Biochemistry and Biophysics Reports最新文献

筛选
英文 中文
Investigating combined hypoxia and stemness indices for prognostic transcripts in gastric cancer: Machine learning and network analysis approaches 研究胃癌预后转录物的缺氧和干性联合指标:机器学习和网络分析方法。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-19 DOI: 10.1016/j.bbrep.2024.101897
Sharareh Mahmoudian-Hamedani , Maryam Lotfi-Shahreza , Parvaneh Nikpour
{"title":"Investigating combined hypoxia and stemness indices for prognostic transcripts in gastric cancer: Machine learning and network analysis approaches","authors":"Sharareh Mahmoudian-Hamedani ,&nbsp;Maryam Lotfi-Shahreza ,&nbsp;Parvaneh Nikpour","doi":"10.1016/j.bbrep.2024.101897","DOIUrl":"10.1016/j.bbrep.2024.101897","url":null,"abstract":"<div><h3>Introduction</h3><div>Gastric cancer (GC) is among the deadliest malignancies globally, characterized by hypoxia-driven pathways that promote cancer progression, including stemness mechanisms facilitating invasion and metastasis. This study aimed to develop a prognostic decision tree using genes implicated in hypoxia and stemness pathways to predict outcomes in GC patients.</div></div><div><h3>Materials and methods</h3><div>GC RNA-seq data from The Cancer Genome Atlas (TCGA) were analyzed to compute hypoxia and stemness scores using Gene Set Variation Analysis (GSVA) and the mRNA expression-based stemness index (mRNAsi). Hierarchical clustering identified clusters with distinct survival outcomes, and differentially expressed genes (DEGs) between clusters were identified. Weighted Gene Co-expression Network Analysis (WGCNA) identified modules and hub genes associated with clinical traits. Overlapping DEGs and hub genes underwent functional enrichment, protein-protein interaction (PPI) network analysis, and survival analysis. A prognostic decision tree was constructed using survival-associated shared genes.</div></div><div><h3>Results</h3><div>Hierarchical clustering identified six clusters among 375 TCGA GC patients, with significant survival differences between cluster 1 (low hypoxia, high stemness) and cluster 4 (high hypoxia, high stemness). Validation in the GSE62254 dataset corroborated these findings. WGCNA revealed modules linked to clinical traits and survival, with functional enrichment highlighting pathways like cell adhesion and calcium signaling. The decision tree, based on genes such as <em>AKAP6</em>, <em>GLRB</em>, and <em>RUNX1T1</em>, achieved an AUC of 0.81 (training) and 0.67 (test), demonstrating the utility of combined scores in patient stratification.</div></div><div><h3>Conclusion</h3><div>This study introduces a novel hypoxia-stemness-based prognostic decision tree for GC. The identified genes show promise as prognostic biomarkers, warranting further clinical validation.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101897"},"PeriodicalIF":2.3,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142977449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The multifaceted role of SMAD4 in immune cell function SMAD4在免疫细胞功能中的多方面作用。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-18 DOI: 10.1016/j.bbrep.2024.101902
Xinmu Cui , Yu Song , Jianfeng Han , Zhaoxin Yuan
{"title":"The multifaceted role of SMAD4 in immune cell function","authors":"Xinmu Cui ,&nbsp;Yu Song ,&nbsp;Jianfeng Han ,&nbsp;Zhaoxin Yuan","doi":"10.1016/j.bbrep.2024.101902","DOIUrl":"10.1016/j.bbrep.2024.101902","url":null,"abstract":"<div><div>The Transforming Growth Factor-beta (TGF-β) signaling pathway, with SMAD4 as its central mediator, plays a pivotal role in regulating cellular functions, including growth, differentiation, apoptosis, and immune responses. While extensive research has elucidated SMAD4's role in tumorigenesis, its functions within immune cells remain underexplored. This review synthesizes current knowledge on SMAD4's diverse roles in various immune cells such as T cells, B cells, dendritic cells, and macrophages, highlighting its impact on immune homeostasis and pathogen response. Understanding SMAD4's role in immune cells is crucial, as its dysregulation can lead to autoimmune disorders, chronic inflammation, and immune deficiencies. The review emphasizes the significance of SMAD4 in immune regulation, proposing that deeper investigation could reveal novel therapeutic targets for immune-mediated conditions. Insights into SMAD4's involvement in processes like T cell differentiation, B cell class switch recombination, and macrophage polarization underscore its potential as a therapeutic target for a range of diseases, including autoimmune disorders and cancer.