Journal of biochemistry最新文献_第2页

Differential regulation between photosynthetic type and non-photosynthetic type Fd:FNRs in the negative cooperativity and pH dependency of the electron transfer activity. 光合型与非光合型FNRs对电子转移活性负协同性和pH依赖性的差异调控。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-03 DOI: 10.1093/jb/mvaf031

Yoko Kimata-Ariga, Shunsuke Miyake, Takato Murakami, Shunsuke Kuwano

{"title":"Differential regulation between photosynthetic type and non-photosynthetic type Fd:FNRs in the negative cooperativity and pH dependency of the electron transfer activity.","authors":"Yoko Kimata-Ariga, Shunsuke Miyake, Takato Murakami, Shunsuke Kuwano","doi":"10.1093/jb/mvaf031","DOIUrl":"10.1093/jb/mvaf031","url":null,"abstract":"In higher plants, ferredoxin (Fd) and Fd-NADP+ reductase (FNR) are each present as distinct isoproteins of photosynthetic type and non-photosynthetic type, which exhibit differential function despite their similarity in the 3D structures. In this study, we addressed differential regulation of Fd/FNR reaction between the two types from two perspectives and investigated the amino acid residues of Fd responsible for the differences. Firstly, pH-dependent profile of Fd/FNR electron transfer activity varied among the combinations of the two types of Fd and FNR; non-photosynthetic type FNR showed similar pattern for the two types of Fds while photosynthetic type FNR was previously shown to exhibit opposite pattern, which was explained by the different pH-dependent profile of Km for the two Fds. Secondly, the extent of the suppression of the affinity (in terms of Km value) between Fd and FNR by NADPH significantly varied among the combinations of the two types of Fd:FNR. The difference was shown to be mainly due to the different property of Fd between the two types. Kinetic analyses using site-directed mutants of Fd showed the contribution of C-terminal residues, together with that of 78th residue of Fd, on the differential profile of Fd/FNR reaction by pH and NADPH.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"171-179"},"PeriodicalIF":1.7,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258162","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

Crystal structure of Klebsiella pneumoniae maltohexaose-producing α-amylase. 肺炎克雷伯菌产麦芽己糖α-淀粉酶的晶体结构。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-03 DOI: 10.1093/jb/mvaf034

Zui Fujimoto, Naomi Kishine, Mitsuru Momma

引用次数: 0

Bisecting GlcNAc modification of angiotensin-related glycoproteins in mouse kidney. GlcNAc对小鼠肾脏血管紧张素相关糖蛋白的修饰。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-03 DOI: 10.1093/jb/mvaf033

Haruka Kawade, Wanxue Bao, Yuko Tokoro, Yoshimasa Ito, Yudai Tsuji, Kazuo Takahashi, Kazuki Nakajima, Miyako Nakano, Yasuhiko Kizuka

{"title":"Bisecting GlcNAc modification of angiotensin-related glycoproteins in mouse kidney.","authors":"Haruka Kawade, Wanxue Bao, Yuko Tokoro, Yoshimasa Ito, Yudai Tsuji, Kazuo Takahashi, Kazuki Nakajima, Miyako Nakano, Yasuhiko Kizuka","doi":"10.1093/jb/mvaf033","DOIUrl":"10.1093/jb/mvaf033","url":null,"abstract":"Structural variations of N-glycans critically regulate glycoprotein functions and are involved in various human diseases. N-Acetylglucosaminyltransferase-III (GnT-III or MGAT3) is highly expressed in the brain and kidney and is an N-glycan branching enzyme that biosynthesizes the unique N-glycan branch designated as bisecting GlcNAc. Its roles in Alzheimer's disease and cancer have been revealed, but the functions of bisecting GlcNAc in the kidney are poorly understood. Here, we show that kidneys in the GnT-III-knockout (KO) mouse exhibit impaired body fluid balance and present interstitial edema. To understand the molecular mechanisms further, we biochemically purified the glycoproteins modified by GnT-III in the mouse kidney and identified these proteins using proteomics. We found that the proteins involved in the pathway for angiotensin II (Ang II) metabolism are modified by GnT-III, and that the subcellular localization of angiotensin-converting enzyme was altered in GnT-III-KO cells. Furthermore, the pathology in models of Ang II-related disease was slightly more severe in GnT-III-KO than in wild-type mice. Our data indicate a protective role for bisecting GlcNAc in the mouse kidney, highlighting a newly described link between specific N-glycan structures and renal functions.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"181-192"},"PeriodicalIF":1.7,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144284438","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

