Biochemistry Biochemistry最新文献_第10页

Identification of a Hidden, Highly Aggregation-Prone Intermediate of Full-Length TDP-43 That Triggers its Misfolding and Amyloid Aggregation. 鉴定全长 TDP-43 的一个隐藏的、高度易聚集的中间体，它能触发 TDP-43 的错误折叠和淀粉样蛋白聚集。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-12 DOI: 10.1021/acs.biochem.4c00389

Abhilasha A Doke, Santosh Kumar Jha

{"title":"Identification of a Hidden, Highly Aggregation-Prone Intermediate of Full-Length TDP-43 That Triggers its Misfolding and Amyloid Aggregation.","authors":"Abhilasha A Doke, Santosh Kumar Jha","doi":"10.1021/acs.biochem.4c00389","DOIUrl":"10.1021/acs.biochem.4c00389","url":null,"abstract":"In cells, TDP-43 is a crucial protein that can form harmful amyloid aggregates linked to fatal and incurable human neurodegenerative disorders. Normally, TDP-43 exists in a smaller soluble native state that prevents aggregation. However, aging and stress can destabilize this native state, leading to the formation of disease-causing amyloid aggregates via the formation of partially unfolded, high-energy intermediates with a greater tendency to aggregate. These intermediates are crucial in the early stages of amyloid formation and are challenging to study due to their low stability. Understanding the structure of these early aggregation-prone states of TDP-43 is essential for designing effective treatments for TDP-43 proteinopathies. Targeting these initial intermediates could be more effective than focusing on fully formed amyloid aggregates. By disrupting the aggregation process at this early stage, we may be able to prevent the progression of diseases related to TDP-43 aggregation. Hence, we decided to uncover the hidden, high-energy intermediates in equilibrium with the native states of TDP-43 by modulating the thermodynamic stability of the soluble native dimer (N form) and monomeric molten globular state (MG form) of full-length TDP-43. The thermodynamic modulation performed in the current study successfully revealed the highly aggregation-prone intermediate of full-length TDP-43, i.e., PUF. Moreover, we observed that along with high aggregation propensity, the aggregation kinetics and mechanisms of PUF differ from previously identified intermediates of full-length TDP-43 (the MG and I forms). The information regarding the initial aggregation-prone state of full-length TDP-43 could lead to therapies for amyloid diseases by halting early protein aggregation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3100-3113"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612587","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

Directed Evolution of an Adenylation Domain Alters Substrate Specificity and Generates a New Catechol Siderophore in Escherichia coli. 腺苷酸化域的定向进化改变了大肠杆菌的底物特异性并产生了一种新的儿茶酚苷元。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-21 DOI: 10.1021/acs.biochem.4c00499

Erin Conley, Caryn S Wadler, Bailey A Bell, Ivy Lucier, Caroline Haynie, Sophie Eldred, Valerie Nguyen, Tim S Bugni, Michael G Thomas

{"title":"Directed Evolution of an Adenylation Domain Alters Substrate Specificity and Generates a New Catechol Siderophore in Escherichia coli.","authors":"Erin Conley, Caryn S Wadler, Bailey A Bell, Ivy Lucier, Caroline Haynie, Sophie Eldred, Valerie Nguyen, Tim S Bugni, Michael G Thomas","doi":"10.1021/acs.biochem.4c00499","DOIUrl":"10.1021/acs.biochem.4c00499","url":null,"abstract":"Nonribosomal peptide synthetases (NRPS) biosynthesize numerous natural products with therapeutic, agricultural, and industrial significance. Reliably altering substrate selection in these enzymes has been a longstanding goal, as this would enable the production of tailor-made peptides with desired activities. In this study, the NRPS EntF and the associated biosynthesis of the siderophore enterobactin (ENT) were used as a model system to interrogate substrate selection by an adenylation (A) domain. We employed a directed evolution pipeline that harnesses an in vivo genetic selection for siderophore production to alter A domain substrate selection. Surprisingly, this led to the formation of a new, physiologically active catechol siderophore in Escherichia coli. We characterized the enzyme variants in vitro and demonstrated transferability of our findings to the well-studied TycC and GrsB NRPSs. This work identifies critical binding pocket residues that allow for altered substrate selection in our model system and expands upon our understanding of iron acquisition in E. coli.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3126-3135"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680313","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

