Biochemistry Biochemistry最新文献_第3页

Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00529

Conor B Abraham, Emily Lewkowicz, Olga Gursky, John E Straub

{"title":"Elucidating the Mechanism of Recognition and Binding of Heparin to Amyloid Fibrils of Serum Amyloid A.","authors":"Conor B Abraham, Emily Lewkowicz, Olga Gursky, John E Straub","doi":"10.1021/acs.biochem.4c00529","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00529","url":null,"abstract":"Amyloid diseases feature pathologic deposition of normally soluble proteins and peptides as insoluble fibrils in vital organs. Amyloid fibrils co-deposit with various nonfibrillar components including heparan sulfate (HS), a glycosaminoglycan that promotes amyloid formation in vitro for many unrelated proteins. HS-amyloid interactions have been proposed as a therapeutic target for inflammation-linked amyloidosis wherein N-terminal fragments of serum amyloid A (SAA) protein deposit in the kidney and liver. The structural basis for these interactions is unclear. Here, we exploit the high-resolution cryoelectron microscopy (cryo-EM) structures of ex vivo murine and human SAA fibrils in a computational study employing molecular docking, Brownian dynamics simulations, and molecular dynamics simulations to elucidate how heparin, a highly sulfated HS mimetic, recognizes and binds to amyloid protein fibrils. Our results demonstrate that negatively charged heparin chains bind to linear arrays of uncompensated positively charged basic residues along the spines of amyloid fibrils facilitated by electrostatic steering. The predicted heparin binding sites match the location of unidentified densities observed in cryo-EM maps of SAA amyloids, suggesting that these extra densities represent bound HS. Since HS is constitutively found in various amyloid deposits, our results suggest a common mechanism for HS-amyloid recognition and binding.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845299","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

ATAD2 and TWIST1 Interaction Promotes MYC Activation in Colorectal Carcinoma.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 DOI: 10.1021/acs.biochem.4c00360

Anirban Roy, Babu Sudhamalla

{"title":"ATAD2 and TWIST1 Interaction Promotes MYC Activation in Colorectal Carcinoma.","authors":"Anirban Roy, Babu Sudhamalla","doi":"10.1021/acs.biochem.4c00360","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00360","url":null,"abstract":"ATPase family AAA domain-containing protein 2 (ATAD2) is significantly up-regulated in many cancer types and contributes to poor patient outcomes. ATAD2 exhibits a multidomain architecture comprising an N-terminal acidic domain, two AAA+ ATPase domains, a bromodomain, and a C-terminal domain. The AAA+ ATPase domain facilitates protein oligomerization and ATP binding, while the bromodomain recognizes acetylated lysine in histones and nonhistone proteins. ATAD2 involvement in cancer extends across multiple signaling pathways, such as Rb-E2F1, PI3K/AKT, and TGF-β1/Smad3, which promotes cell proliferation and cancer progression. Herein, we report that ATAD2 directly interacts with TWIST1, and both N-terminal regions of proteins mediate the interaction. Immunofluorescence experiments suggested that ATAD2 and TWIST1 primarily colocalize in the nucleus. Notably, our qPCR results revealed the functional significance of ATAD2-TWIST1 interaction by demonstrating their synergistic effect on the transcriptional activation of MYC in colorectal carcinoma cell lines. Moreover, the ChIP-qPCR result further indicates that ATAD2 and TWIST1 significantly localize in the promoter of the MYC gene. In addition, analysis of The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) data suggests a correlation between ATAD2, TWIST1, and MYC overexpression and poor survival rates in colorectal carcinoma. Lastly, the overexpression of ATAD2 and TWIST1 enhances cell proliferation, emphasizing their role in colorectal carcinoma progression through MYC activation. Together, these results suggest that ATAD2 is a crucial factor in TWIST1-dependent MYC gene activation, resulting in an active ATAD2-TWIST1-MYC axis that contributes to colon cancer cell proliferation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833201","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

Molecular Basis for Cγ-N Bond Formation by PLP-Dependent Enzyme LolC.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-06 DOI: 10.1021/acs.biochem.4c00588

