Biochemistry Biochemistry最新文献_第8页

Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing 利用单分子相关化学探针对复杂 RNA 的三级结构进行指纹识别

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-10-03 DOI: 10.1021/acs.biochem.4c0034310.1021/acs.biochem.4c00343

Ana C. Tan, Patrick S. Irving, Jordan T. Koehn, Shouhong Jin, David Y. Qiu and Kevin M. Weeks*,

{"title":"Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing","authors":"Ana C. Tan, Patrick S. Irving, Jordan T. Koehn, Shouhong Jin, David Y. Qiu and Kevin M. Weeks*, ","doi":"10.1021/acs.biochem.4c0034310.1021/acs.biochem.4c00343","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00343https://doi.org/10.1021/acs.biochem.4c00343","url":null,"abstract":"Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, information about base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. Here, we introduce mutual information as a filtering metric to isolate tertiary structure communication contained within smCCP data and use this strategy to characterize the structural ensemble of the SAM-III riboswitch. We identified an smCCP fingerprint that is selective for states containing a tertiary structure that forms concurrently with cognate ligand binding. We then successfully applied mutual information filters to independent RNAs and isolated through-space tertiary interactions in riboswitches and large RNAs with complex structures. smCCP, coupled with mutual information criteria, can now be used as a tertiary structure discovery tool, including to identify specific states in an ensemble that have a higher-order structure. These studies pave the way for the use of the straightforward smCCP experiment for discovery and characterization of tertiary structure motifs in complex RNAs.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448983","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

Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model 泛素部分折叠态与近原态之间的缓慢构象交换：多态折叠模型的证据

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-10-01 DOI: 10.1021/acs.biochem.4c0032110.1021/acs.biochem.4c00321

Sri Teja Adhada, and , Siddhartha P. Sarma*,

{"title":"Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model","authors":"Sri Teja Adhada,  and , Siddhartha P. Sarma*, ","doi":"10.1021/acs.biochem.4c0032110.1021/acs.biochem.4c00321","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00321https://doi.org/10.1021/acs.biochem.4c00321","url":null,"abstract":"The mechanism by which small proteins fold, i.e., via intermediates or via a two-state mechanism, is a subject of intense investigation. Intermediate states in the folding pathways of these proteins are sparsely populated due to transient lifetimes under normal conditions rendering them transparent to a majority of the biophysical methods employed for structural, thermodynamic, and kinetic characterization, which attributes are essential for understanding the cooperative folding/unfolding of such proteins. Dynamic NMR spectroscopy has enabled the characterization of folding intermediates of ubiquitin that exist in equilibrium under conditions of low pH and denaturants. At low pH, an unlocked state defined as N′ is in fast exchange with an invisible state, U″, as observed by CEST NMR. Addition of urea to ubiquitin at pH 2 creates two new states F′ and U′, which are in slow exchange (kF′→U′ = 0.14 and kU′→F′ = 0.28 s–1) as indicated by longitudinal ZZ-magnetization exchange spectroscopy. High-resolution solution NMR structures of F′ show it to be in an “unlocked” conformation with measurable changes in rotational diffusion, translational diffusion, and rotational correlational times. U′ is characterized by the presence of just the highly conserved N-terminal β1−β2 hairpin. The folding of ubiquitin is cooperative and is nucleated by the formation of an N-terminal β-hairpin followed by significant hydrophobic collapse of the protein core resulting in the formation of bulk of the secondary structural elements stabilized by extensive tertiary contacts. U′ and F′ may thus be described as early and late folding intermediates in the ubiquitin folding pathway.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450601","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

Periostin Is a Disulfide-Bonded Homodimer and Forms a Complex with Fibronectin in the Human Skin 表皮生长因子是一种二硫键同源二聚体，在人体皮肤中与纤连蛋白形成复合物

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-10-01 DOI: 10.1021/acs.biochem.4c0024010.1021/acs.biochem.4c00240