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101902"},"PeriodicalIF":2.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11721226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessing the prevalence of neutralizing antibodies (NAbs) to SARS-CoV-2 during three years of the COVID-19 pandemic 在COVID-19大流行的三年中评估SARS-CoV-2中和抗体(nab)的流行情况。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-17 DOI: 10.1016/j.bbrep.2024.101903
Marina dos Santos Barreto , Ronaldy Santana Santos , Eloia Emanuelly Dias Silva , Deise Maria Rego Rodrigues Silva , Pedro Henrique Macedo Moura , Pamela Chaves de Jesus , Jessiane Bispo de Souza , Lucas Alves da Mota Santana , Adriana Gibara Guimarães , Lysandro Pinto Borges
{"title":"Assessing the prevalence of neutralizing antibodies (NAbs) to SARS-CoV-2 during three years of the COVID-19 pandemic","authors":"Marina dos Santos Barreto ,&nbsp;Ronaldy Santana Santos ,&nbsp;Eloia Emanuelly Dias Silva ,&nbsp;Deise Maria Rego Rodrigues Silva ,&nbsp;Pedro Henrique Macedo Moura ,&nbsp;Pamela Chaves de Jesus ,&nbsp;Jessiane Bispo de Souza ,&nbsp;Lucas Alves da Mota Santana ,&nbsp;Adriana Gibara Guimarães ,&nbsp;Lysandro Pinto Borges","doi":"10.1016/j.bbrep.2024.101903","DOIUrl":"10.1016/j.bbrep.2024.101903","url":null,"abstract":"<div><div>The development of COVID-19 vaccines has been an important step in the fight against the pandemic. However, it is still necessary to understand the influence of factors that can alter the immune response. In general, doses need to be updated frequently, and care must be taken to control the virus that is still circulating worldwide. In this study, we evaluated the neutralizing antibodies (NAbs) against SARS-CoV-2 in northeast Brazil. The study was divided into three phases (T1, T2, and T3) and included 297 participants. The three phases occurred in three different years of the pandemic (2021, 2022 and 2023). We obtained higher mean NAbs in T2 and T3 when most of the participants had already completed their vaccination program. No significant difference in the distribution of NAbs and sex was observed (p &gt; 0.05). It was shown that there is a difference in the expression of NAbs in the different amounts of doses, with individuals with no dose obtaining a significantly lower average than those who took the vaccine. Regarding age, the average NAbs were higher with increasing age. In this study, we assess the prevalence of NAbs in three pandemic phases, making it possible to understand the importance of vaccine updating in maintaining immunity.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101903"},"PeriodicalIF":2.3,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11721800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioinformatic identification of signature miRNAs associated with fetoplacental vascular dysfunction in gestational diabetes mellitus 与妊娠糖尿病胎儿胎盘血管功能障碍相关的特征mirna的生物信息学鉴定。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-16 DOI: 10.1016/j.bbrep.2024.101888
Yulan Lu , Chunhong Liu , Xiaoxia Pang , Xinghong Chen , Chunfang Wang , Huatuo Huang