Yueqi Xu, Shaonan Liu, Jinmin Gao, Yang Hai

{"title":"Molecular Basis for Cγ-N Bond Formation by PLP-Dependent Enzyme LolC.","authors":"Yueqi Xu, Shaonan Liu, Jinmin Gao, Yang Hai","doi":"10.1021/acs.biochem.4c00588","DOIUrl":"10.1021/acs.biochem.4c00588","url":null,"abstract":"Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyze a diverse array of biochemical transformations, making them invaluable biocatalytic tools for the synthesis of complex bioactive compounds. Here, we report the biochemical characterization of LolC, a PLP-dependent γ-synthase involved in the biosynthesis of loline alkaloids. LolC catalyzes the formation of a Cγ-N bond between O-acetyl--homoserine (OAH) and l-proline, generating a diamino diacid intermediate. Our findings reveal that LolC exhibits strict specificity for proline and its analogues, contrasting with the substrate promiscuity of closely related Cγ-C bond-forming enzyme Fub7. Structural analysis, using an AlphaFold model, identifies key differences in the substrate entrance tunnel of LolC, which is amphiphilic and distinct from the hydrophobic tunnel in Fub7. A mutagenesis study further highlights the functional divergence of a key active site residue between these enzymes. These results provide new insights into the substrate specificity and catalytic function of LolC, offering a valuable comparison to Fub7 and advancing our understanding of PLP-dependent enzymes involved in γ-substitution reactions.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3348-3356"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783333","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

Identification of an Intrinsically Disordered Region (IDR) in Arginyltransferase 1 (ATE1).

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-06 DOI: 10.1021/acs.biochem.4c00512

Misti Cartwright, Rinky Parakra, Ayomide Oduwole, Fangliang Zhang, Daniel J Deredge, Aaron T Smith

{"title":"Identification of an Intrinsically Disordered Region (IDR) in Arginyltransferase 1 (ATE1).","authors":"Misti Cartwright, Rinky Parakra, Ayomide Oduwole, Fangliang Zhang, Daniel J Deredge, Aaron T Smith","doi":"10.1021/acs.biochem.4c00512","DOIUrl":"10.1021/acs.biochem.4c00512","url":null,"abstract":"Arginyltransferase 1 (ATE1) catalyzes arginylation, an important posttranslational modification (PTM) in eukaryotes that plays a critical role in cellular homeostasis. The disruption of ATE1 function is implicated in mammalian neurodegenerative disorders and cardiovascular maldevelopment, while posttranslational arginylation has also been linked to the activities of several important human viruses such as SARS-CoV-2 and HIV. Despite the known significance of ATE1 in mammalian cellular function, past biophysical studies of this enzyme have mainly focused on yeast ATE1, leaving the mechanism of arginylation in mammalian cells unclear. In this study, we sought to structurally and biophysically characterize mouse (Mus musculus) ATE1. Using size-exclusion chromatography (SEC), small-angle X-ray scattering (SAXS), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), assisted by AlphaFold modeling, we found that mouse ATE1 is structurally more complex than yeast ATE1. Importantly, our data indicate the existence of an intrinsically disordered region (IDR) in all mouse ATE1 splice variants. However, comparative HDX-MS analyses show that yeast ATE1 does not have such an IDR, consistent with prior X-ray, cryo-EM, and SAXS analyses. Furthermore, bioinformatics approaches reveal that mammalian ATE1 sequences, as well those as in a large majority of other eukaryotes, contain an IDR-like sequence positioned in proximity to the ATE1 GNAT active-site fold. Computational analysis suggests that the IDR facilitates the formation of a complex between ATE1 and tRNAArg, adding a new complexity to the ATE1 structure and providing new insights for future studies of ATE1 functions.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3236-3249"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789416","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

FRET Probes for Detection of Both Active and Inactive Zika Virus Protease. 用于检测活性和非活性寨卡病毒蛋白酶的 FRET 探针。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-26 DOI: 10.1021/acs.biochem.4c00415

Kristalle G Cruz, Kevin Alexander, Sparsh Makhaik, Jeanne A Hardy

{"title":"FRET Probes for Detection of Both Active and Inactive Zika Virus Protease.","authors":"Kristalle G Cruz, Kevin Alexander, Sparsh Makhaik, Jeanne A Hardy","doi":"10.1021/acs.biochem.4c00415","DOIUrl":"10.1021/acs.biochem.4c00415","url":null,"abstract":"Proteases are a privileged class of enzymes due to their catalysis of an irreversible post translational modification, namely cleavage of substrate proteins. Protease activity is essential for human pathways including inflammation, blood clotting, and apoptosis. Proteases are also essential for the propagation of many viruses due to their role in cleavage of the viral polyprotein. For these reasons, proteases are an attractive and highly exploited class of drug targets. To fully harness the power of proteases as drug targets, it is essential that their presence and function are detectable throughout the course of the protease lifetime, from inactive zymogen to the fully cleaved (mature) protease. A number of methods for detection of proteases have been developed, however, many rely on catalytic activity, so are not useful throughout the proteolytic life cycle. Here, we build on our observation that the MH1 family of benzofuran-aminothiazolopyridine inhibitors of Zika virus protease (ZVP) undergo a unique FRET interaction with tryptophan residues in the protease. The full FRET signal is only observed in higher potency binding interactions. Moreover, this approach can distinguish two inactive variants of ZVP based on their folded or unfolded state. These studies also probe the physicochemical basis of the FRET signal. Exploiting these types of FRET interactions may offer an orthogonal approach for detection of this protease, which takes advantage of the relationship between the novel ligand and the core of the protein and is therefore useful throughout the protease maturation cycle. Depending on chemical properties, this approach may be applicable in other proteases and other protein classes.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3300-3309"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714764","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 Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase. 磷酸丙酮酸脱羧酶 RhiEF 的结构分析：对依赖于焦磷酸硫胺素的异源同分异构体脱羧酶的初步认识。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-25 DOI: 10.1021/acs.biochem.4c00559

