Biochemistry Biochemistry最新文献_第2页

Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes. 总是在移动：核过程中的染色质动力学概述。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-05-01 DOI: 10.1021/acs.biochem.5c00114

Charlotte M Delvaux de Fenffe, Jolijn Govers, Francesca Mattiroli

引用次数: 0

Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity. 离子-DNA相互作用是尿嘧啶DNA糖基化酶活性的关键决定因素。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-05-07 DOI: 10.1021/acs.biochem.5c00067

Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser

{"title":"Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity.","authors":"Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser","doi":"10.1021/acs.biochem.5c00067","DOIUrl":"10.1021/acs.biochem.5c00067","url":null,"abstract":"Because of their ubiquitous presence, ions interact with numerous macromolecules in the cell and affect critical biological processes. Here, we discuss how cations including Mg2+ alter the enzymatic activity of a DNA glycosylase by tuning its affinity for DNA. The response of uracil DNA glycosylase (UNG2) to Mg2+ ions in solution is biphasic and paradoxical, where low concentrations of the ion stimulate the enzyme, but high concentrations inhibit the enzyme. We analyzed this phenomenon by modeling experimental data with a statistical framework that we empirically derived to understand molecular systems that display biphasic behaviors. Parameters from our statistical model indicate that DNA substrates are nearly saturated with cations under ideal conditions for UNG2 activity. However, the enzyme slows rather abruptly when the ionic content becomes too low or too high due to changes in the electrostatic environment that alter protein affinity for DNA. We discuss how ion occupancy on DNA is dependent on DNA length; thus, the sensitivity of UNG2 to cations is also dependent on DNA length. Finally, we found that Mg2+-induced changes in DNA base stacking and dynamics have minimal effects on UNG2, as these outcomes occur at ion concentrations that are much lower than is required for efficient enzyme activity. Altogether, our work demonstrates how cation-DNA interactions, which are likely common in the nucleus, are a key determinant of uracil base excision repair mediated by UNG2.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2332-2344"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Division of Labor among Fission Dynamins Based on Substrate Size. 基于基质尺寸的裂变动力学的分工。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-04-30 DOI: 10.1021/acs.biochem.4c00862

Meghadeepa Sarkar, Thomas J Pucadyil

{"title":"Division of Labor among Fission Dynamins Based on Substrate Size.","authors":"Meghadeepa Sarkar, Thomas J Pucadyil","doi":"10.1021/acs.biochem.4c00862","DOIUrl":"10.1021/acs.biochem.4c00862","url":null,"abstract":"Membrane fission is necessary for the formation of vesicles in the endolysosomal system and for the division of organelles like peroxisomes, mitochondria, and chloroplasts. In these processes, fission is managed by certain members of the dynamin superfamily of proteins (DSPs). These DSPs are soluble proteins that self-assemble into helical scaffolds that hydrolyze GTP and force the constriction of tubular membrane substrates, leading to their fission. Based on where they function, fission DSPs can be operationally categorized into vesicle dynamins (VDs) or organelle dynamins (ODs). Even though they share conserved domains and display largely similar enzymatic properties, recent results reveal fundamental differences with respect to the size of the tubular membrane substrate that certain VDs and ODs can sever. Substrate sizes encountered during vesicle formation and organelle division are quite different and could have served as physical constraints that forced the evolution of VDs and ODs. Here, we briefly review and rationalize mechanisms for the division of labor among DSPs.The structural basis for substrate size-dependent fission activity among VDs and ODs remains unclear and represents an attractive area for future research.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2117-2122"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-05-09 DOI: 10.1021/acs.biochem.5c00217

