Biochemistry Biochemistry最新文献_第5页

Evaluation and Comparison of Candida albicans vs Mammalian 6-O-Phospho-Kinases: Substrate Specificity and Applications. 白色念珠菌与哺乳动物6- o-磷酸激酶的评价和比较：底物特异性和应用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-07 Epub Date: 2024-12-11 DOI: 10.1021/acs.biochem.4c00525

Min Liu, Caroline Williams, Stephen N Hyland, Marina P Vasconcelos, Bella R Carnahan, Rachel Putnik, Sushanta Ratna, Catherine L Grimes

{"title":"Evaluation and Comparison of Candida albicans vs Mammalian 6-O-Phospho-Kinases: Substrate Specificity and Applications.","authors":"Min Liu, Caroline Williams, Stephen N Hyland, Marina P Vasconcelos, Bella R Carnahan, Rachel Putnik, Sushanta Ratna, Catherine L Grimes","doi":"10.1021/acs.biochem.4c00525","DOIUrl":"10.1021/acs.biochem.4c00525","url":null,"abstract":"Sensing of peptidoglycan fragments is essential for inducing downstream signaling in both mammalian and fungal systems. The hexokinases NagK and Hxk1 are crucial enzymes for the phosphorylation of peptidoglycan molecules in order to activate specific cellular responses; however, biochemical characterization of their enzymatic specificity and efficiency has yet to be investigated in depth. Here a mass spectrometry enzymatic screen was implemented to assess substrate specificity, and an ATP coupled assay provided the quantitative kinetic profiles of these two homologous, eukaryotic enzymes. The data show, that while homologous, NagK and Hxk1 have vastly different substrate profiles. NagK accepts a variety of different peptidoglycan-based substrates albeit with reduced efficiency but are still valuable as a tool in large scale chemoenzymatic settings. Conversely, Hxk1 has a smaller substrate scope but can turnover these alternative substrates at similar levels to its natural substrate. These results allow for deeper understanding into the biosynthetic machinery responsible for essential cellular processes including UDP-GlcNAc regulation and immune recognition events in the cell.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"26-31"},"PeriodicalIF":2.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11716661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811427","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

Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNa_V1.5 Channel. 水合作用和氨基酸相互作用在hNaV1.5通道离子渗透机制中的作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-07 Epub Date: 2024-12-17 DOI: 10.1021/acs.biochem.4c00664

Nuria Anguita-Ortiz, Juan J Nogueira

{"title":"Role of Hydration and Amino Acid Interactions on the Ion Permeation Mechanism in the hNaV1.5 Channel.","authors":"Nuria Anguita-Ortiz, Juan J Nogueira","doi":"10.1021/acs.biochem.4c00664","DOIUrl":"10.1021/acs.biochem.4c00664","url":null,"abstract":"This study explores the ion selectivity and conduction mechanisms of the hNaV1.5 sodium channel using classical molecular dynamics simulations under an externally applied electric field. Our findings reveal distinct conduction mechanisms for Na+ and K+, primarily driven by differences in their hydration states when they diffuse close to the channel's selective filter (DEKA) and extracellular ring (EEDD). The Na+ ions undergo partial dehydration in the EEDD region, followed by a rehydration step in the DEKA ring, resulting in longer retention times and a deeper free energy minimum compared to K+. Conversely, the K+ ions exhibit a continuous dehydration process, facilitating a smoother passage through these key regions. These results indicate that ion selectivity and conductance are primarily governed by solvation dynamics, which, in turn, depend on the interactions with key charged residues within the channel. Additionally, we show that the delicate energetic balance between the interactions of the ions with the protein residues and with their solvation shells during the dehydration and rehydration processes is not properly captured by the force field. As a consequence, the selectivity of the channel is not well described, indicating that more accurate computational models must be applied to simulate ion conduction through eukaryotic NaV channels.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"47-56"},"PeriodicalIF":2.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11713869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

How the Electron-Transfer Cascade is Maintained in Chlorophyll-d Containing Photosystem I. 含叶绿素d光系统中电子传递级联是如何维持的。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-07 Epub Date: 2024-12-10 DOI: 10.1021/acs.biochem.4c00521