Three glutamic acid residues in the cytoplasmic N-terminal tail of long-form GlcAT-P define Golgi-to-ER trafficking. 长形GlcAT-P的细胞质n端尾部的三个谷氨酸残基定义了高尔基到内质网的运输。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-03 DOI: 10.1093/jb/mvaf030

Ayaka Okada, Risa Harui, Tomonari Ishida, Katsuaki Higashi, Motohiro Nonaka, Shogo Oka, Jyoji Morise

{"title":"Three glutamic acid residues in the cytoplasmic N-terminal tail of long-form GlcAT-P define Golgi-to-ER trafficking.","authors":"Ayaka Okada, Risa Harui, Tomonari Ishida, Katsuaki Higashi, Motohiro Nonaka, Shogo Oka, Jyoji Morise","doi":"10.1093/jb/mvaf030","DOIUrl":"10.1093/jb/mvaf030","url":null,"abstract":"Glucuronyltransferase GlcAT-P is a rate-limiting enzyme involved in the biosynthesis of the Human Natural Killer-1 carbohydrate and is essential for acquiring higher brain functions. Alternative splicing produces two isoforms, short-form GlcAT-P (sGlcAT-P) and long-form GlcAT-P (lGlcAT-P), which share identical peptide sequences except for an additional 13 amino acids (AA) in the cytoplasmic N-terminal tail of lGlcAT-P. Although sGlcAT-P localizes to the Golgi apparatus (GA), where many glycosyltransferases reside, lGlcAT-P is distributed in both the GA and endoplasmic reticulum (ER). However, the mechanisms responsible for this distinct intracellular distribution remain poorly understood. In this study, we explored the role of the 13 AA in the cytoplasmic N-tail of lGlcAT-P in trafficking between the GA and the ER using the Retention Using Selective Hooks system. Our findings revealed that lGlcAT-P undergoes enhanced retrograde trafficking from the GA to the ER, whereas its anterograde trafficking from the ER to the GA remains largely unaffected. In addition, three glutamic acid residues within the 13 AA of lGlcAT-P were identified as crucial for promoting retrograde trafficking. These results suggest that the ER distribution of lGlcAT-P is primarily governed by Golgi-to-ER trafficking regulated by specific sequences in its cytoplasmic N-tail.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"161-170"},"PeriodicalIF":1.7,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248033","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

Maintaining a neutral range disperses myosin molecules under salt-free conditions. 在无盐条件下保持中性范围分散肌球蛋白分子。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-03 DOI: 10.1093/jb/mvaf036