Sang-Choul Im, Hwei-Ming Peng, Lucy Waskell, Richard J Auchus

{"title":"Similar Rates of Second Electron Transfer and Single-Turnover Dehydroepiandrosterone Formation for Oxyferrous Human Cytochrome P450 17A1 (Steroid 17-Hydroxylase/17,20-lyase)-17-hydroxypregnenolone Complex with Either Human Cytochrome P450-Oxidoreductase or Human Cytochrome b5.","authors":"Sang-Choul Im, Hwei-Ming Peng, Lucy Waskell, Richard J Auchus","doi":"10.1021/acs.biochem.5c00217","DOIUrl":"10.1021/acs.biochem.5c00217","url":null,"abstract":"The 17-hydroxylase and 17,20-lyase activities of cytochrome P450 17A1 are required for androgen biosynthesis, which is the target of the prostate-cancer drug abiraterone acetate. Cytochrome b5 (b5) stimulates the 17,20-lyase activity 8-fold in reconstituted systems containing P450-oxidoreductase (POR); however, the mechanism of the b5 effect and the rate-limiting step(s) of these catalytic cycles are not known. Using stopped flow spectroscopy and rapid chemical quench under single-turnover conditions, we determined the effects of b5 on rates of individual steps of the 17-hydroxylase and 17,20-lyase reactions. Steps prior to and including oxygen binding were rapid for both reactions (>9 s-1), and rates of dehydroepiandrosterone release (4-5 s-1) were also fast and not increased by b5. Starting with 17-hydroxypregnenolone-bound oxyferrous P450 17A1, the electron transfer rate was slower from b5 than from POR (2.9 ± 0.2 versus 7.4 ± 0.1 s-1), whereas return to ferric P450 17A1 was faster with b5 than from POR (1.7 ± 0.3 versus 1.3 ± 0.1 s-1). Using the same conditions as electron transfer experiments for rapid chemical quench, rates of dehydroepiandrosterone formation were equivalent with reduced POR or b5 (2.4 ± 0.4 versus 2.3 ± 0.3 s-1, respectively); b5 reduced hydrogen peroxide formation under multiple turnover conditions. We conclude that rates of electron transfer and product formation for the 17,20-lyase reaction starting with reduced oxyferrous P450 17A1 are similar and partially rate-limiting to either POR or b5. These data suggest that the b5 effect on the 17,20-lyase reaction manifests only during multiple turnover conditions rather than enhancing single-turnover kinetics.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2306-2317"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Glycosylation Weakens Skp1 Homodimerization in Toxoplasma gondii by Interrupting a Fuzzy Interaction. 糖基化通过中断模糊相互作用削弱刚地弓形虫Skp1同型二聚化。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-04-29 DOI: 10.1021/acs.biochem.4c00859

Donovan A Cantrell, Ramona J Bieber Urbauer, Hyun W Kim, Robert J Woods, Jeffrey L Urbauer, Zachary A Wood, Christopher M West

{"title":"Glycosylation Weakens Skp1 Homodimerization in Toxoplasma gondii by Interrupting a Fuzzy Interaction.","authors":"Donovan A Cantrell, Ramona J Bieber Urbauer, Hyun W Kim, Robert J Woods, Jeffrey L Urbauer, Zachary A Wood, Christopher M West","doi":"10.1021/acs.biochem.4c00859","DOIUrl":"10.1021/acs.biochem.4c00859","url":null,"abstract":"Skp1/Cullin-1/F-Box protein (SCF) complexes represent a major class of E3 ubiquitin ligases responsible for proteomic control throughout eukaryotes. Target specificity is mediated by a large set of F-box proteins (FBPs) whose F-box domains interact with Skp1 in a conserved, well-organized fashion. In the social amoeba Dictyostelium, Skp1 is regulated by oxygen-dependent glycosylation which alters Skp1's FBP interactome and inhibits homodimerization that is mediated in part by an ordered interface which overlaps with that of FBPs. Based on sedimentation velocity experiments, Skp1 from the intracellular pathogen Toxoplasma gondii exhibits a homodimerization Kd comparable to that of a previously measured FBP/Skp1 interaction. Glycosylation of Skp1's disordered C-terminal region (CTR) distal to the ordered homodimer interface significantly weakens Skp1 homodimerization, an effect reproduced by CTR deletion. Replacement with a randomized CTR sequence retains high affinity excluding an extension of the ordered dimer interface. Substitution by poly serine weakens the homodimer to a degree equal to its deletion, indicating a composition dependent effect. The contribution of the CTR to Skp1 homodimerization is canceled by high salt consistent with an electrostatic mechanism. All-atom molecular dynamics simulations suggest that the CTR promotes homodimerization via charge cluster interactions. Taken together, the data indicate that glycosylation weakens homodimerization by disrupting a C-terminal fuzzy interaction that functions in tandem with the ordered dimer interface, thereby freeing Skp1 for FBP binding. Thus, the CTR contributes to Skp1/Skp1 and Skp1/FBP interactions via independent mechanisms that are each influenced by O2, indicating multiple constraints on the evolution of its sequence.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2262-2279"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeting Apicomplexan Parasites: Structural and Functional Characterization of Cryptosporidium Thioredoxin Reductase as a Novel Drug Target. 靶向顶复合体寄生虫：新型药物靶点隐孢子虫硫氧还蛋白还原酶的结构和功能表征。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-04-30 DOI: 10.1021/acs.biochem.5c00059