Akira Nakamura, Ayaka Shiina, Tsubasa Fukaya, Yurie Seki, Mizuki Momiyama, Shuichi Kojima

{"title":"Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase.","authors":"Akira Nakamura, Ayaka Shiina, Tsubasa Fukaya, Yurie Seki, Mizuki Momiyama, Shuichi Kojima","doi":"10.1021/acs.biochem.4c00559","DOIUrl":"10.1021/acs.biochem.4c00559","url":null,"abstract":"The RhiE and RhiF proteins work together as RhiEF and function as a thiamine pyrophosphate (TPP)-dependent phosphonopyruvate decarboxylase to produce phosphonoacetaldehyde in the rhizocticin biosynthesis pathway. In this study, we determined the crystal structure of the RhiEF complexed with TPP and Mg2+. RhiEF forms a dimer of heterodimers, and the cofactor TPP is bound at the heterotetrameric subunit interface. Structural analysis of RhiEF revealed that the RhiE and RhiF moieties correspond to the pyrimidine-binding (PYR) and pyrophosphate-binding (PP) domains commonly found in TPP-dependent enzymes, respectively, as predicted by amino acid sequence alignment analysis. In contrast to other TPP-dependent enzymes with known structures, RhiEF has no domains other than the PYR and PP domains. Furthermore, structure-based evolutionary and sequence-based phylogenetic analyses have suggested that heteromultimeric enzymes such as RhiEF are ancestral types. These results indicate that RhiEF is one of the smallest and most ancient TPP-dependent decarboxylases. Based on the structural comparisons of RhiEF with other TPP-dependent decarboxylases, we identified the amino acid residues responsible for the catalytic mechanism of TPP-dependent decarboxylation in RhiEF.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3250-3260"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714765","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

Flavin-Mediated Reductive Deiodination: Conformational Events and Reactivity Pattern in the Active Site of Human Iodotyrosine Deiodinase. 黄素介导的还原脱碘反应：人类碘酪氨酸脱碘酶活性位点的构象变化和反应模式。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-27 DOI: 10.1021/acs.biochem.4c00639

Soumyajit Karmakar, Sabyashachi Mishra

{"title":"Flavin-Mediated Reductive Deiodination: Conformational Events and Reactivity Pattern in the Active Site of Human Iodotyrosine Deiodinase.","authors":"Soumyajit Karmakar, Sabyashachi Mishra","doi":"10.1021/acs.biochem.4c00639","DOIUrl":"10.1021/acs.biochem.4c00639","url":null,"abstract":"Human iodotyrosine deiodinase (hIYD) catalyzes the reductive deiodination of iodotyrosine using a flavin mononucleotide cofactor to maintain the iodine concentration in the body. Mutations in the hIYD gene are linked to human hypothyroidism, emphasizing its role in thyroid function regulation. The present work employs microsecond-scale molecular dynamics simulations and quantum chemical calculations to elucidate the conformational dynamics and reactivity in the active site at various stages of hIYD enzymatic cycle. The flavin is found to employ a unique butterfly motion of its isoalloxazine ring accompanied by a novel active-and-resting state of its ribose 2'-OH group at different stages of the enzymatic cycle. The flavin dynamics are found to control substrate binding affinity, the active site lid closure, and NADPH recognition. The predicted hIYD model shows enhanced stabilization of NADPH due to additional interactions with the N-terminal and intermediate domains. The enzyme uses a group of basic residues (R100, R101, R104, K182, and R279) to stabilize flavin in different stages of catalysis, suggesting potential mutations to control enzyme activity. The reactivity descriptors and stereoelectronic analysis predict the N5 nitrogen of flavin as a proton source during the reductive deiodination, while the anisotropic charge distribution on the halogen atom has negligible structural and electronic effects. The present findings provide key insights into the molecular basis of hIYD activity and lay the groundwork for future research aimed at therapeutic interventions and industrial applications.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3310-3323"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724507","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