Toru Hayakawa, Yu Shishido, Yuki Ikeuchi, Jun-Ichi Wakamatsu, Haruto Kumura

{"title":"Maintaining a neutral range disperses myosin molecules under salt-free conditions.","authors":"Toru Hayakawa, Yu Shishido, Yuki Ikeuchi, Jun-Ichi Wakamatsu, Haruto Kumura","doi":"10.1093/jb/mvaf036","DOIUrl":"10.1093/jb/mvaf036","url":null,"abstract":"Skeletal muscle myosin is generally considered insoluble under physiological, low ionic strength, or salt-free conditions due to its tendency to self-assemble into filamentous polymers in vitro. Our previous study showed that myosin can be solubilized in low ionic strength solutions containing l-histidine. However, another report suggested that 1-methylhistidine could not solubilize myosin, and the factors essential for myosin solubilization remain unclear. To elucidate the role of l-histidine in the water solubilization of myosin, we examined myosin solubility and the molecular properties of its rod domain, l-meromyosin, using structurally related buffer compounds. Under salt-free conditions, solubility depended heavily on the acid dissociation constant of buffer, indicating that maintaining a neutral pH is critical. The rod domain showed molecular elongation regardless of the buffer type, yet surface charge and hydrophobicity remained comparable to conditions with high ionic strength. These results suggest that myosin is inherently soluble and maintains its structural integrity under neutral, salt-free conditions. The apparent insolubility under such conditions is likely to result from hydrochloric acid used for pH adjustment. Since l-histidine and imidazole achieve neutrality without acid addition, they are ideal buffers for myosin solubilization.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":"209-215"},"PeriodicalIF":1.7,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144505776","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

Elucidating the effects of Fisetin on hALDH4 activity and stability: A multidisciplinary approach using spectroscopy and molecular dynamics simulations. 阐明非塞汀对hALDH4活性和稳定性的影响：使用光谱和分子动力学模拟的多学科方法。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-01 DOI: 10.1093/jb/mvaf053

Ayodele O Kolawole, Mary Ayoola Bukoye, Adejoke N Kolawole, Babatunde A Falese, Showkat Ahmad Mir, Binata Nayak

{"title":"Elucidating the effects of Fisetin on hALDH4 activity and stability: A multidisciplinary approach using spectroscopy and molecular dynamics simulations.","authors":"Ayodele O Kolawole, Mary Ayoola Bukoye, Adejoke N Kolawole, Babatunde A Falese, Showkat Ahmad Mir, Binata Nayak","doi":"10.1093/jb/mvaf053","DOIUrl":"https://doi.org/10.1093/jb/mvaf053","url":null,"abstract":"Human Aldehyde Dehydrogenase IV (hALDH4) role in the metabolism of aldehydic compounds is apodictic. Fisetin, a bioactive flavonoid, having myriad of pharmacological activities with inexhaustible therapeutic potentials. Howbeit, the interactive mechanism and inhibitory potential of fisetin on hALDH4 still remain unclear and untold. Here, multi spectroscopic technique, molecular modelling and dynamic simulations were comprehensively explored to elucidate this. Fisetin quenching the intrinsic fluorescence of hALDH4. Fisetin showed a significant inhibitory effect on the hALDH4 (IC50 = 17.45 μM) with kinetic inhibition constant, KI, of 25.97 μM. It reversibly inhibited the enzyme in a mixed competitive manner. The interaction, though predominantly electrostatic interaction, perturbed the intrinsic hALDH4 conformation by compromising the predominant α-helix structure. hALDH4 has one ligand competent site for fisetin with a binding constant (Ka) of 3.80 x 104 L.mol-1 at 25°C. The molecular docking and atomistic simulations demonstrated affinity of fisetin for hALDH4 causing the protein structural strain, resulting in unusual conformations but stable. This investigation provided important insights on kinetics and thermodynamics of fisetin and hALDH4 interaction shedding light on the potential treatment of hALDH-implicated pathological conditions.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955630","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

Identification of a PCNA-binding motif in human translesion DNA polymerase REV1 and structural basis of its interaction with PCNA. 人翻译DNA聚合酶REV1中PCNA结合基序的鉴定及其与PCNA相互作用的结构基础。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-09-01 DOI: 10.1093/jb/mvaf054

Asami Hishiki, Naoya Hoshino, Kokona Okawara, Sotaro Fuchigami, Kodai Hara, Hiroshi Hashimoto