{"title":"Bioinformatic identification of signature miRNAs associated with fetoplacental vascular dysfunction in gestational diabetes mellitus","authors":"Yulan Lu ,&nbsp;Chunhong Liu ,&nbsp;Xiaoxia Pang ,&nbsp;Xinghong Chen ,&nbsp;Chunfang Wang ,&nbsp;Huatuo Huang","doi":"10.1016/j.bbrep.2024.101888","DOIUrl":"10.1016/j.bbrep.2024.101888","url":null,"abstract":"<div><h3>Background</h3><div>Intrauterine exposure to gestational diabetes mellitus (GDM) poses significant risks to fetal development and future metabolic health. Despite its clinical importance, the role of microRNAs (miRNAs) in fetoplacental vascular endothelial cell (VEC) programming in the context of GDM remains elusive. This study aims to identify signature miRNA genes involved in this process using bioinformatics analysis via multiple algorithms.</div></div><div><h3>Methods</h3><div>The dataset used in this study was acquired from Gene Expression Omnibus (GEO). Firstly, differentially expressed miRNA genes (DEMGs) were evaluated using limma package. Thereafter, an enrichment analysis of DEMGs was performed. Then, the least absolute shrinkage and selection operator (LASSO) and support vector machine (SVM) were used as the other algorithms for screening candidate signature miRNA genes. Genes from the intersection of limma, LASSO, and SVM genes were used as the final signature miRNA genes. The receiver operator characteristic curve (ROC), the nomogram diagram, gene set enrichment analysis (GSEA), and signature miRNAs-target genes interaction network were implemented further to explore the features and functions of signature genes.</div></div><div><h3>Results</h3><div>A total of 32 DEMGs, with 21 upregulated and 11 downregulated miRNA genes, were obtained from limma analysis. LASSO and SVM analyses identified 15 and 12 candidate signature miRNA genes, respectively. After the intersection of genes from limma, LASSO, and SVM analyses, MIR34A and MIR186 were found as the final signature genes related to fetoplacental VEC programming. MIR34A and MIR186 were highly expressed and were associated with an increased risk of fetoplacental VEC programming in GDM mothers. The area under the curve (AUC) of ROC for MIR34A and MIR186 were 0.960 and 0.935, respectively. GSEA analysis revealed that these signature genes positively participate in cellular processes related to VEC migration, cell differentiation, angiogenesis, programmed cell death, and inflammatory response. Finally, miRNAs-target genes interaction network analysis provides the interaction of signature miRNAs and their critical target genes, which may help further studies for miR-34a and miR-186 in GDM.</div></div><div><h3>Conclusions</h3><div>MIR34A and MIR186 are novel signature miRNA genes related to fetoplacental VEC programming that may represent critical genes associated with placental function and fetal programming under GDM conditions.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101888"},"PeriodicalIF":2.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11720096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spectroscopic and calorimetric study of the interaction between Nile blue and double-stranded RNA 尼罗蓝与双链RNA相互作用的光谱和量热研究。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-14 DOI: 10.1016/j.bbrep.2024.101899
Md Dulal Hossain Khan, Ramya Ayyalasomayajula, Mare Cudic, Renjie Wang
{"title":"Spectroscopic and calorimetric study of the interaction between Nile blue and double-stranded RNA","authors":"Md Dulal Hossain Khan,&nbsp;Ramya Ayyalasomayajula,&nbsp;Mare Cudic,&nbsp;Renjie Wang","doi":"10.1016/j.bbrep.2024.101899","DOIUrl":"10.1016/j.bbrep.2024.101899","url":null,"abstract":"<div><div>Nile blue has been widely used in histological staining, fluorescence labeling, and DNA probing, with its intercalation behavior into the DNA helix being well documented. Here, we present a comprehensive investigation to address a current knowledge gap regarding the binding properties of Nile blue to two types of double-stranded RNA (dsRNA): poly(A·U) and poly(I·C), using various biophysical techniques. Absorption and fluorescence spectroscopic studies suggest a significant binding interaction between Nile blue and the two designated dsRNAs, specifically indicating an intercalation binding mode with poly(A·U) and demonstrating a noticeably higher binding affinity compared to poly(I·C). The binding stoichiometry was further determined by Job's plot to be 0.47 for poly(A·U) and 1.0 for poly(I·C). The increased relative viscosity and changes in the circular dichroism (CD) ellipticity of dsRNA after interacting with Nile blue indicate the stacking of Nile blue dyes between the RNA duplexes. These changes suggest a conformational alteration of the dsRNAs and confirm the intercalation mode of binding. The thermal dynamic analysis demonstrates that both binding were favored by negative enthalpy and primarily driven by the hydrophobic effect.