Journal of biochemistry最新文献_第4页

CDC42 missense mutations and human diseases: from neurodevelopmental disorders to autoinflammation. CDC42错义突变与人类疾病：从神经发育障碍到自身炎症。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-07-31 DOI: 10.1093/jb/mvaf021

Takahiro Yasumi

引用次数: 0

The crystal structure of the small zinc-finger protein ZifS from Thermus thermophilus HB8. 嗜热热菌HB8小锌指蛋白ZifS的晶体结构。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-07-31 DOI: 10.1093/jb/mvaf028

Saki Kurinami, Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Hiroki Okanishi, Yoshikatsu Kanai, Takato Yano, Ryoji Masui

{"title":"The crystal structure of the small zinc-finger protein ZifS from Thermus thermophilus HB8.","authors":"Saki Kurinami, Kenji Fukui, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Hiroki Okanishi, Yoshikatsu Kanai, Takato Yano, Ryoji Masui","doi":"10.1093/jb/mvaf028","DOIUrl":"10.1093/jb/mvaf028","url":null,"abstract":"Zinc finger domains are important interaction modules for binding to nucleic acids, proteins, lipids and small molecules. Many small-sized zinc finger proteins are encoded in bacterial genomes, but most of them have not been functionally annotated. We focused on TTHA0897, ZifS, as a small zinc finger protein from the extremely thermophilic eubacterium Thermus thermophilus HB8. In vivo experiments suggested that the cellular function of ZifS is related to the growth transition of T. thermophilus from the lag to the exponential phase under nutritionally limited conditions. In vitro biochemical experiments, including electrophoretic mobility shift assay and pull-down assay, yielded no clues about molecular functions of ZifS. X-ray crystallographic analysis revealed that the dimeric ZifS globally forms a cylinder-like structure, although ZifS dimer has no overall structural similarity to other known zinc finger proteins. The zinc ion-binding manner of ZifS fitted the characteristics of the zinc ribbon fold, which are mostly found in domains from proteins involved in the transcriptional and translational machinery. The crystal structure of ZifS is the first experimental insight into the molecular structure of this protein family, revealing several conserved features that may be functionally relevant.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"121-133"},"PeriodicalIF":1.7,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Innate immune signals triggered on organelle membranes. 先天免疫信号触发细胞器膜。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-07-31 DOI: 10.1093/jb/mvaf016

Yoshihiko Kuchitsu, Tomohiko Taguchi

引用次数: 0

Correction to: Innate immune signals triggered on organelle membranes. 修正：先天免疫信号触发细胞器膜。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-07-31 DOI: 10.1093/jb/mvaf035

引用次数: 0

NMR analysis of interaction between RNA structure elements and small molecules. RNA结构元件与小分子相互作用的核磁共振分析。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-07-01 DOI: 10.1093/jb/mvaf020

Megumi Tomemori, Rika Ichijo, Yoko Shinohara, Kaori Hatta, Kazuhiko Nakatani, Gota Kawai

引用次数: 0

Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells. Atg7敲低抑制自噬增强吉西他滨/紫杉醇耐药胰腺癌MIAPaCa2细胞的化疗敏感性。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-07-01 DOI: 10.1093/jb/mvaf022

Yudai Kudo, Kotaro Hirota, Honoka Tsuzuki, Shinya Kawano, Tomofumi Saka, Riri Hayashi, Yuta Yoshino, Akira Ikari, Satoshi Endo