Christian E. Rusbjerg-Weberskov, Carsten Scavenius, Jan J. Enghild* and Nadia Sukusu Nielsen,

{"title":"Periostin Is a Disulfide-Bonded Homodimer and Forms a Complex with Fibronectin in the Human Skin","authors":"Christian E. Rusbjerg-Weberskov, Carsten Scavenius, Jan J. Enghild* and Nadia Sukusu Nielsen, ","doi":"10.1021/acs.biochem.4c0024010.1021/acs.biochem.4c00240","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00240https://doi.org/10.1021/acs.biochem.4c00240","url":null,"abstract":"The protein periostin is a matricellular protein that is expressed in connective tissue. It is composed of five globular domains arranged in an elongated structure with an extensive disordered C-terminal tail. Periostin contains 11 cysteine residues, of which one is unpaired and the rest form five intramolecular disulfide bonds. Periostin plays an important role during wound healing and is also involved in driving the inflammatory state in atopic diseases. This study provides a comprehensive biochemical characterization of periostin in human skin and in dermal and pulmonary fibroblasts in vitro. Through the application of Western blotting, co-immunoprecipitation, and LC-MS/MS, we show for the first time that periostin is a disulfide-bonded homodimer and engages in a novel disulfide-bonded complex with fibronectin both in vivo and in vitro. This inherent characteristic of periostin holds the potential to redefine our approach to exploring and understanding its functional role in future research endeavors.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142436880","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

How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase. ATP 和 dATP 如何作为分子开关调节原型细菌 Ia 类核糖核苷酸还原酶的酶活性？

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-10-01 Epub Date: 2024-08-20 DOI: 10.1021/acs.biochem.4c00329

Michael A Funk, Christina M Zimanyi, Gisele A Andree, Allison E Hamilos, Catherine L Drennan

{"title":"How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.","authors":"Michael A Funk, Christina M Zimanyi, Gisele A Andree, Allison E Hamilos, Catherine L Drennan","doi":"10.1021/acs.biochem.4c00329","DOIUrl":"10.1021/acs.biochem.4c00329","url":null,"abstract":"Class Ia ribonucleotide reductases (RNRs) are allosterically regulated by ATP and dATP to maintain the appropriate deoxyribonucleotide levels inside the cell for DNA biosynthesis and repair. RNR activity requires precise positioning of the β2 and α2 subunits for the transfer of a catalytically essential radical species. Excess dATP inhibits RNR through the creation of an α-β interface that restricts the ability of β2 to obtain a position that is capable of radical transfer. ATP breaks the α-β interface, freeing β2 and restoring enzyme activity. Here, we investigate the molecular basis for allosteric activity regulation in the well-studied Escherichia coli class Ia RNR through the determination of six crystal structures and accompanying biochemical and mutagenesis studies. We find that when dATP is bound to the N-terminal regulatory cone domain in α, a helix unwinds, creating a binding surface for β. When ATP displaces dATP, the helix rewinds, dismantling the α-β interface. This reversal of enzyme inhibition requires that two ATP molecules are bound in the cone domain: one in the canonical nucleotide-binding site (site 1) and one in a site (site 2) that is blocked by phenylalanine-87 and tryptophan-28 unless ATP is bound in site 1. When ATP binds to site 1, histidine-59 rearranges, prompting the movement of phenylalanine-87 and trytophan-28, and creating site 2. dATP hydrogen bonds to histidine-59, preventing its movement. The importance of site 2 in the restoration of RNR activity by ATP is confirmed by mutagenesis. These findings have implications for the design of bacterial RNR inhibitors.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007838","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

Human CSTF2 RNA Recognition Motif Domain Binds to a U-Rich RNA Sequence through a Multistep Binding Process. 人类 CSTF2 RNA 识别动点域通过多步结合过程与 U-Rich RNA 序列结合。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-10-01 Epub Date: 2024-09-21 DOI: 10.1021/acs.biochem.4c00408

