Biochemistry Biochemistry最新文献

In Vivo Ribosome-Amplified MetaBOlism, RAMBO, Effect Observed by Real Time Pulse Chase, RTPC, NMR Spectroscopy. 体内核糖体放大代谢，RAMBO，实时脉冲追踪效应观察，RTPC，核磁共振波谱。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-27 DOI: 10.1021/acs.biochem.5c00086

Jianchao Yu, Nicholas Sciolino, Leonard Breindel, Qishan Lin, David S Burz, Alexander Shekhtman

引用次数: 0

Cryo-Electron Microscopy Provides Mechanistic Insights into Solution-Dependent Polymorphism and Cross-Aggregation Phenomena of the Human and Rat Islet Amyloid Polypeptides. 冷冻电子显微镜为人类和大鼠胰岛淀粉样多肽的溶液依赖性多态性和交叉聚集现象提供了机制见解。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-26 DOI: 10.1021/acs.biochem.5c00042

Dylan Valli, Saik Ann Ooi, Ibrahim Kaya, Asger Berg Thomassen, Himanshu Chaudhary, Tobias Weidner, Per E Andrén, Michał Maj

{"title":"Cryo-Electron Microscopy Provides Mechanistic Insights into Solution-Dependent Polymorphism and Cross-Aggregation Phenomena of the Human and Rat Islet Amyloid Polypeptides.","authors":"Dylan Valli, Saik Ann Ooi, Ibrahim Kaya, Asger Berg Thomassen, Himanshu Chaudhary, Tobias Weidner, Per E Andrén, Michał Maj","doi":"10.1021/acs.biochem.5c00042","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00042","url":null,"abstract":"Inhibitors targeting amyloids formed by the human Islet Amyloid Polypeptide (hIAPP) are promising therapeutic candidates for type 2 diabetes. Peptide formulations derived from the nonamyloidogenic rat IAPP (rIAPP) sequence are currently used as hIAPP mimetics to support insulin therapy. rIAPP itself acts as a peptide inhibitor; yet, the structural-level consequences of such inhibition, particularly its impact on amyloid polymorphism, have not been studied in detail. Here, we conduct coaggregation experiments with varying rIAPP-to-hIAPP concentration ratios and employ high-resolution cryo-electron microscopy (Cryo-EM) to elucidate the polymorphism of the resulting fibril structures. Our results demonstrate that the polymorphism of hIAPP amyloids is highly sensitive to the electrostatic environment, which can be modulated by buffer composition, the concentration of the inhibitor, and cosolvents such as hexafluoroisopropanol (HFIP). Under native conditions, rIAPP associates with hIAPP but does not cross-aggregate, resulting in fibrils primarily composed of hIAPP. Significant inhibition is observed at relatively high concentrations of rIAPP. However, trace amounts of HFIP disrupt this inhibition, leading to increased fibril concentrations due to the formation of cross-seeded products composed of both hIAPP and rIAPP, as evidenced by mass spectrometry and two-dimensional infrared (2D IR) spectroscopy. These findings highlight the critical role of experimental conditions, particularly the electrostatic environment, in modulating amyloid polymorphism, cross-seeding, and inhibition. By providing structural insights into these processes, this study advances our understanding of peptide aggregation and offers valuable guidance for the rational design of more effective therapeutic inhibitors targeting hIAPP-related amyloidosis.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140869","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

A Geranylated Natural Product Simamycin Disrupts the Allosteric Catalysis of tRNA-2-selenouridine Synthase SelU. 香叶酰化天然产物西霉素破坏trna -2-硒尿嘧啶合成酶SelU的变构催化作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-25 DOI: 10.1021/acs.biochem.5c00053

Stephen J Dansereau, Alexander Shekhtman, Francesco Epifano, Salvatore Genovese, Serena Fiorito, Thomas J Begley, Jia Sheng

{"title":"A Geranylated Natural Product Simamycin Disrupts the Allosteric Catalysis of tRNA-2-selenouridine Synthase SelU.","authors":"Stephen J Dansereau, Alexander Shekhtman, Francesco Epifano, Salvatore Genovese, Serena Fiorito, Thomas J Begley, Jia Sheng","doi":"10.1021/acs.biochem.5c00053","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00053","url":null,"abstract":"tRNA-2-selenouridine synthase (SelU) is a tRNA-modifying enzyme that is instrumental to bacterial translation by exploiting certain chalcogens. Specifically, this enzyme catalyzes the geranylation of 2-thiouridine at the wobble position of three bacterial tRNAs to enhance the recognition of codons ending in guanosine over adenosine using geranyl pyrophosphate as the cofactor. In addition, SelU is also the working enzyme for a selenation process at the same tRNA position in the presence of selenophosphate. How this enzyme conducts two mechanistically different reactions is a fundamentally interesting question. In order to gain more details about the substrate recognition of SelU, in this work, we identified a small natural compound simamycin (5'-O-geranyluridine) with strong interactions with this enzyme. Further, through biophysical affinity assays and NMR structural studies, we postulated an allosteric mechanism of SelU catalysis involving cooperativity among each domain and a conformational rearrangement around the active site of its N-terminal domain. This conclusion is supported by the bimolecular quenching constants, number of binding sites, and thermodynamic parameters calculated for this compound complexed with the N-terminal domain of SelU.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140868","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