Tomoyasu Noji, Keisuke Saito, Hiroshi Ishikita

{"title":"How the Electron-Transfer Cascade is Maintained in Chlorophyll-d Containing Photosystem I.","authors":"Tomoyasu Noji, Keisuke Saito, Hiroshi Ishikita","doi":"10.1021/acs.biochem.4c00521","DOIUrl":"10.1021/acs.biochem.4c00521","url":null,"abstract":"Photosystem I (PSI) from Acaryochloris marina utilizes chlorophyll d (Chld) with a formyl group as its primary pigment, which is more red-shifted than chlorophyll a (Chla) in PSI from Thermosynechococcus elongatus. Using the cryo-electron microscopy structure and solving the linear Poisson-Boltzmann equation, here we report the redox potential (Em) values in A. marina PSI. The Em(Chld) values at the paired chlorophyll site, [PAPB], are nearly identical to the corresponding Em(Chla) values in T. elongatus PSI, despite Chld having a 200 mV lower reduction power. The accessory chlorophyll site, A-1, in the B branch exhibits an extensive H-bond network with its ligand water molecule, contributing to Em(A-1B) being lower than Em(A-1A). The substitution of pheophytin a (Pheoa) with Chla at the electron acceptor site, A0, decreases Em(A0), resulting in an uphill electron transfer from A-1. The impact of the A-1 formyl group on Em(A0) is offset by the reorientation of the A0 ester group. It seems likely that Pheoa is necessary for A. marina PSI to maintain the overall electron-transfer cascade characteristic of PSI in its unique light environment.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"203-212"},"PeriodicalIF":2.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11716663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798620","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

Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor. 重组表达的hUGDH的冷冻电镜结构揭示了一种隐藏的替代变构抑制剂。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-07 Epub Date: 2024-12-16 DOI: 10.1021/acs.biochem.4c00555

John H O'Brien, Renuka Kadirvelraj, Po-Sen Tseng, Nolan Ross-Kemppinen, David Crich, Richard M Walsh, Zachary A Wood

{"title":"Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor.","authors":"John H O'Brien, Renuka Kadirvelraj, Po-Sen Tseng, Nolan Ross-Kemppinen, David Crich, Richard M Walsh, Zachary A Wood","doi":"10.1021/acs.biochem.4c00555","DOIUrl":"10.1021/acs.biochem.4c00555","url":null,"abstract":"Human UDP-glucose dehydrogenase (hUGDH) catalyzes the oxidation of UDP-glucose into UDP-glucuronic acid, an essential substrate in the Phase II metabolism of drugs. hUGDH is a hexamer that exists in an equilibrium between an active (E) state and an inactive (EΩ) state, with the latter being stabilized by the binding of the allosteric inhibitor UDP-xylose (UDP-Xyl). The allosteric transition between EΩ and E is slow and can be observed as a lag in progress curves. Previous analysis of the lag suggested that unliganded hUGDH exists mainly as EΩ, but two unique crystal forms suggest that the enzyme favors the E state. Resolving this discrepancy is necessary to fully understand the allosteric mechanism of hUGDH. Here, we used cryo-EM to show that recombinant hUGDH expressed in Escherichia coli copurifies with UDP-4-keto-xylose (UX4O), which mimics the UDP-Xyl inhibitor and favors the EΩ state. Cryo-EM studies show that removing UX4O from hUGDH shifts the ensemble to favor the E state. This shift is consistent with progress curve analysis, which shows the absence of a lag for unliganded hUGDH. Inhibition studies show that hUGDH has similar affinities for UDP-Xyl and UX4O. The discovery that UX4O inhibits allosteric hUGDH suggests that UX4O may be the physiologically relevant inhibitor of allosteric UGDHs in bacteria that do not make UDP-Xyl.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"92-104"},"PeriodicalIF":2.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11713868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833202","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

Re-evaluation of the C-Glucosyltransferase IroB Illuminates Its Ability to C-Glucosylate Non-native Triscatecholate Enterobactin Mimics. 对c -葡萄糖基转移酶IroB的重新评估阐明了其对非天然三儿茶酚酸肠杆菌模拟物c -葡萄糖基化的能力。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-24 DOI: 10.1021/acs.biochem.4c00581