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101899"},"PeriodicalIF":2.3,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11714696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recombinant expression and characterization of the family 5 cellulase from Bacillus velezensis in Escherichia coli BL21-CodonPlus (DE3)-RIPL velezensis家族5纤维素酶在大肠杆菌BL21-CodonPlus (DE3)-RIPL中的重组表达及特性研究
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-14 DOI: 10.1016/j.bbrep.2024.101898
Dinh Minh Tran , Thi Huyen Nguyen , To Uyen Huynh , Iuliia Pentekhina
{"title":"Recombinant expression and characterization of the family 5 cellulase from Bacillus velezensis in Escherichia coli BL21-CodonPlus (DE3)-RIPL","authors":"Dinh Minh Tran ,&nbsp;Thi Huyen Nguyen ,&nbsp;To Uyen Huynh ,&nbsp;Iuliia Pentekhina","doi":"10.1016/j.bbrep.2024.101898","DOIUrl":"10.1016/j.bbrep.2024.101898","url":null,"abstract":"<div><div>B. velezensis RB. IBE29 is a chitinolytic bacterium originally isolated from agricultural soil of Vietnam. Previous studies demonstrated this bacterium was a promising chitinase producer, biocontrol agent, and biofertilizer for crop production. The complete genome sequence of the bacterium was reported and possesses the gene encoding family 5 cellulase; however, role of this enzyme has not been experimentally characterized. This work aimed to express and biologically characterize family 5 cellulase of strain RB. IBE29. The ORF (without signal peptide) of the <em>celA</em> of strain RB. IBE29 was expressed in <em>E. coli</em> BL21-CodonPlus (DE3)-RIPL using the vector pColdII, and the corresponding product (rBvCelA, 55.17 kDa) was successfully purified using the HisTrap FF column. The purified rBvCelA showed the highest cellulase activity against CMC, followed by sugarcane bagasse and rice straw, and had optimal temperature and pH at 60 °C and 6.0, respectively. Metal salts ZnCl<sub>2</sub>, FeCl<sub>2</sub>, MgCl<sub>2</sub>, CuSO<sub>4</sub>, and MnCl<sub>2</sub> enhanced the cellulase activity by 103.85, 124.24, 109.38, 105.64, and 115.12 %, respectively. In addition, the supplementation of the purified rBvCelA in the feed enhanced the growth and improved the feed intake of broiler chickens by 5.88 and 5.19 %, respectively. These results indicated that family 5 cellulase of <em>B. velezensis</em> has a promising role in crop production and poultry breeding. As far as we know, this is the first report describing the contribution of family 5 cellulase from <em>B. velezensis</em> in broiler breeding.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101898"},"PeriodicalIF":2.3,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reduced expression of the serotonin transporter impacts mitochondria in a sexually dimorphic manner 5 -羟色胺转运体的表达减少以两性二态的方式影响线粒体。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-13 DOI: 10.1016/j.bbrep.2024.101895
Bryony N. Thorne , Bart A. Ellenbroek , Darren J. Day
{"title":"Reduced expression of the serotonin transporter impacts mitochondria in a sexually dimorphic manner","authors":"Bryony N. Thorne ,&nbsp;Bart A. Ellenbroek ,&nbsp;Darren J. Day","doi":"10.1016/j.bbrep.2024.101895","DOIUrl":"10.1016/j.bbrep.2024.101895","url":null,"abstract":"<div><div>Neuropsychiatric and neurodevelopmental disorders are complex conditions that arise from a variety of interacting genetic and environmental factors. Among these factors, altered serotonergic signalling and mitochondrial dysfunction are strongly implicated, with a growing body of evidence to suggesting that serotonergic