{"title":"Inhibition of autophagy by Atg7 knockdown enhances chemosensitivity in gemcitabine/paclitaxel-resistant pancreatic cancer MIAPaCa2 cells.","authors":"Yudai Kudo, Kotaro Hirota, Honoka Tsuzuki, Shinya Kawano, Tomofumi Saka, Riri Hayashi, Yuta Yoshino, Akira Ikari, Satoshi Endo","doi":"10.1093/jb/mvaf022","DOIUrl":"10.1093/jb/mvaf022","url":null,"abstract":"The 5-year survival rate for pancreatic cancer is extremely low, at ~12%, primarily because most patients present with advanced and unresectable tumours. Chemotherapy regimens, such as gemcitabine (GEM) plus paclitaxel (PTX) and FOLFIRINOX, are standard treatments; however, resistance to these therapies remains a major challenge. Autophagy has been implicated in this resistance. Both the Atg8 and Atg12 conjugation systems are essential for autophagosome maturation, and the ubiquitin-like protein activator Atg7 plays an essential role in these systems. This study investigated the effects of Atg7 knockdown on GEM/PTX sensitivity in GEM/PTX-resistant pancreatic cancer MIAPaCa2 (GP-R) cells. GP-R cells exhibited reduced sensitivity to GEM/PTX, increased expression of autophagy-related factors, and elevated basal autophagy compared to parental cells. Atg7 knockdown in GP-R cells effectively inhibited both basal and GEM/PTX-induced autophagy, significantly increased total and mitochondrial reactive oxygen species (ROS), and led to the induction of apoptotic cell death. These findings suggest that autophagy inhibition via Atg7 knockdown enhances GEM/PTX sensitivity in GP-R cells. In conclusion, targeting Atg7 to inhibit autophagy may be a promising approach to improving the efficacy of GEM/PTX therapy in pancreatic cancer.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"11-24"},"PeriodicalIF":2.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ZNRF1-dependent regulation of AKT activity modulates Nav subcellular localization and AIS position in neurons to regulate fear-related behaviour. 依赖znrf1的AKT活性调节神经元中Nav亚细胞定位和AIS位置，从而调节恐惧相关行为。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-07-01 DOI: 10.1093/jb/mvaf024

Moeka Ohno, Shuji Wakatsuki, Hiroshi Kuniishi, Masayuki Sekiguchi, Eri Takeuchi, Keizo Takao, Megumi Watase, Takaya Abe, Toshiyuki Araki

引用次数: 0

Valosin-containing protein mediates DNA-dependent protein kinase activation in response to DNA topoisomerase II-associated DNA double-strand breaks. 在DNA拓扑异构酶ii相关DNA双链断裂的反应中，含缬草苷蛋白介导DNA依赖性蛋白激酶激活。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-07-01 DOI: 10.1093/jb/mvaf025

Ryo Sakasai, Yumi Sunatani, Tadashi Matsui, Kuniyoshi Iwabuchi

{"title":"Valosin-containing protein mediates DNA-dependent protein kinase activation in response to DNA topoisomerase II-associated DNA double-strand breaks.","authors":"Ryo Sakasai, Yumi Sunatani, Tadashi Matsui, Kuniyoshi Iwabuchi","doi":"10.1093/jb/mvaf025","DOIUrl":"10.1093/jb/mvaf025","url":null,"abstract":"DNA topoisomerase II (Top2) induces DNA double-strand breaks (DSBs) to relieve the torsional stress associated with DNA replication and transcription. Etoposide (ETP), a Top2 poison in clinical use as an anticancer drug, traps Top2 reactive intermediates, resulting in the accumulation of DSBs, coupled with the formation of Top2-DNA protein crosslinks (Top2-DPC) at the ends of DSBs. Proteasome-dependent processing of trapped Top2 is necessary for some cellular responses to ETP-induced DSBs; however, the effect of suppressing Top2 removal on DSB repair is not well understood. In this study, we focused on valosin-containing protein (VCP), a proteasome mediator, to analyse the effect of the suppression of Top2-DPC resolution on the repair of ETP-induced DSBs. ETP-induced activation of DNA-dependent protein kinase (DNA-PK), a non-homologous end-joining (NHEJ) factor, was suppressed by VCP inhibitors, similar to the effects observed in proteasome-inhibited cells. Consistent with this finding, VCP inhibition suppressed repair activity in response to ETP-induced DSBs. Additionally, VCP inhibition delayed the resolution of ETP-induced Top2-DPC. These results suggest that the processing of trapped Top2 via the VCP-proteasome pathway is important for efficient DNA-PK activation and subsequent repair in response to ETP-induced DSBs.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"51-60"},"PeriodicalIF":2.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improvement of a FRET-based redox probe Redoxfluor through circular permutation and effects of substitution of cysteine residues on its redox properties. 基于fret的氧化还原探针Redoxfluor的循环置换改进及半胱氨酸残基取代对其氧化还原性能的影响。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-07-01 DOI: 10.1093/jb/mvaf023