Rachel N Motz, Jaden K Anderson, Elizabeth M Nolan

{"title":"Re-evaluation of the C-Glucosyltransferase IroB Illuminates Its Ability to C-Glucosylate Non-native Triscatecholate Enterobactin Mimics.","authors":"Rachel N Motz, Jaden K Anderson, Elizabeth M Nolan","doi":"10.1021/acs.biochem.4c00581","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00581","url":null,"abstract":"The pathogen-associated C-glucosyltransferase IroB is involved in the biosynthesis of salmochelins, C-glucosylated derivatives of enterobactin (Ent), which is a triscatecholate siderophore of enteric bacteria including Salmonella enterica and Escherichia coli. Here, we reassess the ability of IroB to C-glucosylate non-native triscatecholate mimics of Ent, which may have utility in the design and development of siderophore-based therapeutics and diagnostics. We establish TRENCAM (TC) and MECAM (MC), synthetic Ent analogs with tris(2-aminoethyl)amine- or mesitylene-derived backbones replacing the trilactone core of Ent, respectively, and their monoglucosylated congeners as substrates of IroB. Time course analyses and steady-state kinetic studies, which were performed under conditions that provide enhanced activity relative to prior studies, inform the substrate selectivity and catalytic efficiencies of this enzyme. We extend these findings to the preparation of a siderophore-antibiotic conjugate composed of monoglucosylated TC and ampicillin (MGT-Amp). Examination of its antibacterial activity and receptor specificity demonstrates that MGT-Amp targets pathogenicity because it shows specificty for the pathogen-associated outer membrane receptor IroN. Overall, our findings extend the biochemical characterization of IroB and its substrate scope and illustrate the ability to leverage a bacterial C-glucosyltransferase for non-native chemoenzymatic transformations along with potential applications of salmochelin mimics.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880620","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

Impact of Guanidinium Hydrochloride on the Shapes of Prothymosin-α and α-Synuclein Is Dramatically Different. 盐酸胍对原胸腺肽-α和α-突触核蛋白形状的影响有显著差异。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-24 DOI: 10.1021/acs.biochem.4c00654

Zhenxing Liu, D Thirumalai

{"title":"Impact of Guanidinium Hydrochloride on the Shapes of Prothymosin-α and α-Synuclein Is Dramatically Different.","authors":"Zhenxing Liu, D Thirumalai","doi":"10.1021/acs.biochem.4c00654","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00654","url":null,"abstract":"The effects of guanidinium hydrochloride (GdmCl) on two intrinsically disordered proteins (IDPs) are investigated using simulations of the self-organized polymer-IDP (SOP-IDP) model. The impact of GdmCl is taken into account using the molecular transfer model (MTM). We show that due to the dramatic reduction in the stiffness of the highly charged Prothymosin-α (ProTα) with increasing concentration of GdmCl ([GdmCl]), the radius of gyration (Rg) decreases sharply until about 1.0 M. Above 1.0 M, ProTα expands, caused by the swelling effect of GdmCl. In contrast, Rg of α-Synuclein (αSyn) swells as continuously as [GdmCl] increases, with most of the expansion occurring at concentrations less than 0.2 M. Strikingly, the amplitude of the small-angle X-ray scattering (SAXS) profiles for ProTα increases until [GdmCl] ≈ 1.0 M and decreases beyond 1.0 M. The [GdmCl]-dependent SAXS profiles for αSyn, which has a pronounced bump at small wave vector (q ∼ 0.5 nm-1) at low [GdmCl] (≤0.2 M), monotonically decrease at all values of [GdmCl]. The contrasting behavior predicted by the combination of MTM and SOP-IDP simulations may be qualitatively understood by modeling ProTα as a strongly charged polyelectrolyte with nearly uniform density of charges along the chain contour and αSyn as a nearly neutral polymer, except near the C-terminus, where the uncompensated negatively charged residues are located. The precise predictions for the SAXS profiles as a function of [GdmCl] can be readily tested.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142884799","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

QM/MM Calculations on Excited-State Proton Transfer and Photoisomerization of a Red Fluorescent Protein mKeima with Large Stokes Shift. 大斯托克斯位移红色荧光蛋白mKeima激发态质子转移和光异构化的QM/MM计算。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-23 DOI: 10.1021/acs.biochem.4c00586