signalling is an important regulator of mitochondrial biogenesis. The serotonin transporter (SERT) functions to regulate synaptic 5-HT, and human allelic variants of the serotonin reuptake transporter-linked polymorphic region (5-HTTLPR) are associated with reduced SERT expression and increased susceptibility for developing neuropsychiatric disorders. Using the heterozygous (HET) variant of the SERT knockout rat to model reduced SERT expression, Western blotting was used to measure the abundance of TOMM20 and the complex I protein MT-CO1 as metrics for mitochondrial mass and abundance of respiratory complex IV. Mitochondrial activity was determined by dye reduction. We found sex-based and region-specific differences in mitochondrial mass and activity and that male and females show differing responses to reduced SERT expression. Our findings suggest that the sexually dimorphic differences in serotonergic signalling impact mitochondrial function and that these differences may be important for understanding sex differences in neuropsychiatric and neurodevelopmental disorders.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101895"},"PeriodicalIF":2.3,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Construction and evaluation of a prognostic model of autophagy-related genes in hepatocellular carcinoma 肝细胞癌自噬相关基因预后模型的构建与评价。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-12 DOI: 10.1016/j.bbrep.2024.101893
Yutao He , Bin Du , Weiran Liao , Wei Wang, Jifeng Su, Chen Guo, Kai Zhang, Zhitian Shi
{"title":"Construction and evaluation of a prognostic model of autophagy-related genes in hepatocellular carcinoma","authors":"Yutao He ,&nbsp;Bin Du ,&nbsp;Weiran Liao ,&nbsp;Wei Wang,&nbsp;Jifeng Su,&nbsp;Chen Guo,&nbsp;Kai Zhang,&nbsp;Zhitian Shi","doi":"10.1016/j.bbrep.2024.101893","DOIUrl":"10.1016/j.bbrep.2024.101893","url":null,"abstract":"<div><h3>Background</h3><div>Hepatocellular carcinoma (HCC) is a globally prevalent disease. Our article evaluates risk models based on autophagy- and HCC-related genes and their prognostic value by bioinformatics analytical methods to provide a scientific basis for clinical treatment.</div></div><div><h3>Methods</h3><div>Prognostic genes were identified by univariate and multivariate Cox analyses, and risk scores were calculated. The value of risk models was analysed by receiver operating characteristic curve (ROC), immune microenvironment and drug sensitivity. Prognostic gene-related regulatory mechanisms based on network database.</div></div><div><h3>Results</h3><div>We screened four prognosis-related genes (SQSTM1, GABARAPL1, CDKN2A, HSPB8) for model construction. The AUC for 1-, 2- and 3-year survival was higher than 0.6 in both the training and validation sets. The nomogram constructed based on risk scores, pathologic_T predicted the outcome better. There were differences in the tumour microenvironment between the high and low risk groups, as evidenced by differences in the distribution of immune cells and differences in the expression of immune checkpoints.</div></div><div><h3>Conclusion</h3><div>Our results illustrate that models, nomograms and risk scores were valuable for tumour progression.</div></div><div><h3>Clinical trial number</h3><div>Not applicable.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101893"},"PeriodicalIF":2.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11700244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure/function of ATP sulfurylase domain of human 3′-phosphoadenosine 5′-phosphosulfate synthase (hPAPSS) 人3′-磷酸腺苷5′-磷酸硫酸合酶ATP硫化酶结构域的结构/功能
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-12 DOI: 10.1016/j.bbrep.2024.101892
K.V. Venkatachalam , Dhiraj Sinha , Chris Soha , Rudi H. Ettrich