Elahe Masoumzadeh, Michael P Latham

{"title":"Human CSTF2 RNA Recognition Motif Domain Binds to a U-Rich RNA Sequence through a Multistep Binding Process.","authors":"Elahe Masoumzadeh, Michael P Latham","doi":"10.1021/acs.biochem.4c00408","DOIUrl":"10.1021/acs.biochem.4c00408","url":null,"abstract":"The RNA recognition motif (RRM) is a conserved and ubiquitous RNA-binding domain that plays essential roles in mRNA splicing, polyadenylation, transport, and stability. RRM domains exhibit remarkable diversity in binding partners, interacting with various sequences of single- and double-stranded RNA, despite their small size and compact fold. During pre-mRNA cleavage and polyadenylation, the RRM domain from CSTF2 recognizes U- or G/U-rich RNA sequences downstream from the cleavage and polyadenylation site to regulate the process. Given the importance of alternative cleavage and polyadenylation in increasing the diversity of mRNAs, the exact mechanism of binding of RNA to the RRM of CSTF2 remains unclear, particularly in the absence of a structure of this RRM bound to a native RNA substrate. Here, we performed a series of NMR titration and spin relaxation experiments, which were complemented by paramagnetic relaxation enhancement measurements and rigid-body docking, to characterize the interactions of the CSTF2 RRM with a U-rich ligand. Our results reveal a multistep binding process involving differences in ps-ns time scale dynamics and potential structural changes, particularly in the C-terminalα-helix. These results provide insights into how the CSTF2 RRM domain binds to U-rich RNA ligands and offer a greater understanding for the molecular basis of the regulation of pre-mRNA cleavage and polyadenylation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277253","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

Extraction of In-Cell β-Amyloid Fibrillar Aggregates for Studying Molecular-Level Structural Propagations Using Solid-State NMR Spectroscopy 提取细胞内β-淀粉样蛋白纤维聚集体，利用固态核磁共振波谱研究分子级结构传播

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-09-30 DOI: 10.1021/acs.biochem.4c0039510.1021/acs.biochem.4c00395

June M. Kenyaga, and , Wei Qiang*,

{"title":"Extraction of In-Cell β-Amyloid Fibrillar Aggregates for Studying Molecular-Level Structural Propagations Using Solid-State NMR Spectroscopy","authors":"June M. Kenyaga,  and , Wei Qiang*, ","doi":"10.1021/acs.biochem.4c0039510.1021/acs.biochem.4c00395","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00395https://doi.org/10.1021/acs.biochem.4c00395","url":null,"abstract":"Molecular-level structural polymorphisms of β-amyloid (Aβ) fibrils have recently been recognized as pathologically significant. High-resolution solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been utilized to study these structural polymorphisms, particularly in ex-vivo fibrils seeded from amyloid extracts of post-mortem brain tissues of Alzheimer’s disease (AD) patients. One unaddressed question in current ex-vivo seeding protocol is whether fibrillation from exogenous monomeric Aβ peptides, added to the extracted seeds, can be quantitatively suppressed. Addressing this issue is critical because uncontrolled fibrillation could introduce biased molecular structural polymorphisms in the resulting fibrils. Here, we present a workflow to optimize the key parameters of ex-vivo seeding protocols, focusing on the quantification of amyloid extraction and the selection of exogenous monomeric Aβ concentrations to minimize nonseeded fibrillation. We validate this workflow using three structurally different 40-residue Aβ (Aβ40) fibrillar seeds, demonstrating their ability to propagate their structural features to exogenous wild-type Aβ40.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142437586","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

Modeling Enzyme Kinetics: Current Challenges and Future Perspectives for Biocatalysis 酶动力学建模：生物催化的当前挑战和未来展望

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-09-26 DOI: 10.1021/acs.biochem.4c0050110.1021/acs.biochem.4c00501

