments, and neurotoxicity.


2021 ◽  
Vol 6 (2) ◽  
pp. 117
Author(s):  
Nishia Waya Meray ◽  
Suharti Suharti ◽  
Akhmaloka Akhmaloka

Pada penelitian sebelumnya fragmen gen 1,9 kb telah berhasil diisolasi dari Kawah Domas, Jawa Barat melalui pendekatan metagenom. Fragmen tersebut diketahui mengandung daerah Open Reading Frame (ORF) utuh dari gen pengkode aldolase kelas II dari uncultured Acidilobus sp. yang kemudian disebut sebagai aldII. Fragmen gen aldII tersebut berhasil diekspresikan menjadi protein termostabil aldolase kelas II yang kemudian disebut sebagai AldII. Penelitian ini bertujuan untuk melakukan studi bioinformasi terhadap protein AldII tersebut. Protein AldII kemudian diketahui memiliki massa molekul ~21,2 kDa dengan rumus molekul C940H1539N261O281S8. Total residu bermuatan negatif (Asp + Glu) sebanyak 22 residu, sedangkan total residu bermuatan positif (Arg + Lys) adalah 18 residu. Nilai pI teoritis AldII sebesar 5,86. Hasil perhitungan indeks kestabilan protein ini adalah 36,61 dan diklasifikasikan sebagai protein yang stabil. Lewat penjajaran dengan homologi terdekat, ditemukan daerah lestari yang dapat menunjukan residu yang mungkin berperan dalam pengikatan logam dan sisi aktif. Prediksi struktur 3D dilakukan secara ab initio, menunjukan adanya 6 struktur β-sheet dan 6 struktur α-heliks. Dengan demikian dapat disimpulkan bahwa protein AldII dari uncultured Acidilobus sp. diduga memiliki aktivitas enzimatik.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261123
Author(s):  
Thu-Thuy Nguyen ◽  
Trang Hoang ◽  
Kiet N. Tran ◽  
Hyeonji Kim ◽  
Sei-Heon Jang ◽  
...  

Thioredoxin (Trx), a small redox protein, exhibits thermal stability at high temperatures regardless of its origin, including psychrophiles. Trxs have a common structure consisting of the central β-sheet flanked by an aliphatic cluster on one side and an aromatic cluster on the other side. Although the roles of aromatic amino acids in the folding and stability of proteins have been studied extensively, the contributions of aromatic residues to the stability and function of Trx, particularly Trxs from cold-adapted organisms, have not been fully elucidated. This study examined the roles of aromatic amino acids in the aromatic cluster of a Trx from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621 (SpTrx). The aromatic cluster of SpTrx was comprised of W11, F26, F69, and F80, in which F26 at the β2 terminus was buried inside. The substitution of tyrosine for F26 changed the SpTrx conformation substantially compared to that of F69 and F80. Further biochemical and spectroscopic investigations on F26 showed that the F26Y, F26W, and F26A mutants resulted in structural instability of SpTrx in both urea- and temperature-induced unfolding and lower insulin reduction activities. The Trx reductase (SpTR) showed lower catalytic efficiencies against F26 mutants compared to the wild-type SpTrx. These results suggest that buried F26 is essential for maintaining the active-site conformation of SpTrx as an oxidoreductase and its structural stability for interactions with SpTR at colder temperatures.


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