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Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2 AlphaFold3 和 AlphaFold2 预测的血红素蛋白中血红素结合位点的结构比较
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-22 DOI: 10.1093/chemle/upae148
Hiroko X Kondo, Yu Takano
{"title":"Structure comparison of heme-binding sites in heme protein predicted by AlphaFold3 and AlphaFold2","authors":"Hiroko X Kondo, Yu Takano","doi":"10.1093/chemle/upae148","DOIUrl":"https://doi.org/10.1093/chemle/upae148","url":null,"abstract":"AlphaFold3 can predict protein–ligand complex structures. In this study, we examined the accuracy of prediction of heme–protein interactions by AlphaFold3. AlphaFold3 succeeded in predicting heme–protein interactions for most heme proteins except for those without homologous proteins in the Protein Data Bank. Our comparison of predictions by AlphaFold3 and AlphaFold2 suggests that heme–protein structures can be predicted from amino acid sequences of proteins alone using AlphaFold2.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"408 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase 甲醇脱氢酶中配体结合的分子动力学计算见解
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-22 DOI: 10.1093/chemle/upae153
One-Sun Lee, Sung Haeng Lee
{"title":"Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase","authors":"One-Sun Lee, Sung Haeng Lee","doi":"10.1093/chemle/upae153","DOIUrl":"https://doi.org/10.1093/chemle/upae153","url":null,"abstract":"Methanol dehydrogenase is a promising biocatalyst for industrial use, converting methanol to formaldehyde. Our molecular modeling revealed methanol binds to methanol dehydrogenase with ∼7 kcal/mol free energy, while formaldehyde binds with ∼4 kcal/mol. This suggests that methanol remains longer in the active site, and formaldehyde exits more readily postreaction. These insights are crucial for designing more efficient methanol dehydrogenase variants for industrial applications.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"2 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Constructing a novel I-BiOBr/CQD composite for near-infrared–driven photocatalysis 构建用于近红外驱动光催化的新型 I-BiOBr/CQD 复合材料
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-16 DOI: 10.1093/chemle/upae151
Maozhou Fan
{"title":"Constructing a novel I-BiOBr/CQD composite for near-infrared–driven photocatalysis","authors":"Maozhou Fan","doi":"10.1093/chemle/upae151","DOIUrl":"https://doi.org/10.1093/chemle/upae151","url":null,"abstract":"In this study, a novel composite of Iodine-doped bismuth oxybromide (I-BiOBr)/carbon quantum dots was synthesized using a simple chemical precipitation method at ambient temperature. The bandgap energy of bismuth oxybromide (BiOBr) can be reduced from 2.78 to 2.28 eV by introducing I-ions, aligning it with the upconverted emission spectrum of carbon quantum dots. Consequently, the photodegradation efficiency of I-BiOBr/carbon quantum dots reached a 95% degradation rate for methyl orange after 120 min of visible light irradiation, which is 4.2 times than that of BiOBr.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"35 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
UV-induced Controlled Radical Polymerization Using Titanium Dioxide Nanoparticles Via the RAFT Process 通过 RAFT 工艺使用二氧化钛纳米粒子进行紫外线诱导的受控自由基聚合反应
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-16 DOI: 10.1093/chemle/upae165
Shuji Zenke, Tomonari Tanaka