Structural Insights into Selectively Targeting Candida albicans Hsp90. 选择性靶向白色念珠菌Hsp90的结构见解。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-21 DOI: 10.1021/acs.biochem.5c00015

Mark E Kowalewski, Sebastian Zagler, Matthew R Redinbo

{"title":"Structural Insights into Selectively Targeting Candida albicans Hsp90.","authors":"Mark E Kowalewski, Sebastian Zagler, Matthew R Redinbo","doi":"10.1021/acs.biochem.5c00015","DOIUrl":"https://doi.org/10.1021/acs.biochem.5c00015","url":null,"abstract":"The threat of drug-resistant pathogens continues to rise and underscores the need for new antimicrobial and antifungal strategies. Diverse chemical scaffolds have been shown with high affinity to bind the human heat-shock protein Hsp90. Orthologous proteins are present in microbial pathogens and have been shown to be particularly abundant in these organisms, suggesting they may serve as therapeutic targets. Here, we examine the potency and selectivity of human Hsp90 ligands for their capacity to bind to the nucleotide binding domain of Hsp90 from the pathogenic fungi, Candida albicans. Using a series of biochemical, structural, and fragment and in silico screening investigations, we define key chemical features that lead to effective C. albicans Hsp90 (CaHsp90) binding. We support these studies with crystal structures of five diverse human Hsp90 ligands in complex with CaHsp90, as well as the structure of this protein with a nonhydrolyzable ATP analog. We demonstrate the structural basis for the selectivity of the human Hsp90 inhibitor TAS116 for CaHsp90, features that may be exploited in the future development of improved CaHsp90 inhibitors.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118370","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

A Role for Two Conserved Arginine Residues in Protected Persulfide Transfer by SufE-Dependent SufS Cysteine Desulfurases. 两个保守的精氨酸残基在sufe依赖的SufS半胱氨酸脱硫酶的保护过硫转移中的作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-21 DOI: 10.1021/acs.biochem.4c00705

Rajleen K Gogar, Juliana V Conte, Nidhi Chhikara, Jack A Dunkle, Patrick A Frantom

{"title":"A Role for Two Conserved Arginine Residues in Protected Persulfide Transfer by SufE-Dependent SufS Cysteine Desulfurases.","authors":"Rajleen K Gogar, Juliana V Conte, Nidhi Chhikara, Jack A Dunkle, Patrick A Frantom","doi":"10.1021/acs.biochem.4c00705","DOIUrl":"10.1021/acs.biochem.4c00705","url":null,"abstract":"Under stress conditions, iron-sulfur cluster biogenesis in Escherichia coli is initiated by the cysteine desulfurase, SufS, via the SUF pathway. SufS is a type II cysteine desulfurase that catalyzes the PLP-dependent breakage of an l-cysteine C-S bond to generate l-alanine and a covalent active site persulfide. The cysteine desulfurase activity of SufS is activated by SufE, which accepts the covalent persulfide from SufS to regenerate the active site. Based on analysis of the SufS/SufE structure, it was hypothesized that two conserved arginine residues in the SufS active site, R56 and R359, could be important for persulfide transfer from SufS to SufE by regulating the positioning of the α3-α4 loop on SufS. To investigate this hypothesis, site-directed mutagenesis was used to obtain R56A/K and R359A/K SufS variants. Alanine substitution at either position caused defects to SufE-dependent SufS activity, with more conservative lysine substitutions resulting in varying levels of rescued activity. Fluorescence polarization binding assays showed that the loss of SufS activity was not due to a defect in forming the SufS/SufE complex. Surprisingly, the R359A substitution resulted in a 10-fold improvement in the KD value for complex formation. The structure of R359A SufS explains this result as it exhibits a conformational change in the α3-α4 loop allowing SufE better access to the SufS active site. Taken together, the kinetic, binding, and structural data support a mechanism where R359 plays a role in linking SufS catalysis with modulation of the α3-α4 loop to promote a close-approach interaction of SufS and SufE conducive to persulfide transfer.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109047","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

Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge. 氟喹诺酮衍生物KG022与单凸起rna的特异性相互作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-05-20 Epub Date: 2025-03-11 DOI: 10.1021/acs.biochem.4c00669

Rika Ichijo, Gota Kawai

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

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

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