{"title":"Identification of a PCNA-binding motif in human translesion DNA polymerase REV1 and structural basis of its interaction with PCNA.","authors":"Asami Hishiki, Naoya Hoshino, Kokona Okawara, Sotaro Fuchigami, Kodai Hara, Hiroshi Hashimoto","doi":"10.1093/jb/mvaf054","DOIUrl":"https://doi.org/10.1093/jb/mvaf054","url":null,"abstract":"REV1 is a eukaryotic error-prone DNA polymerase belonging to the Y-family, with a central role in translesion DNA synthesis (TLS) to continue DNA replication even in the presence of DNA damage in the template strand. TLS is stimulated by mono-ubiquitination of proliferating cell nuclear antigen (PCNA), a toroidal-shaped protein functioning as a scaffold for DNA polymerases and repair enzymes. Mammals possess four types of Y-family DNA polymerases: Pol η, Pol κ, Pol ι, and REV1. Among those, Pol η, Pol κ, and Pol ι interact with PCNA through PCNA-binding motifs, low-affinity variants of PCNA-interacting protein box (PIP-box). To date, several studies have reported that REV1 interacts with PCNA, but identified PCNA-binding regions are inconsistent; therefore, a structural basis for interaction between REV1 and PCNA also remains unclear. Here, we identified a signature sequence conserved within vertebrates REV1 responsible for PCNA-binding. Furthermore, we unveiled a mechanism underlying the physical interaction between the PCNA-binding motif of human REV1 and PCNA by X-ray crystallography, thus revealing that REV1 binds to PCNA through a PIP-box variant located in the C-terminal side of the little finger domain. Our study provides a convincing answer for a long-standing controversy regarding the physical interaction between REV1 and PCNA.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955618","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

Phosphatidylinositol-Specific Phospholipase C Across Biological Kingdoms: Domain Organization, Functions, and Regulation. 磷脂酰肌醇特异性磷脂酶C跨越生物王国：结构域组织、功能和调控。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-08-28 DOI: 10.1093/jb/mvaf051

Kaori Kanemaru, Yoshikazu Nakamura

引用次数: 0

Commentary for The Incorporation of Extracellular Vesicle Markers Varies Among Vesicles with Distinct Surface Charges. 细胞外囊泡标记物的结合在具有不同表面电荷的囊泡中是不同的。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-08-27 DOI: 10.1093/jb/mvaf052

Kenji Matsuzawa, Junichi Ikenouchi

{"title":"Commentary for The Incorporation of Extracellular Vesicle Markers Varies Among Vesicles with Distinct Surface Charges.","authors":"Kenji Matsuzawa, Junichi Ikenouchi","doi":"10.1093/jb/mvaf052","DOIUrl":"https://doi.org/10.1093/jb/mvaf052","url":null,"abstract":"Extracellular vesicles (EVs) have emerged as critical mediators of intercellular communication, transporting diverse molecular cargoes such as proteins, lipids, and nucleic acids. Despite their growing importance in both basic biology and clinical applications, the remarkable heterogeneity of EVs remains a major obstacle to their functional characterization. In a recent study, Maeda and colleagues developed a highly sensitive and quantitative method for monitoring EV release using HiBiT-tagged marker proteins, combined with a novel chromatographic approach that fractionates EVs based on surface charge properties. This strategy enabled the identification of distinct EV subpopulations harboring specific protein markers and differing in their biogenesis and intracellular origin. By integrating CRISPR-mediated tagging, live-cell luminescence assays, and ion-exchange chromatography, the study establishes surface charge as a new physicochemical parameter for EV classification. These findings offer a powerful framework for dissecting EV heterogeneity and lay the foundation for the development of more precise EV-based diagnostic strategies.","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955669","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

De novo synthesis of peroxisomes: How they are born. 过氧化物酶体的新生合成：它们是如何产生的。

IF 1.7 4区生物学

Journal of biochemistry Pub Date : 2025-08-26 DOI: 10.1093/jb/mvaf048

Ayumu Sugiura

引用次数: 0