Guang-Ning Pan, Xiang-Yang Liu, Ganglong Cui, Wei-Hai Fang

{"title":"QM/MM Calculations on Excited-State Proton Transfer and Photoisomerization of a Red Fluorescent Protein mKeima with Large Stokes Shift.","authors":"Guang-Ning Pan, Xiang-Yang Liu, Ganglong Cui, Wei-Hai Fang","doi":"10.1021/acs.biochem.4c00586","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00586","url":null,"abstract":"Large Stokes shift red fluorescent proteins (LSS-RFPs) are of growing interest for multicolor bioimaging applications. However, their photochemical mechanisms are not fully understood. Here, we employed the QM(XDW-CASPT2//CASSCF)/MM method to investigate the excited-state proton transfer and photoisomerization processes of the LSS-RFP mKeima starting from its cis neutral isomer. Upon excitation to the bright S1 state in the Franck-Condon region, mKeima relaxes to a metastable minimum-energy state. From this short-lived species, two competing deactivation pathways are available: the excited-state proton transfer in the S1 state, and the S1 decay via the S1/S0 conical intersection as a result of the cis-trans photoisomerization. In comparison, the former is a dominant excited-state relaxation pathway, leading to the cis anionic isomer of mKeima in the S1 state. This anionic intermediate then undergoes cis-trans photoisomerization after overcoming a barrier of approximately 10 kcal/mol in the S1 state, which is followed by an excited-state decay via the S1/S0 conical intersection region. The efficient nonadiabatic decay of the cis anionic isomer of mKeima in the S1 state inhibits the radiative process, leading to a weak emission around 520 nm observed experimentally. These findings shed important mechanistic light on the experimental observations and provide valuable insights that could help in the design of LSS-RFPs with superior fluorescence properties.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880609","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

Disruption of Molecular Interactions between the G3BP1 Stress Granule Host Protein and the Nucleocapsid (NTD-N) Protein Impedes SARS-CoV-2 Virus Replication. G3BP1应激颗粒宿主蛋白与核衣壳蛋白（NTD-N）分子相互作用的破坏阻碍了SARS-CoV-2病毒复制

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-21 DOI: 10.1021/acs.biochem.4c00536

Preeti Dhaka, Ankur Singh, Sanketkumar Nehul, Shweta Choudhary, Prasan Kumar Panda, Gaurav Kumar Sharma, Pravindra Kumar, Shailly Tomar

{"title":"Disruption of Molecular Interactions between the G3BP1 Stress Granule Host Protein and the Nucleocapsid (NTD-N) Protein Impedes SARS-CoV-2 Virus Replication.","authors":"Preeti Dhaka, Ankur Singh, Sanketkumar Nehul, Shweta Choudhary, Prasan Kumar Panda, Gaurav Kumar Sharma, Pravindra Kumar, Shailly Tomar","doi":"10.1021/acs.biochem.4c00536","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00536","url":null,"abstract":"The Ras GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a formidable barrier to viral replication by generating stress granules (SGs) in response to viral infections. Interestingly, viruses, including SARS-CoV-2, have evolved defensive mechanisms to hijack SG proteins like G3BP1 for the dissipation of SGs that lead to the evasion of the host's immune responses. Previous research has demonstrated that the interaction between the NTF2-like domain of G3BP1 (G3BP1NTF-2) and the intrinsically disordered N-terminal domain (NTD-N1-25) of the N-protein plays a crucial role in regulating viral replication and pathogenicity. Interestingly, the current study identified an additional upstream stretch of residues (128KDGIIWVATEG138) (N128-138) within the N-terminal domain of the N-protein (NTD-N41-174) that also forms molecular contacts with the G3BP1 protein, as revealed through in silico analysis, site-directed mutagenesis, and biochemical analysis. Remarkably, WIN-62577, and fluspirilene, the small molecules targeting the conserved peptide-binding pocket in G3BP1NTF-2, not only disrupted the protein-protein interactions (PPIs) between NTD-N41-174 and G3BP1NTF-2 but also exhibited significant antiviral efficacy against SARS-CoV-2 replication with EC50 values of ∼1.8 and ∼1.3 μM, respectively. The findings of this study, validated by biophysical thermodynamics and biochemical investigations, advance the potential of developing therapeutics targeting the SG host protein against SARS-CoV-2, which may also serve as a broad-spectrum antiviral target.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870575","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