Rigidifying the β2-α2 Loop in the Mouse Prion Protein Slows down Formation of Misfolded Oligomers. 使小鼠朊病毒蛋白中的β2-α2环刚性化，减缓错误折叠低聚物的形成

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-20 DOI: 10.1021/acs.biochem.4c00435

Suman Pal, Jayant B Udgaonkar

{"title":"Rigidifying the β2-α2 Loop in the Mouse Prion Protein Slows down Formation of Misfolded Oligomers.","authors":"Suman Pal, Jayant B Udgaonkar","doi":"10.1021/acs.biochem.4c00435","DOIUrl":"10.1021/acs.biochem.4c00435","url":null,"abstract":"Transmissible Spongiform Encephalopathies are fatal neurodegenerative diseases caused by the misfolding of the cellular prion protein (PrPC) into its pathological isoform (PrPSc). Efficient transmission of PrPSc occurs within the same species, but a species barrier limits interspecies transmission. While PrP structure is largely conserved among mammals, variations at the β2-α2 loop are observed, and even minor changes in the amino acid sequence of the β2-α2 loop can significantly affect transmission efficiency. The present study shows that the introduction of the elk/deer-specific amino acid substitutions at positions 169 (Ser to Asn) and 173 (Asn to Thr) into the mouse prion protein, which are associated with the structural rigidity of the β2-α2 loop, has a substantial impact on protein dynamics as well as on the misfolding pathways of the protein. Native state hydrogen-deuterium exchange studies coupled with mass spectrometry, show that the rigid loop substitutions stabilize not only the β2-α2 loop but also the C-terminal end of α3, suggesting that molecular interactions between these two segments are strengthened. Moreover, the energy difference between the native state and multiple misfolding-prone partially unfolded forms (PUFs) present at equilibrium, is increased. The decreased accessibility of the PUFs from the native state leads to a slowing down of the misfolding of the protein. The results of this study provide important insights into the early events of conformational conversion of prion protein into β-rich oligomers, and add to the evidence that the β2-α2 loop is a key determinant in prion protein aggregation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3114-3125"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674587","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

Channel Gating in a Post-Translational Protein Translocase 翻译后蛋白转位酶中的通道门控

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 DOI: 10.1021/acs.biochem.9b0014910.1021/acs.biochem.9b00149

Shu-ou Shan*,

引用次数: 0

Probing Aromatic Side Chains Reveals the Site-Specific Melting in the SUMO1 Molten Globule. 探测芳香族侧链可揭示 SUMO1 熔融球中的特定位点熔化。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-14 DOI: 10.1021/acs.biochem.4c00366