Federica Gabriele, Jala A Bogard, Marta Palerma, Matteo Ardini, Margaret E Byrne, Xian-Ming Chen, Pavel A Petukhov, Rodolfo Ippoliti, Francesco Angelucci, David L Williams

{"title":"Targeting Apicomplexan Parasites: Structural and Functional Characterization of Cryptosporidium Thioredoxin Reductase as a Novel Drug Target.","authors":"Federica Gabriele, Jala A Bogard, Marta Palerma, Matteo Ardini, Margaret E Byrne, Xian-Ming Chen, Pavel A Petukhov, Rodolfo Ippoliti, Francesco Angelucci, David L Williams","doi":"10.1021/acs.biochem.5c00059","DOIUrl":"10.1021/acs.biochem.5c00059","url":null,"abstract":"Cryptosporidiosis poses a significant health threat to young children and immunocompromised individuals due to the lack of effective therapies. Here, we demonstrate that the Cryptosporidium parvum redox system is fundamentally different from their human host. Humans possess independent glutathione (GSH) and thioredoxin (Trx) pathways. Cryptosporidium lacks authentic glutathione reductase (GR), and we hypothesize that it most likely utilizes the Trx reductase (TrxR) plus Trx couple to maintain GSH in its reduced state. Given the central role of CpTrxR in the parasite's redox homeostasis, we focus on its functional and structural characterization. We find that the combination of CpTrxR andC. parvum Trx efficiently reduces oxidized GSH, in effect functioning as a GR. Auranofin, a gold-containing compound, is known to kill parasites in culture, and here we demonstrate that CpTrxR is irreversibly inhibited by this compound. The crystallographic structures of CpTrxR, a type II TrxR characterized by the distinctive C-terminal -CGGGKCG motif found exclusively in apicomplexan parasites, including Plasmodium spp., the causative agents of malaria, are presented. Our study characterizes three unprecedented catalytically competent intermediates of the C-terminal tail in the so-called \"in\" conformations, providing insights into the structural and functional properties of type II TrxR. These findings offer valuable information for the design of CpTrxR inhibitors, addressing the pressing need for new therapeutic options against cryptosporidiosis, particularly in populations where current treatments are insufficiently effective.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2212-2225"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12092171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How Omecamtiv Modulates Myosin Motion. Omecamtiv如何调节肌球蛋白运动。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-05-06 DOI: 10.1021/acs.biochem.4c00807

Ritaban Halder, Arieh Warshel

{"title":"How Omecamtiv Modulates Myosin Motion.","authors":"Ritaban Halder, Arieh Warshel","doi":"10.1021/acs.biochem.4c00807","DOIUrl":"10.1021/acs.biochem.4c00807","url":null,"abstract":"Myosin VI is a unique reverse-directed motor protein in the myosin family. The D179Y mutation in Myosin VI is associated with deafness in mammals. This mutation destroys the processive motion of myosin and inhibits its functional activity due to an elevated phosphate release rate. The current work explores the way by which this mutation affects the phosphate release rate and changes the action of Myosin VI. Our study involves a wide range of approaches comprising free energy-based simulations, contact map analysis, binding energy investigation, structural inspection, renormalization simulation, multiple sequence alignment, and bioinformatics analysis. It is found that when the evolutionary conserved aspartic acid (D179) of Myosin VI is mutated to tyrosine (Y179), it leads to premature phosphate release from Myosin VI. Most importantly, the drug omecamtiv rescues the processivity of the mutant by slowing down the actin-independent phosphate release from Myosin VI. Thus, we also explore the molecular mechanism behind the premature phosphate release of the D179Y mutant of Myosin VI and the actin-independent slowing down of the phosphate release in the presence of omecamtiv. This phosphate release modulation is related to Myosin VI's processivity as found experimentally. Overall, our proposed model indicates that omecamtiv significantly alters the interaction between the P-loop of Myosin VI and the interfacial residues, which is the driving force behind the slowing down of the phosphate release of the D179Y mutant in the presence of omecamtiv. Finally, our study provides additional support to our proposal that the directionality of myosins is determined by the highest barrier along the cycle and not by any dynamical effect.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2318-2331"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Biochemical Studies of a Cyanobacterial Halogenase Support the Involvement of a Dimetal Cofactor. 一种蓝藻卤化酶的生化研究支持双金属辅助因子的参与。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-04-29 DOI: 10.1021/acs.biochem.4c00720