{"title":"UV-induced Controlled Radical Polymerization Using Titanium Dioxide Nanoparticles Via the RAFT Process","authors":"Shuji Zenke, Tomonari Tanaka","doi":"10.1093/chemle/upae165","DOIUrl":"https://doi.org/10.1093/chemle/upae165","url":null,"abstract":"Herein, we report the UV-induced controlled radical polymerization facilitated by titanium dioxide nanoparticles and trithiocarbonate derivatives, serving as photocatalysts and chain transfer agents, respectively. The polymerization proceeded through a reversible addition–fragmentation chain transfer (RAFT) process. The resulting polymers exhibited well-controlled molecular weights and relatively low polydispersity. Additionally, the chain extension reaction via UV-induced RAFT polymerization using titanium dioxide nanoparticles yielded higher-molecular weight polymer products.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"17 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Short steps synthesis of unsymmetrical acetylenes from tetrachloroethylene and arylboronic acids using Suzuki coupling reaction and improvement of mild dechlorinations 利用铃木偶联反应短步合成四氯乙烯和芳基硼酸中的不对称乙炔以及改进温和的脱氯反应
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-14 DOI: 10.1093/chemle/upae079
Hiyono Suzuki, Akane Togo, Junya Kikuzawa, Kazuki Miyamoto, Shinsuke Marumoto, Akiko Kuwabara, Masafumi Kobayashi, Kouichi Matsumoto
{"title":"Short steps synthesis of unsymmetrical acetylenes from tetrachloroethylene and arylboronic acids using Suzuki coupling reaction and improvement of mild dechlorinations","authors":"Hiyono Suzuki, Akane Togo, Junya Kikuzawa, Kazuki Miyamoto, Shinsuke Marumoto, Akiko Kuwabara, Masafumi Kobayashi, Kouichi Matsumoto","doi":"10.1093/chemle/upae079","DOIUrl":"https://doi.org/10.1093/chemle/upae079","url":null,"abstract":"Short steps synthesis of unsymmetrical acetylenes from tetrachloroethylene and arylboronic acids, and the use of the metal Mg as the mild reagent for dechlorinations has been developed. Unsymmetrical acetylenes including the donor and acceptor diarylacetylenes were produced in good yields. The reaction optimization, scope and limitations, the scale-up reaction, and the evaluation of the step were studied for this paper.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"473 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis of Terminus-Decorated Aza[9]helicenes: Control of Interlayer Interaction 末端蜕变的氮杂[9]螺旋烯的合成：层间相互作用的控制
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-12 DOI: 10.1093/chemle/upae159
Yusuke Matsuo, Shu Seki, Takayuki Tanaka
{"title":"Synthesis of Terminus-Decorated Aza[9]helicenes: Control of Interlayer Interaction","authors":"Yusuke Matsuo, Shu Seki, Takayuki Tanaka","doi":"10.1093/chemle/upae159","DOIUrl":"https://doi.org/10.1093/chemle/upae159","url":null,"abstract":"Azahelicenes are intriguing luminescent materials with a planar chirality. The properties of aza[9]helicene can be perturbed by attaching substituent at the termini. The impact of the terminal-decoration has been investigated in view of structural and electronic aspects, leading to the control of interlayer interaction.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"73 1 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of diazirine–alkyne tag for protein–ligand interaction analysis with photoaffinity labeling 开发重氮烷基标签，利用光亲和标记分析蛋白质与配体的相互作用
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-08 DOI: 10.1093/chemle/upae142
Masatoshi Nakatani, Shohei Ebihara, Masaki Kita
{"title":"Development of diazirine–alkyne tag for protein–ligand interaction analysis with photoaffinity labeling","authors":"Masatoshi Nakatani, Shohei Ebihara, Masaki Kita","doi":"10.1093/chemle/upae142","DOIUrl":"https://doi.org/10.1093/chemle/upae142","url":null,"abstract":"We have developed a diazirine–alkyne tag for target protein–ligand interaction analysis. A sulfonamide photoaffinity probe was readily prepared using copper-catalyzed azide–alkyne cycloaddition (CuAAC), which site-specifically formed a covalent bond with human carbonic anhydrase 1 (∼30% labeling yield). The photolabeled position (E58–H64 region) was determined based on the results of a tandem mass spectrometry (MS/MS) analysis of tryptic peptides and was supported by molecular modeling studies. Our method may be useful for determining unknown ligand-binding sites of various target biomolecules.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"73 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141949054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis of ε-NbN and δ-NbN by metathesis reaction of NaNbO3 and BN 通过 NaNbO3 和 BN 的偏合成反应合成 ε-NbN 和 δ-NbN