Simran Arora, Sri Rama Koti Ainavarapu

{"title":"Probing Aromatic Side Chains Reveals the Site-Specific Melting in the SUMO1 Molten Globule.","authors":"Simran Arora, Sri Rama Koti Ainavarapu","doi":"10.1021/acs.biochem.4c00366","DOIUrl":"10.1021/acs.biochem.4c00366","url":null,"abstract":"The conventional idea that a well-defined protein structure governs its functions is being challenged by the evolving significance of conformational flexibility and disorder in influencing protein activity. Here, we focus on the Small Ubiquitin-like MOdifier 1 (SUMO1) protein, a post-translational modifier, which binds various target proteins during the process of SUMOylation. We present evidence supporting the presence of both folded and \"ordered\" molten globule (MG) states in SUMO1 under physiological conditions. We investigate the MG state using a combination of near-UV and far-UV circular dichroism (CD) experiments. Moreover, we dissect the information from the near-UV CD data to gain specific insights about the MG intermediate. This is achieved by mutating specific aromatic amino acids, particularly creating a single-tyrosine mutant S1Y51 (by introducing Y21F and Y91F mutations) and a tryptophan mutant S1F66W. Spectroscopic studies of the mutants as a function of temperature revealed multiple insights. The transition from the folded to the MG state involves a site-specific loss of tertiary packing near Y51 but the region surrounding F66 retained most of its tertiary contacts, suggesting an ordered MG structure. We further demonstrate the increased solvent exposure of Y51 in the MG state by using time-resolved fluorescence and steady-state quenching experiments. The observed conformational flexibility and solvent accessibility, particularly around Y51 that is known to be involved in binding the cognate ligands such as PIASX and its peptide analogues, have biological and functional implications in mediating protein-protein interactions during the SUMOylation process.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3090-3099"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612588","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

Inactivation of CYP2D6 by Berberrubine and the Chemical Mechanism. 小檗碱对 CYP2D6 的灭活作用及其化学机制

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-21 DOI: 10.1021/acs.biochem.4c00450

Jinqiu Rao, Tianwang Wang, Leran Yu, Kai Wang, Feng Qiu

{"title":"Inactivation of CYP2D6 by Berberrubine and the Chemical Mechanism.","authors":"Jinqiu Rao, Tianwang Wang, Leran Yu, Kai Wang, Feng Qiu","doi":"10.1021/acs.biochem.4c00450","DOIUrl":"10.1021/acs.biochem.4c00450","url":null,"abstract":"Berberrubine (BRB), belonging to the benzylisoquinoline alkaloid, is a main metabolite of berberine in vivo. BRB was previously proven to undergo metabolic activation mediated by P450s. In this study, the chemical interactions between BRB and CYP2D6 enzyme were investigated. First, a variety of P450s participated in the metabolism of berberine transformed to BRB, but CYP2D6 was the most involved enzyme. A time-, concentration-, and nicotinamide adenine dinucleotide phosphate (NADPH)-dependent inhibition of CYP2D6 was caused by BRB. The inhibitory effect of BRB on CYP2D6 was irreversible. The maximum reaction rate constants of inactivation (kinact) and half-maximal inactivation (KI) of BRB on CYP2D6 were 0.0410 min-1 and 3.798 μM, respectively. Metoprolol, a classic substrate of CYP2D6, attenuated CYP2D6 from inactivation by BRB. Glutathione (GSH) and catalase/superoxide dismutase failed to protect against the inactivation of CYP2D6 caused by BRB. Three cys-based adducts derived from the reaction of electrophilic metabolites of BRB with CYP2D6 were detected by ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS. The reactive metabolites derived from BRB might be responsible for the inactivation of CYP2D6. In summary, BRB was characterized as a mechanism-based inactivator of CYP2D6.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3078-3089"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680315","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

Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product. 桧烯合成酶的结构和功能--一种产生高强度 [3.1.0] 双环产物的单萜环化酶。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-11-11 DOI: 10.1021/acs.biochem.4c00476