Jürgen Pleiss*,

{"title":"Modeling Enzyme Kinetics: Current Challenges and Future Perspectives for Biocatalysis","authors":"Jürgen Pleiss*, ","doi":"10.1021/acs.biochem.4c0050110.1021/acs.biochem.4c00501","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00501https://doi.org/10.1021/acs.biochem.4c00501","url":null,"abstract":"Biocatalysis is becoming a data science. High-throughput experimentation generates a rapidly increasing stream of biocatalytic data, which is the raw material for mechanistic and novel data-driven modeling approaches for the predictive design of improved biocatalysts and novel bioprocesses. The holistic and molecular understanding of enzymatic reaction systems will enable us to identify and overcome kinetic bottlenecks and shift the thermodynamics of a reaction. The full characterization and modeling of reaction systems is a community effort; therefore, published methods and results should be findable, accessible, interoperable, and reusable (FAIR), which is achieved by developing standardized data exchange formats, by a complete and reproducible documentation of experimentation, by collaborative platforms for developing sustainable software and for analyzing data, and by repositories for publishing results together with raw data. The FAIRification of biocatalysis is a prerequisite to developing highly automated laboratory infrastructures that improve the reproducibility of scientific results and reduce the time and costs required to develop novel synthesis routes.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142437449","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

G-Quadruplex-Mediated Transcriptional Regulation of SYT7: Implications for Tumor Progression and Therapeutic Strategies G-四叠体介导的 SYT7 转录调控：对肿瘤进展和治疗策略的影响

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-09-25 DOI: 10.1021/acs.biochem.4c0035910.1021/acs.biochem.4c00359

Ying Ma, Jiarong Guo, Xinyi Song, Haipeng Rao, Jinxin Zhang, Miao Miao, Feiyan Pan* and Zhigang Guo*,

{"title":"G-Quadruplex-Mediated Transcriptional Regulation of SYT7: Implications for Tumor Progression and Therapeutic Strategies","authors":"Ying Ma, Jiarong Guo, Xinyi Song, Haipeng Rao, Jinxin Zhang, Miao Miao, Feiyan Pan* and Zhigang Guo*, ","doi":"10.1021/acs.biochem.4c0035910.1021/acs.biochem.4c00359","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00359https://doi.org/10.1021/acs.biochem.4c00359","url":null,"abstract":"Synaptotagmin 7 (SYT7), a member of the synaptotagmin family, exhibits high expression in various tumors and is closely associated with patient prognosis. The tight regulation of SYT7 expression assumes paramount significance in the progression of tumorigenesis. In this study, we detected a high GC content in the first 1000 bp of the promoter region of SYT7, suggesting a potential role of the G-quadruplex in its transcriptional regulation. Circular dichroism spectroscopy results showed that −187 to −172 bp sequence can form a typical parallel G-quadruplex structure, and site mutation revealed the critical role of the ninth guanine in its formation. Then, treatment of two ligands of G-quadruplex (TMPyP4 and Pyridostatin) reduced both the expression of SYT7 and subsequent tumor proliferation, demonstrating the potential of the G-quadruplex as a targeted therapy for tumors. By shedding light on the pivotal role of the G-quadruplex in regulating SYT7 transcription, our study not only advances our comprehension of this intricate regulatory mechanism but also emphasizes the significance of SYT7 in tumor proliferation. These findings collectively contribute to a more comprehensive understanding of the interplay between G-quadruplex regulation and SYT7 function in tumor development.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142450651","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 Dynamics of the CCCH-Type Tandem Zinc Finger Domain of POS-1 and Implications for RNA Binding Specificity POS-1 的 CCCH 型串联锌指结构域的结构和动力学及其对 RNA 结合特异性的影响

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-09-25 DOI: 10.1021/acs.biochem.4c0025910.1021/acs.biochem.4c00259