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-08 DOI: 10.1093/chemle/upae154
Tenshin Osaka, Toshiya Ikenobe, Zenji Hiroi, Hisanori Yamane, Takahiro Yamada
{"title":"Synthesis of ε-NbN and δ-NbN by metathesis reaction of NaNbO3 and BN","authors":"Tenshin Osaka, Toshiya Ikenobe, Zenji Hiroi, Hisanori Yamane, Takahiro Yamada","doi":"10.1093/chemle/upae154","DOIUrl":"https://doi.org/10.1093/chemle/upae154","url":null,"abstract":"δ-NbN powder with particles of approximately 1 µm in size was obtained by heating a mixture of NaNbO3 and BN powders at 1373 K for 1 h, while agglomerates composed of ε-NbN platelet grains up to 50 µm in size were obtained by heating the mixture at the same temperature for 10 h. Metathesis reaction in which sodium borate was formed with replacement of the oxygen and nitrogen from NaNbO3 and BN occurred with the NbN formation. Wavelength-dispersive X-ray analysis showed that the molar ratios of Nb to N in the synthesized δ-NbN and ε-NbN were approximately 1:1. Magnetic susceptibility measurements showed that the δ-NbN powder was a superconductor with a transition temperature of approximately 16 K. In comparison, the ε-NbN agglomerates did not exhibit superconductivity above 2 K.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"2 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141949053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Anion effects on the structure and stability of 3D domain-swapped cytochrome c dimer 阴离子对三维结构域互换的细胞色素 c 二聚体的结构和稳定性的影响
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-08-02 DOI: 10.1093/chemle/upae150
Kodai Fujiwara, Michiko Ryuzaki, Masaru Yamanaka, Tsuyoshi Mashima, Tomonori Saotome, Shun-ichi Kidokoro, Shun Hirota
{"title":"Anion effects on the structure and stability of 3D domain-swapped cytochrome c dimer","authors":"Kodai Fujiwara, Michiko Ryuzaki, Masaru Yamanaka, Tsuyoshi Mashima, Tomonori Saotome, Shun-ichi Kidokoro, Shun Hirota","doi":"10.1093/chemle/upae150","DOIUrl":"https://doi.org/10.1093/chemle/upae150","url":null,"abstract":"The structure and stability of proteins are affected by ions. We have previously reported that cytochrome c can form a 3D domain-swapped dimer. The structure of the cytochrome c domain-swapped dimer becomes more compact in the presence of kosmotropic anions, whereas the thermal stability of the dimer decreased with addition of chaotropic anions based on the Hofmeister series. Dimers were formed by incubating cytochrome c at 50 °C in the presence of citrate ions.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"44 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141881290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
[Ti]-YNU-5: a large-pore titanosilicate as an efficient catalyst for selective oxidations [钛]-YNU-5：作为选择性氧化高效催化剂的大孔钛硅酸盐
IF 1.6 4区 化学
Chemistry Letters Pub Date : 2024-07-27 DOI: 10.1093/chemle/upae130
Shengxiang Zhang, Kai Asanuma, Satoshi Inagaki, Yoshihiro Kubota
{"title":"[Ti]-YNU-5: a large-pore titanosilicate as an efficient catalyst for selective oxidations","authors":"Shengxiang Zhang, Kai Asanuma, Satoshi Inagaki, Yoshihiro Kubota","doi":"10.1093/chemle/upae130","DOIUrl":"https://doi.org/10.1093/chemle/upae130","url":null,"abstract":"A novel large-pore titanosilicate with YFI topology, [Ti]-YNU-5, was prepared via post-synthetic isomorphous substitution of Ti for Al in the YFI framework. It exhibited the enhanced catalytic performances in the liquid-phase epoxidation of bulky alkenes and the oxidation of phenol with hydrogen peroxide. Hydrophobicity was found to be an important factor.","PeriodicalId":9862,"journal":{"name":"Chemistry Letters","volume":"17 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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