{"title":"Structure/function of ATP sulfurylase domain of human 3′-phosphoadenosine 5′-phosphosulfate synthase (hPAPSS)","authors":"K.V. Venkatachalam ,&nbsp;Dhiraj Sinha ,&nbsp;Chris Soha ,&nbsp;Rudi H. Ettrich","doi":"10.1016/j.bbrep.2024.101892","DOIUrl":"10.1016/j.bbrep.2024.101892","url":null,"abstract":"<div><div>3′-phosphoadenosine 5′-phosphosulfate (PAPS) is synthesized by PAPS synthase (PAPSS) in two steps. In the first step ATP sulfurylase (ATPS) transfers sulfate group onto adenylyl moiety of ATP to form adenosine 5′-phosphosulfate (APS) and PPi. APS-kinase (APSK) then transfers the gamma-phosphoryl from ATP onto 3′-OH of APS to form PAPS and ADP. Mutations of histidine's (H<sub>425</sub>/H<sub>428</sub>) of hPAPSS isoform1 knocked out ATPS and not APSK. <em>In silico</em> ATP binding and molecular dynamics experiments exhibited an unfavorable binding energy for mutant enzymes. Thus, requirements of H<sub>425</sub>NGH<sub>428</sub> motif for ATPS is established. The N<sub>426</sub> residue in various organisms is substituted with R. We mutated hPAPSS1 with basic residue K. The N<sub>426</sub> to K<sub>426</sub> (N–K) mutant exhibited slightly lower Km (3.7 mM) and higher Vmax (3X) for ATP compared to wildtype (WT, Km 4.3 mM). The Km for sulfate for N–K mutant was nearly same as WT but the Vmax was ∼4X higher for N–K. The catalytic efficiency (Vmax/Km) of N–K was ∼3 fold higher than WT. The full length hPAPSS1 evinced bimodal response against ATP, a paradigm that was deduced to be a trait of PAPSS that requires 2 mol of ATP/PAPS formed. This bimodal kinetics with ATP was lost when the N-terminal APSK was deleted from the C-terminal ATPS domain. The C-terminal domain contained ATPS activity, exhibited Km of 2.2 mM for ATP and Km of 0.53 mM for Sulfate and much higher catalytic efficiency compared to full length hPAPSS1. Thus, fused ATPS-APSK must be structurally and kinetically different than individual domains influenced by inter-domain residues.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101892"},"PeriodicalIF":2.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The consequences of climate change and male reproductive health: A review of the possible impact and mechanisms 气候变化与男性生殖健康的后果:可能的影响和机制综述。
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2024-12-05 DOI: 10.1016/j.bbrep.2024.101889
R.E. Akhigbe , P.A. Oyedokun , T.M. Akhigbe , M.A. Hamed , F.B. Fidelis , A.I. Omole , A.E. Adeogun , M.D. Akangbe , A.A. Oladipo
{"title":"The consequences of climate change and male reproductive health: A review of the possible impact and mechanisms","authors":"R.E. Akhigbe ,&nbsp;P.A. Oyedokun ,&nbsp;T.M. Akhigbe ,&nbsp;M.A. Hamed ,&nbsp;F.B. Fidelis ,&nbsp;A.I. Omole ,&nbsp;A.E. Adeogun ,&nbsp;M.D. Akangbe ,&nbsp;A.A. Oladipo","doi":"10.1016/j.bbrep.2024.101889","DOIUrl":"10.1016/j.bbrep.2024.101889","url":null,"abstract":"<div><div>A global decline in male fertility has been reported, and climate change is considered a major cause of this. Climate change refers to long-term shifts in temperatures and weather patterns, and results from greenhouse gas emissions like carbon dioxide and methane that act as a blanket wrapped around the earth, trapping heat and elevating temperatures. Sad to say, the consequences of climatic variation are beyond the dramatic elevated temperature, they include cold stress, increased malnutrition, air pollution, cardiovascular diseases respiratory tract infections, cancer, sexually transmitted infections, mental stress, and heat waves. These negative effects of climate change impair male reproductive function through multiple pathways, like ROS-sensitive signaling, suppression of steroidogenic markers, and direct damage to testicular cells. The present study aimed to describe the impact of the consequences of climate change on male reproductive health with details of the various mechanisms involved. This will provide an in-depth understanding of the pathophysiological and molecular basis of the possible climatic variation-induced decline in male fertility, which will aid in the development of preventive measures to abate the negative effects of climate change on male reproductive function.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101889"},"PeriodicalIF":2.3,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信