Kosuke Shiraishi, Banri Kitamura, Kaho Aramaki, Yasuyoshi Sakai, Jun Hoseki

{"title":"Improvement of a FRET-based redox probe Redoxfluor through circular permutation and effects of substitution of cysteine residues on its redox properties.","authors":"Kosuke Shiraishi, Banri Kitamura, Kaho Aramaki, Yasuyoshi Sakai, Jun Hoseki","doi":"10.1093/jb/mvaf023","DOIUrl":"10.1093/jb/mvaf023","url":null,"abstract":"The properties of a FRET-based redox probe Redoxfluor have been improved for its sensitivity and dynamic range. Substitution of the Citrine portion of Redoxfluor with circular permutated (cp) Citrine improved the dynamic range without affecting the redox potential. The cp158 mutant, referred to as Redoxfluor 2, possessed the most extended dynamic range and detected intracellular redox changes in yeast and bacteria, while the original did not. Investigation of the glutathione-redox dependency of the FRET ratio of various cysteine-substituted mutants revealed that Cys230 in the linker between Cerulean and the C-terminal cysteine-rich domain (CRD) and Cys385 in Citrine are essential for glutathione redox sensing. Although neither cysteine residues in CRD is essential for glutathione redox sensing, substitution of the CRD cysteine residues prominently affected the dynamic range of redox sensing and the redox potential titrated with glutathione. One of the CRD cysteine-substituted mutants (C259A) showed a greatly extended dynamic range and a substantially reducing redox potential compared to the original Redoxfluor. Redoxfluor 2 and the C259A mutant are suitable for versatile uses including sensitive detection of aberrant redox states, redox visualization in the more reducing intracellular compartments and high-throughput screening of redox modulators active against pathologically abnormal redox states.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"25-38"},"PeriodicalIF":2.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Suicide substrate reaction-like modification of mouse serine racemase with L-serine. l -丝氨酸修饰小鼠丝氨酸消旋酶的自杀底物样反应。

IF 2.1 4区生物学

Journal of biochemistry Pub Date : 2025-05-30 DOI: 10.1093/jb/mvaf019

Akari Hata, Tomokazu Ito, Hitoshi Mori, Takuya Ogawa, Tatsuo Kurihara, Hisashi Hemmi, Tohru Yoshimura

{"title":"Suicide substrate reaction-like modification of mouse serine racemase with L-serine.","authors":"Akari Hata, Tomokazu Ito, Hitoshi Mori, Takuya Ogawa, Tatsuo Kurihara, Hisashi Hemmi, Tohru Yoshimura","doi":"10.1093/jb/mvaf019","DOIUrl":"10.1093/jb/mvaf019","url":null,"abstract":"A pyridoxal 5'-phosphate-dependent fold-type II serine racemase (SR) is responsible for the synthesis of D-Ser, which serves as a co-agonist of N-methyl-D-aspartate glutamate receptor. In addition to racemization, SR catalyzes the dehydration of D- and L-Ser. SR is suggested to be involved in the D-Ser degradation in vivo, but this has not been confirmed. In this study, we found that mouse SR (mSR) underwent a suicide substrate reaction-like modification with its substrate, resulting in a remarkable change in its reaction specificity. mSR gradually lost its activity by the incubation with L- and D-Ser, but not completely. mSR was labelled with [14C]-L-Ser. ESI-MS analysis revealed that the molecular mass of SR increased by 84 Da by the incubation with L-Ser. Taken together with the results of previous crystallographic studies of fission yeast SR, we concluded that the active site lysine residue of mSR was modified with an α-aminoacrylate intermediate generated from L-Ser and converted to a lysinoalanine residue. The modification significantly decreased the racemization and L-Ser dehydration activities, while dramatically increased the D-Ser dehydration activity by the ~100 times reduction of the Km value. This is probably advantageous for the D-Ser degradation by mSR under physiological conditions.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"437-445"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0