Matthew N Gaynes, Kristin R Osika, David W Christianson

{"title":"Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product.","authors":"Matthew N Gaynes, Kristin R Osika, David W Christianson","doi":"10.1021/acs.biochem.4c00476","DOIUrl":"10.1021/acs.biochem.4c00476","url":null,"abstract":"Sabinene is a plant natural product with a distinctive strained [3.1.0] bicyclic ring system that is used commercially as a spicy and pine-like fragrance with citrus undertones. This unusual monoterpene has also been studied as an antifungal and anti-inflammatory agent as well as a next-generation biofuel. In order to understand the molecular determinants of [3.1.0] bicyclic ring formation in sabinene biosynthesis, we now report three X-ray crystal structures of sabinene synthase from Western red cedar, Thuja plicata (TpSS), with open and partially closed active site conformations at 2.21-2.72 Å resolution. We additionally report the complete biochemical characterization of sabinene synthase, including steady-state kinetics, active site mutagenesis, and product array profiling. The catalytic metal ion requirement is unexpectedly broad for a class I terpene cyclase: optimal catalytic activity was measured using Mn2+ or Co2+, with more modest activity observed using Mg2+ or Ni2+. Kinetic parameters were determined for both full-length TpSS and a deletion variant lacking the putative N-terminal plastidial targeting sequence, designated ΔTpSS. Monoterpene product profiles for both indicated similar product arrays independent of the catalytic metal ion used, with sabinene comprising nearly 90% of the total products generated. Site-directed mutagenesis was utilized to probe the function of active site residues, and several mutants yielded altered product arrays. Most notably, the G458A substitution converted ΔTpSS into a high-activity α-pinene synthase. α-Pinene contains a bicyclic [3.1.1] ring system; structural and mechanistic analyses suggest a molecular rationale for the reprogrammed transannulation reaction, leading to the alternative bicyclic product.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3147-3159"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11614673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142612589","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

Delivery Aspects for Implementing siRNA Therapeutics for Blood Diseases. 实施血液病 siRNA 治疗的传输方面。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 Epub Date: 2024-10-10 DOI: 10.1021/acs.biochem.4c00327

Saba Abbasi Dezfouli, Marcel E Michailides, Hasan Uludag

{"title":"Delivery Aspects for Implementing siRNA Therapeutics for Blood Diseases.","authors":"Saba Abbasi Dezfouli, Marcel E Michailides, Hasan Uludag","doi":"10.1021/acs.biochem.4c00327","DOIUrl":"10.1021/acs.biochem.4c00327","url":null,"abstract":"Hematological disorders result in significant health consequences, and traditional therapies frequently entail adverse reactions without addressing the root cause. A potential solution for hematological disorders characterized by gain-of-function mutations lies in the emergence of small interfering RNA (siRNA) molecules as a therapeutic option. siRNAs are a class of RNA molecules composed of double-stranded RNAs that can degrade specific mRNAs, thereby inhibiting the synthesis of underlying disease proteins. Therapeutic interventions utilizing siRNA can be tailored to selectively target genes implicated in diverse hematological disorders, including sickle cell anemia, β-thalassemia, and malignancies such as lymphoma, myeloma, and leukemia. The development of efficient siRNA silencers necessitates meticulous contemplation of variables such as the RNA backbone, stability, and specificity. Transportation of siRNA to specific cells poses a significant hurdle, prompting investigations of diverse delivery approaches, including chemically modified forms of siRNA and nanoparticle formulations with various biocompatible carriers. This review delves into the crucial role of siRNA technology in targeting and treating hematological malignancies and disorders. It sheds light on the latest research, development, and clinical trials, detailing how various pharmaceutical approaches leverage siRNA against blood disorders, mainly concentrating on cancers. It outlines the preferred molecular targets and physiological barriers to delivery while emphasizing the growing potential of various therapeutic delivery methods. The need for further research is articulated in the context of overcoming the shortcomings of siRNA in order to enrich discussions around siRNA's role in managing blood disorders and aiding the scientific community in advancing more targeted and effective treatments.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3059-3077"},"PeriodicalIF":2.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142398687","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

Channel Gating in a Post-Translational Protein Translocase. 翻译后蛋白转位酶中的通道门控。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 DOI: 10.1021/acs.biochem.9b00149

Shu-Ou Shan

引用次数: 0

Correction to Conformational Features of Tau Fibrils from Alzheimer's Disease Brain Are Faithfully Propagated by Unmodified Recombinant Protein. 未经修饰的重组蛋白对阿尔茨海默病脑Tau原纤维构象特征的校正。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-03 DOI: 10.1021/acs.biochem.6b01240

Olga A Morozova, Zachary M March, Anne S Robinson, David W Colby

引用次数: 0