Asli Ertekin, Brittany R. Morgan, Sean P. Ryder and Francesca Massi*,

{"title":"Structure and Dynamics of the CCCH-Type Tandem Zinc Finger Domain of POS-1 and Implications for RNA Binding Specificity","authors":"Asli Ertekin, Brittany R. Morgan, Sean P. Ryder and Francesca Massi*, ","doi":"10.1021/acs.biochem.4c0025910.1021/acs.biochem.4c00259","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00259https://doi.org/10.1021/acs.biochem.4c00259","url":null,"abstract":"CCCH-type tandem zinc finger (TZF) motifs are found in many RNA-binding proteins involved in regulating mRNA stability, translation, and splicing. In Caenorhabditis elegans, several RNA-binding proteins that regulate embryonic development and cell fate determination contain CCCH TZF domains, including POS-1. Previous biochemical studies have shown that despite high levels of sequence conservation, POS-1 recognizes a broader set of RNA sequences compared to the human homologue tristetraprolin. However, the molecular basis of these differences remains unknown. In this study, we refined the consensus RNA sequence and determined the differing binding specificities of the two zinc fingers of POS-1. We also determined the solution structure and characterized the internal dynamics of the TZF domain of POS-1. From the structure, we identified unique features that define the RNA binding specificity of POS-1. We also observed that the TZF domain of POS-1 is in equilibrium between interconverting conformations. Transitions between these conformations require internal motions involving many residues with correlated dynamics in each ZF. We propose that the correlated dynamics are necessary to allow allosteric communication between the nucleotide-binding pockets observed in the N-terminal ZF. Our study shows that both the structure and conformational plasticity of POS-1 are important in ensuring recognition of its RNA binding targets.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142437190","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

Glycerol 3-Phosphate Dehydrogenase Catalyzed Hydride Transfer: Enzyme Activation by Cofactor Pieces 甘油 3-磷酸脱氢酶催化的氢化物转移：辅因子片段激活酶

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-09-25 DOI: 10.1021/acs.biochem.4c0032410.1021/acs.biochem.4c00324

Rania Hegazy, Judith R. Cristobal and John P. Richard*,

{"title":"Glycerol 3-Phosphate Dehydrogenase Catalyzed Hydride Transfer: Enzyme Activation by Cofactor Pieces","authors":"Rania Hegazy, Judith R. Cristobal and John P. Richard*, ","doi":"10.1021/acs.biochem.4c0032410.1021/acs.biochem.4c00324","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00324https://doi.org/10.1021/acs.biochem.4c00324","url":null,"abstract":"Glycerol 3-phosphate dehydrogenase catalyzes reversible hydride transfer from glycerol 3-phosphate (G3P) to NAD+ to form dihydroxyacetone phosphate; from the truncated substrate ethylene glycol to NAD+ in a reaction activated by the phosphite dianion substrate fragment; and from G3P to the truncated nicotinamide riboside cofactor in a reaction activated by adenosine 5′-diphosphate, adenosine 5′-monophosphate, and ribose 5-phosphate cofactor fragments. The sum of the stabilization of the transition state for GPDH-catalyzed hydride transfer reactions of the whole substrates by the phosphodianion fragment of G3P and the ADP fragment of NAD+ is 25 kcal/mol. Fourteen kcal/mol of this transition state stabilization is recovered as phosphite dianion and AMP activation of the reactions of the substrate and cofactor fragments. X-ray crystal structures for unliganded GPDH, for a binary GPDH·NAD+ complex, and for a nonproductive ternary GPDH·NAD+·DHAP complex show that the ligand binding energy is utilized to drive an extensive protein conformational change that creates a caged complex for these ligands. The phosphite dianion and AMP fragments are proposed to activate GPDH for the catalysis of hydride transfer by stabilization of this active caged complex. The closure of a conserved loop [292-LNGQKL-297] during substrate binding stabilizes the G3P and NAD+ complexes by interactions, respectively, with the Q295 and K296 loop side chains. The appearance and apparent conservation of two side chains that interact with the hydride donor and acceptor to stabilize the active closed enzyme are proposed to represent a significant improvement in the catalytic performance of GPDH.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142577708","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