Michelle L Wang, Nathaniel R Glasser, Mrutyunjay A Nair, Carsten Krebs, J Martin Bollinger, Emily P Balskus

{"title":"Biochemical Studies of a Cyanobacterial Halogenase Support the Involvement of a Dimetal Cofactor.","authors":"Michelle L Wang, Nathaniel R Glasser, Mrutyunjay A Nair, Carsten Krebs, J Martin Bollinger, Emily P Balskus","doi":"10.1021/acs.biochem.4c00720","DOIUrl":"10.1021/acs.biochem.4c00720","url":null,"abstract":"Halogenation is a prominent transformation in natural product biosynthesis, with over 5000 halogenated natural products known to date. Biosynthetic pathways accomplish the synthetic challenge of selective halogenation, especially at unactivated sp3 carbon centers, using halogenase enzymes. The halogenase CylC, discovered as part of the cylindrocyclophane (cyl) biosynthetic pathway, performs a highly selective chlorination reaction on an unactivated sp3 carbon center and is proposed to use a dimetal cofactor. Putative dimetal halogenases are widely distributed across cyanobacterial biosynthetic pathways. However, rigorous in vitro biochemical and structural characterization of these enzymes has been challenging. Here, we report additional bioinformatic analyses of putative dimetal halogenases and the biochemical characterization of a newly identified CylC homologue. Site-directed mutagenesis identifies highly conserved putative metal-binding residues, and Mössbauer spectroscopy provides direct evidence for the presence of a diiron cofactor in these halogenases. These insights suggest mechanistic parallels between diiron and mononuclear nonheme iron halogenases, with the potential to guide further characterization and engineering of this unique subfamily of metalloenzymes.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2173-2180"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Obligately Tungsten-Dependent Enzymes─Catalytic Mechanisms, Models and Applications. 专性钨依赖酶─催化机理、模型及应用

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-05-05 DOI: 10.1021/acs.biochem.5c00116

Maciej Szaleniec, Johann Heider

{"title":"Obligately Tungsten-Dependent Enzymes─Catalytic Mechanisms, Models and Applications.","authors":"Maciej Szaleniec, Johann Heider","doi":"10.1021/acs.biochem.5c00116","DOIUrl":"10.1021/acs.biochem.5c00116","url":null,"abstract":"Tungsten-dependent enzymes incorporate a tungsten ion into their active site in the form of a complex with two pyranometallopterin (MPT) molecules, also known as tungsten cofactor (W-co). W-co-containing enzymes are found in several bacteria and archaea, predominantly in enzymes involved in anaerobic metabolism. While some enzymes occur with either molybdenum or tungsten in their active sites, we concentrate here on enzymes obligately depending on W-co, which are not functional as isoenzymes with Mo-co. These are represented by several subtypes of aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductase (BCRs) and acetylene hydratase (AHs). They catalyze either low-potential redox reactions or the unusual hydration reaction of acetylene. In this review, we analyze the catalytic and structural properties of these enzymes and focus on various mechanistic hypotheses proposed to describe their catalytic action, including hypothetical mechanistic patterns common to all of these enzymes. The biochemical characterization of the enzymes is supported by studies with functional inorganic models that help in the elucidation of their spectroscopic and catalytic features. Finally, we discuss a range of ongoing biotechnological applications utilizing obligately tungsten-dependent enzymes in producing value-added chemicals, indicating the expected advantages of incorporating these enzymes into biotechnological processes despite their intrinsic oxygen-sensitivity and the requirement of special recombinant expression platforms.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"2154-2172"},"PeriodicalIF":2.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemical Identification of [Fe(III)(OH)(H₂O)]²⁺ Complex Ion at the Ferroxidase Active Site in Cryo-EM Maps. [Fe(III)(OH)(H2O)]2+配合物在铁氧化酶活性位点的化学鉴定。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-04-29 DOI: 10.1021/acs.biochem.4c00738

Jimin Wang

引用次数: 0