Autoregulation of TRF2 through G-Quadruplex-Specific Interaction between the Gene and N-Terminal Domain of the Protein. 通过基因与蛋白n端结构域之间的g -四重体特异性相互作用对TRF2的自动调节。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2024-12-20 DOI: 10.1021/acs.biochem.4c00287

Xiaojuan Xu, Tao Wang

{"title":"Autoregulation of TRF2 through G-Quadruplex-Specific Interaction between the Gene and N-Terminal Domain of the Protein.","authors":"Xiaojuan Xu, Tao Wang","doi":"10.1021/acs.biochem.4c00287","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00287","url":null,"abstract":"Telomere repeat-binding factor 2 (TRF2) is a key component of the shelterin complex which guards the integrity of the telomere. Most of the TRF2 discussed previously was focused on the telomere, and relatively less is discussed on aspects other than that. It is proved that TRF2 also localizes to other potential G-quadruplex-forming sequences among the whole genome besides the telomere. Therefore, it may participate in regulating genes generally except for the well-known function of protecting telomeres. Here, we demonstrate that the N-terminal basic domain of TRF2 (TRF2B) can interact with the G-quadruplex formed by the 5'-UTR sequence of its gene. Subsequently, this interaction was identified as G-quadruplex-specific. Using a reporter gene system, we proved that the translation of the reporter gene was dramatically reduced, triggered by the interaction between TRF2B and the G-quadruplex. Altogether, we propose that TRF2 can be \"auto-regulated\" through the G-quadruplex formed by its own gene sequence. This finding indicates a potential feedback mechanism in the regulation of the TRF2 gene. Additionally, it suggests a common mode in gene regulation involving the cooperation of TRF2 and the G-quadruplex.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869271","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

Determining the Electrostatic Contributions of GTPase-GEF Complexes on Interfacial Drug Binding Specificity: A Case Study of a Protein-Drug-Protein Complex. 确定 GTPase-GEF 复合物对界面药物结合特异性的静电贡献：蛋白质-药物-蛋白质复合物案例研究。

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.4c00313

Frank A Jermusek, Lauren J Webb

{"title":"Determining the Electrostatic Contributions of GTPase-GEF Complexes on Interfacial Drug Binding Specificity: A Case Study of a Protein-Drug-Protein Complex.","authors":"Frank A Jermusek, Lauren J Webb","doi":"10.1021/acs.biochem.4c00313","DOIUrl":"10.1021/acs.biochem.4c00313","url":null,"abstract":"Understanding the factors that contribute to specificity of protein-protein interactions allows for design of orthosteric small molecules. Within this environment, a small molecule requires both structural and electrostatic complementarity. While the structural contribution to protein-drug-protein specificity is well characterized, electrostatic contributions require more study. To this end, we used a series of protein complexes involving Arf1 bound to guanine nucleotide exchange factors (GEFs) that are sensitive or resistant to the small molecule brefeldin A (BFA). By comparing BFA-sensitive Arf1-Gea1p and Arf1-ARNO with different combinations of four BFA sensitizing ARNO mutations (ARNOwt, ARNO1M, ARNO3M, and ARNO4M), we describe how electrostatic environments at each interface guide BFA binding specificity. We labeled Arf1 with cyanocysteine at several interfacial sites and measured by nitrile adsorption frequencies to map changes in electric field at each interface using the linear Stark equation. Temperature dependence of nitrile vibrational spectra was used to investigate differences in hydrogen bonding environments. These comparisons showed that interfacial electric field at the surface of Arf1 varied substantially depending on the GEF. The greatest differences were seen between Arf1-ARNOwt and Arf1-ARNO4M, suggesting a greater change in electric field is required for BFA binding to Arf1-ARNO. Additionally, rigidity of the interface of the Arf1-ARNO complex correlated strongly with BFA sensitivity, indicating that flexible interfaces are sensitive to disruption upon orthosteric small molecule binding. These findings demonstrate a qualitatively consistent electrostatic environment for Arf1 binding and more subtle differences preventing BFA specificity. We discuss how these results will guide improved design of other small molecules that can target protein-protein interfaces.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"3220-3235"},"PeriodicalIF":2.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714763","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