Flavones Suppress Aggregation and Amyloid Fibril Formation of Human Lysozyme under Macromolecular Crowding Conditions. 黄酮类化合物抑制大分子拥挤条件下人溶菌酶的聚集和淀粉样纤维的形成

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-10-09 DOI: 10.1021/acs.biochem.4c00362

Shabnam, Rajiv Bhat

{"title":"Flavones Suppress Aggregation and Amyloid Fibril Formation of Human Lysozyme under Macromolecular Crowding Conditions.","authors":"Shabnam, Rajiv Bhat","doi":"10.1021/acs.biochem.4c00362","DOIUrl":"10.1021/acs.biochem.4c00362","url":null,"abstract":"The crowded milieu of a biological cell significantly impacts protein aggregation and interactions. Understanding the effects of macromolecular crowding on the aggregation and fibrillation of amyloidogenic proteins is crucial for the treatment of many amyloid-related disorders. Most in vitro studies of protein amyloid formation and its inhibition by small molecules are conducted in dilute buffers, which do not mimic the complexity of the cellular environment. In this study, we used PEGs to simulate macromolecular crowding and examined the inhibitory effects of flavones DHF, baicalein, and luteolin on human lysozyme (HuL) aggregation at pH 2. Naturally occurring flavones have been effective inhibitors of amyloid formation in some proteins. Our findings indicate that while flavones inhibit HuL aggregation and fibrillation in dilute buffer solutions, complete inhibition is observed with a combination of flavones and PEGs, as shown by ThT fluorescence, light scattering, TEM, and AFM studies. The species formed in the presence of PEG 8000 and flavones were less hydrophobic, less toxic, and α-helix-rich compared to control samples, which were hydrophobic and β-sheet-rich, as demonstrated by ANS hydrophobicity, MTT assay, and CD spectroscopy. Fluorescence titration studies of flavones with HuL showed a significant increase in binding constant values under crowding conditions. These findings highlight the importance of macromolecular crowding in modulating protein aggregation and amyloid inhibition. Further studies using disease-causing mutants of HuL and other amyloidogenic proteins are needed to explore the role of macromolecular crowding in small-molecule-mediated modulation and inhibition of protein aggregation and amyloid formation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3194-3212"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386373","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

Hydrated Magnesium Ion-Uracil and Magnesium Chloride-Uracil Clusters Revealed by Ab Initio Study. 通过 Ab Initio 研究发现的水合镁离子-乌拉基尔和氯化镁-乌拉基尔簇。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-11-26 DOI: 10.1021/acs.biochem.4c00374

Lei Hu, Xiao-Yang Xu, Ren-Zhong Li

{"title":"Hydrated Magnesium Ion-Uracil and Magnesium Chloride-Uracil Clusters Revealed by Ab Initio Study.","authors":"Lei Hu, Xiao-Yang Xu, Ren-Zhong Li","doi":"10.1021/acs.biochem.4c00374","DOIUrl":"10.1021/acs.biochem.4c00374","url":null,"abstract":"The study focuses on the interaction between canonical uracil and its rare tautomers with Mg2+ and MgCl2 in the microcosmic water environment and aims to elucidate how ions interact with nucleobase and the cation-anion correlation effect involved using density functional theory calculations. The structures of the Ura-Mg2+(H2O)0-6 and Ura-MgCl2(H2O)0-6 clusters are characterized and show that the water molecules preferentially interact with Mg2+/MgCl2, and Mg2+ adopts a hexacoordination pattern in both Ura-Mg2+(H2O)0-6 and Ura-MgCl2(H2O)0-6 clusters. When uracil interacts with Mg2+ in (H2O)0-6 environments, it tends to favor the formation of keto-enol structures. However, in the presence of Cl- cooperating with Mg2+, the Ura-MgCl2(H2O)0-6 complexes prefer to form diketo structures. The proton transfer mechanism shows that the initial solvation can promote the change from the keto-enol structure to the diketo structure, which is strengthened by the analysis of the Ura-Mg2+(H2O)6 and Ura-MgCl2(H2O)6 structures in the aqueous phase using the PCM model. Additionally, reduced density gradient, atom in molecules, and energy decomposition analysis combined with charge transfer analysis were carried out to obtain the variation law of the interactions between Mg2+ and Ura with the water number increasing, thereby revealing the interaction mechanism of uracil with magnesium ion and the effect of Cl- on the interaction between Mg2+ and uracil.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3395-3409"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724508","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

Initiation, Propagation, and Termination in the Chemistry of Radical SAM Enzymes.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-17 Epub Date: 2024-12-03 DOI: 10.1021/acs.biochem.4c00518

Mark W Ruszczycky, Hung-Wen Liu

引用次数: 0